H3K9me1/2 methylation limits the lifespan of daf-2 mutants in C. elegans

  1. Meng Huang
  2. Minjie Hong
  3. Xinhao Hou
  4. Chengming Zhu
  5. Di Chen  Is a corresponding author
  6. Xiangyang Chen  Is a corresponding author
  7. Shouhong Guang  Is a corresponding author
  8. Xuezhu Feng  Is a corresponding author
  1. The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, China
  2. State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Institute for Brain Sciences, Nanjing University, China
  3. CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, China

Abstract

Histone methylation plays crucial roles in the development, gene regulation, and maintenance of stem cell pluripotency in mammals. Recent work shows that histone methylation is associated with aging, yet the underlying mechanism remains unclear. In this work, we identified a class of putative histone 3 lysine 9 mono/dimethyltransferase genes (met-2, set-6, set-19, set-20, set-21, set-32, and set-33), mutations in which induce synergistic lifespan extension in the long-lived DAF-2 (insulin growth factor 1 [IGF-1] receptor) mutant in Caenorhabditis elegans. These putative histone methyltransferase plus daf-2 double mutants not only exhibited an average lifespan nearly three times that of wild-type animals and a maximal lifespan of approximately 100 days, but also significantly increased resistance to oxidative and heat stress. Synergistic lifespan extension depends on the transcription factor DAF-16 (FOXO). mRNA-seq experiments revealed that the mRNA levels of DAF-16 Class I genes, which are activated by DAF-16, were further elevated in the daf-2;set double mutants. Among these genes, tts-1, F35E8.7, ins-35, nhr-62, sod-3, asm-2, and Y39G8B.7 are required for the lifespan extension of the daf-2;set-21 double mutant. In addition, treating daf-2 animals with the H3K9me1/2 methyltransferase G9a inhibitor also extends lifespan and increases stress resistance. Therefore, investigation of DAF-2 and H3K9me1/2 deficiency-mediated synergistic longevity will contribute to a better understanding of the molecular mechanisms of aging and therapeutic applications.

Editor's evaluation

This work presents important findings which pertain to how the length of an organism's lifespan can be affected by the presence of post-translational histone modifications, namely histone H3 lysine 9 mono- or di-methylation (H3K9me1/2). The authors find that the presence or absence of these marks plays a key role in modulating lifespan and stress resistance that synergizes with a long-lived insulin-pathway (daf-2) model. This work adds an important layer to aging regulation in organisms where a repressive chromatin state in specific genomic regions may limit the extent of lifespan. Hence, proper elucidation of this mechanism would be valuable to attain a comprehensive understanding of aging control and the reasons why these limits exist.

https://doi.org/10.7554/eLife.74812.sa0

Introduction

Lifespan is governed by complex interactions between genetic and environmental factors. The perturbation of insulin/insulin-like signaling, target of rapamycin (TOR) pathway, and mitochondrial functions have been shown to extensively modulate lifespan and health (Fontana et al., 2010; Kenyon, 2010; López-Otín et al., 2013). These genetic manipulations often lead to significant changes in gene expression at both the transcriptional and translational levels. Inhibition of DAF-2, the Caenorhabditis elegans ortholog of the insulin growth factor 1 (IGF-1) receptor, doubles adult lifespan by activating the DAF-16 (FOXO) transcription factor to regulate downstream genes involved in stress resistance, detoxification, and metabolism (Kenyon et al., 1993; Kimura et al., 1997; Lin et al., 1997; Ogg et al., 1997; Murphy et al., 2003; McElwee et al., 2004).

In addition to genetic regulation, aging is also modulated by epigenetic processes. Epigenetic marks, including histone acetylation and methylation, as well as the associated chromatin states, are altered during aging. Aging-dependent loss of chromatin repression is correlated with alterations in gene expression patterns, which have been documented in species ranging from C. elegans to humans (Lee et al., 2000; Lund et al., 2002; Bennett-Baker et al., 2003; Lu et al., 2004). For example, the methylation of histone 3 lysine 4 methylation (H3K4me) is one of the posttranslational histone modifications that marks on regions of active transcription (Shilatifard, 2008). H3K4me is deposited by the MLL/COMPASS complex, which travels with elongating RNA Polymerase II during transcription (Wood et al., 2007). In C. elegans, animals with reductions in COMPASS complex subunits (wdr-5, ash-2, and set-2) live longer than wild-type individuals (Greer et al., 2010).

However, little is known about the importance of repressive histone modification for aging marks. The H3K27me3 demethylase UTX-1 regulates lifespan independently of the presence of the germline but in a manner that depends on the insulin-FOXO signaling pathway (Maures et al., 2011). MET-2, a mammalian H3K9 methyltransferase SETDB1 homolog (Loyola et al., 2006), likely monomethylates and dimethylates H3K9 in C. elegans (Towbin et al., 2012). MET-2 is necessary both for a normal lifespan (Tian et al., 2016) and for the lifespan extension of wdr-5 mutants (Lee et al., 2019). SET-6 is a putative H3K9me2/3 methyltransferase but not H3K9me1. Although the depletion of SET-6 does not significantly increase the lifespan of C. elegans, it may increase healthy aging (Yuan et al., 2020). SET-25 is a putative trimethylase for H3K9 (Towbin et al., 2012; Padeken et al., 2021). However, the deletion of SET-25 does not significantly change the worm lifespan (Woodhouse et al., 2018).

The enzymes responsible for histone lysine methylation are called histone methyltransferases (HMTs). HMTs typically contain a conserved catalytic domain called SET, which stems from Su(var)3–9, Enhancer of zeste, and Trithorax, the first HMTs known to carry this domain (Tschiersch et al., 1994). The C. elegans genome encodes 38 SET domain-containing proteins, of which 5 are essential for viability (Andersen and Horvitz, 2007; Ni et al., 2012). However, the biological roles of most SET proteins are largely unknown.

To investigate the function of repressive histone methylation in lifespan regulation, we selected a number of putative H3K9 methyltransferases as well as methyltransferases that may indirectly regulate H3K9me and tested whether the loss-of-function of these SET proteins could change the lifespan of C. elegans. Interestingly, we found that the H3K9me1/2, but not H3K9me3, mutants exhibited a synergistic lifespan extension with daf-2 mutation. These animals showed an average lifespan of approximately 60 days, which is approximately 70% longer than that of daf-2 worms and is three times as long as that of wild-type N2 animals. The double mutants exhibited a maximal lifespan of approximately 100 days. The synergistic lifespan extension of DAF-2 and lifespan-limiting HMT mutants depend on the transcription factor DAF-16 (FOXO). mRNA-seq experiments showed that DAF-16 Class I genes (genes that are activated by DAF-16) are activated in long-lived worms. Therefore, we conclude that H3K9me1/2 may limit the lifespan of daf-2 animals by repressing the expression of DAF-16 Class I genes.

Results

The depletion of set-21 extends lifespan and enhances stress resistance in daf-2 mutant

SET-21 is a homolog of human isoform 1 of histone-lysine N-methyltransferase SUV39H2, with functions unknown in C. elegans (Wenzel et al., 2011). We accidentally found that set-21(ok2320) significantly extended lifespan in daf-2 mutants, but did not change the lifespan of N2 animals (Figure 1A, Supplementary file 1 Statistical analyses of lifespan experiments). To confirm the function of SET-21 in lifespan regulation, we first generated a number of additional deletion alleles of set-21 by CRISPR/Cas9 technology (Figure 1—figure supplement 1A). The deletion of set-21 did not significantly extend the lifespan or change the brood size in N2 background (Figure 1A, Figure 1—figure supplement 1B). Strikingly, in daf-2(e1370) mutant worms, knocking out set-21 reduced the brood size and significantly extended lifespan (Figure 1A, Figure 1—figure supplement 1B). The average lifespan of daf-2(e1370);set-21(ust68) were 55% longer than that of daf-2(e1370) animals (Figure 1A). And the maximal lifespan of daf-2;set-21 animals achieved approximately 100 days, which is three times as long as that of N2 animals.

Figure 1 with 1 supplement see all
Synergistic lifespan extension and stress resistance in daf-2;set-21 mutants.

(A) (Left) Survival curves of indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Mean ± s.e.m. of two independent experiments. The percentage of change was compared to the average lifespan of control animals. Asterisks indicate significant differences using log rank tests. ** 0.001< p < 0.01; ****p<0.0001. n.s., not significant, p>0.05. Lifespan data were summarized in Supplementary file 1. (B) (Left) Survival curves of indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Mean ± s.e.m. of two independent experiments. Asterisks indicate significant differences using log rank tests. ****p<0.0001. Lifespan data were summarized in Supplementary file 1. (C, D) Survival curves of the indicated animals. (C) Oxidative and (D) heat stress. Data in each panel are presented as the mean ± s.e.m. of five independent experiments. Asterisks indicate significant differences using two-tailed t tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05. The same oxidative stress data of control N2 and daf-2 animals were used in (C) Figures 2 and 3 and Figure 3—figure supplement 3A. The same heat stress data of control N2 and daf-2 animals were used in (D) Figures 2 and 3 and Figure 3—figure supplement 3B.

eat-2 mutant is a genetic model in dietary restriction (DR) research in C. elegans. The mutation of eat-2 renders a non-efficient pharynx in grinding bacteria and results in DR on regular media plates (Raizen et al., 1995). eat-2 animals exhibit phenotypes similar to those observed in other species subjected to DR, including an ~36% longer lifespan (Figure 1B; Lakowski and Hekimi, 1998). Similarly, knocking out set-21 further extended the lifespan of eat-2(ad465) mutant worms (Figure 1B). The average lifespan of eat-2(ad465);set-21(ust68) were 16% longer than that of eat-2(ad465) animals, suggesting a broader effect of these lifespan-limiting SET proteins.

The extended lifespan of nematodes has been shown to correlate with the activation of stress response genes and increased stress resistance (Lithgow et al., 1995; Murphy et al., 2003; Samuelson et al., 2007). The deletion of set-21 did not significantly change the stress resistance in N2 background animals (Figure 1C–D). The daf-2 mutation led to a higher resistance to oxidative stress and heat-shock stress than N2 animals. Strikingly, daf-2;set-21 worms revealed a much higher resistance to oxidative stress via hydrogen peroxide treatment and heat-shock stress than daf-2 animals (Figure 1C–D).

The depletion of met-2 extends lifespan in daf-2 mutant worms and enhances stress resistance

The remarkable lifespan extension in daf-2;set-21 animals inspired us to re-investigate the role of histone H3 lysine 9 methylation in C. elegans. MET-2 is the mammalian SETDB1 homolog, which is involved in mono- and dimethylation of H3K9 (Figure 2A; Loyola et al., 2006; Towbin et al., 2012). The brood size of met-2 mutant is approximately half of that of wild-type N2 animals (Figure 2B). Interestingly, daf-2;met-2 double mutant exhibited synthetic defect and had a significantly reduced brood size. met-2 mutants exhibited a modest shorter lifespan than wild-type N2 animals (Figure 2C; Tian et al., 2016). Strikingly, daf-2;met-2 double mutants revealed an average lifespan of approximately 47 days, which is 30% longer than that of daf-2 mutation alone and is 2.3 times as long as that of wild-type N2 animals (Figure 2C). The depletion of met-2 enhanced the oxidative stress resistance and heat stress resistance in both N2 and daf-2 mutant worms (Figure 2D–E). These results suggest that met-2 and H3K9me1/2 may play different roles in lifespan regulation in N2 and daf-2 animals. Alternatively, the depletion of daf-2 may provide a sensitized genetic background to identify genes that are involved in aging and lifespan regulation.

daf-2;met-2 mutants revealed extended lifespan and increased resistance to oxidative and heat stress compared to daf-2 animals.

(A) Western blotting of L4 stage animals with the indicated antibodies. Numbers indicate the scanned density by ImageJ. (B) Brood size of indicated animals at 20°C. (C) (Left) Survival curves of indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Mean ± s.e.m. of three independent experiments. Asterisks indicate significant differences using log rank tests. ****p<0.0001. Lifespan data were summarized in Supplementary file 1. (D, E) Survival curves of the indicated animals. (D) Oxidative and (E) heat stress. Data in each panel are presented as the mean ± s.e.m. of five independent experiments. Asterisks indicate significant differences using two-tailed t tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05.

SET-25 is a putative trimethylase for H3K9 (Figure 2A; Towbin et al., 2012). However, deletion of SET-25 did not significantly change the worm lifespan or stress resistance in either the wild-type N2 or daf-2 background animals (Figure 2C–E). The deletion of SET-25 only moderately enhanced the oxidative stress resistance in daf-2 mutant worms (Figure 2D–E).

Identification of set genes required for lifespan limitation in daf-2 animals

C. elegans’ genome encodes 38 proteins containing SET domains, most of which have unknown function (Andersen and Horvitz, 2007). To investigate the function of H3K9 methylation in lifespan regulation, we searched for other SET proteins that exhibit sequence similarity to SET-21 (Figure 3A, Figure 3—figure supplement 1). We selected seven additional SET proteins, including SET-6, SET-13, SET-15, SET-19, SET-20, SET-32, and SET-33, which are most closely related to the SET-21 in the dendrogram. All these proteins contain conserved catalytic SET domains and are annotated as putative H3K9 methyltransferases, as well as methyltransferases that may indirectly regulate H3K9me. Among them, SET-6 is required for H3K9me2/3 methylation (Yuan et al., 2020) and SET-32 is required for nuclear RNAi-directed H3K9me3 in C. elegans (Mao et al., 2015; Kalinava et al., 2017; Spracklin et al., 2017). Using N2 and the sensitized daf-2 background, we assayed the lifespan of these putative H3K9 methyltransferase mutants.

Figure 3 with 3 supplements see all
Synergistic lifespan extension of set-6, set-19, set-20, set-32, and set-33 with daf-2 animals.

(A) Dendrogram comparing the protein sequences of SET proteins that are putative H3K9 methyltransferases or methyltransferases that may indirectly regulate H3K9me in Caenorhabditis elegans. The numbers indicate the length of each protein. (B) (Left) Survival curves of indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Mean ± s.e.m. of two independent experiments. The percentage of change was compared to the average lifespan of N2 animals. Asterisks indicate significant differences using log rank tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05. Lifespan data were summarized in Supplementary file 1. (C) (Left) Survival curves of indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Mean ± s.e.m. of two independent experiments. The percentage of change was compared to the average lifespan of daf-2 animals. Asterisks indicate significant differences using log rank tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05. (D, E) Survival curves of the indicated animals. (D) Oxidative and (E) heat stress. Data are presented as the mean ± s.e.m. of five independent experiments. Asterisks indicate significant differences using two-tailed t tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05.

We acquired additional set mutants from CGC and also generated alleles by CRISPR/Cas9 technology (Figure 3—figure supplement 2A). Among them, the deletion of set-6, set-19, set-20, and set-32 modestly increased the lifespan compared to that of wild-type N2 animals (Figure 3B). However, in the daf-2 mutant background, mutations of set-6, set-19, set-20, set-32, and set-33 exhibited a striking synergistic lifespan extension. While the lifespan of daf-2;set-20 and daf-2;set-32 are approximately 60% longer than that of daf-2 worms, the daf-2;set-6 and daf-2;set-19 live 70% longer than that of daf-2 animals (Figure 3C). Especially, daf-2;set-19 exhibits a maximal lifespan of approximately 100 days, which is five times as long as the average lifespan of N2 animals. daf-2;set-6, daf-2;set-19, daf-2;set-20, daf-2;set-32, daf-2;set-33 had fewer brood sizes than the single set gene mutants (Figure 3—figure supplement 2B). The long-lived animals were also much more resistant than control animals to the oxidative stress induced by hydrogen peroxide (Figure 3D, Figure 3—figure supplement 3A) and heat stress (Figure 3E, Figure 3—figure supplement 3B) in daf-2 mutant worms but not in N2 background animals. set-32(ok1457) revealed a higher resistance to heat stress but not oxidative stress than N2 animals.

To test whether SET-6, SET-19, SET-20, SET-21, SET-32, and SET-33 act in the same genetic pathway to regulate lifespan in daf-2 animals, we crossed set-21(ust68) to other set mutants. As expected, the triple mutants daf-2;set-21;set-6, daf-2;set-21;set-19, daf-2;set-21;set-20, daf-2;set-21;set-32, and daf-2;set-21;set-33 did not significantly further extend the lifespan than the double mutants (Figure 4A). Thus, these set genes probably act in the same genetic pathway to regulate lifespan.

Figure 4 with 1 supplement see all
Genetic pathway analysis of set genes in lifespan regulation in daf-2 mutants.

(A–D) (Left) Survival curves of the indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Means ± s.e.m. of two independent experiments. The percentage change was compared to the lifespan of control animals. Asterisks indicate significant differences using log rank tests. ** 0.001< p < 0.01; ****p<0.0001; n.s., not significant, p>0.05. Lifespan data were summarized in Supplementary file 1.

We speculated that there might be a correlation between the expression pattern and lifespan extension of the set genes Thus, we generated in situ single-copy 3xFLAG-GFP tagged SET-21, SET-25, and SET-32 transgenes by CRISPR/Cas9 technology and single-copy GFP-3xFlAG-tagged SET-13 transgenic strains using the Mos1-mediated single-copy insertion (MosSCI) technology. These animals were imaged in N2 and daf-2 background at embryonic and larva stages, respectively, to figure out the expression patterns and cellular localizations of SET proteins (Figure 4—figure supplement 1). However, we failed to find a clear correlation between their expression pattern with the lifespan extension phenotype. The depletion of SET-21 and SET-32 extended the lifespan of daf-2 animals, but GFP::SET-21 and GFP::SET-32 showed different expression patterns and subcellular localizations. GFP::SET-21 exclusively located in the nucleus but GFP::SET-32 located in both the nucleus and cytoplasm in embryos. At larval stage, GFP::SET-21 was expressed in soma but GFP::SET-32 was expressed in germline. Both set-13 and set-25 mutants did not show lifespan extension in N2 and daf-2 background worms. SET-13 and SET-25 were enriched in the nucleus. SET-13::GFP was expressed through eight-cell stage to late-embryonic stage, while SET-25::GFP was expressed in the whole embryonic stage and the germline in young adults.

H3K9me3 is a hallmark of heterochromatin and is often enriched on repetitive sequences (Peters et al., 2003; Guenatri et al., 2004; Martens et al., 2005). The heterochromatin protein 1 (HP1) is a highly conserved small nonhistone protein, which was first identified in Drosophila, and recognizes H3K9me3 (James and Elgin, 1986). C. elegans has two HP1 paralogs: HP1 Like 1 and 2 (HPL-1 and HPL-2) (Couteau et al., 2002). The chromatin binding pattern of HPL-2 most closely resembles H3K9me1 and H3K9me2 and less closely resembles H3K9me3 (Garrigues et al., 2015). hpl-2(tm1489) mutation has been shown to extend lifespan (Meister et al., 2011). However, both daf-2;hpl-1 and daf-2;hpl-2 double mutants did not exhibit further lifespan extension compared to the daf-2 mutant (Figure 4B). SET-25 colocalized with both H3K9me3 and HPL-1, but did not colocalize with HPL-2 (Towbin et al., 2012). SET-25 is required for H3K9me3 methylation but is not involved in lifespan limitation (Figure 2A and C), further supporting that H3K9me3 may be dispensable for lifespan regulation in daf-2 animals.

Previous work has shown that knocking out the H3K4me3 methyltransferase SET-2 extended worm lifespan of N2 animals (Greer et al., 2010). To test whether SET-2-dependent H3K4me3 and lifespan-limiting H3K9 methyltransferases act in the same genetic pathway to regulate lifespan, we crossed set-2 to daf-2;set-21 animals. The double mutants daf-2;set-2 and daf-2;set-21 and the triple mutants daf-2;set-2;set-21 exhibited similar lifespan extensions relative to that of daf-2 animals (Figure 4C), suggesting that H3K4me3 and H3K9me1/2 may function in the same genetic pathway or regulate the same cohorts of target genes for lifespan modulation.

Inhibition of RSKS-1 (S6K), the TOR pathways, extends lifespan in C. elegans (Hansen et al., 2007; Pan et al., 2007), and the double mutant of daf-2;rsks-1 leads to synergistically prolonged longevity (Chen et al., 2013). However, the triple mutants daf-2(e1370);rsks-1(ok1255);set-21(ust68) revealed similar lifespan as long as those of daf-2(e1370);rsks-1(ok1255) and daf-2(e1370);set-21(ust68) double mutants (Figure 4D), suggesting that either rsks-1 and set-21 act in the same molecular pathway to regulate lifespan or there is likely an upceiling of maximal lifespan of approximately 100 days for C. elegans. Interesting, a report suggested that in a mutant of age-1, which encodes the class-I phosphatidylinositol 3-kinase catalytic subunit (PI3K(CS)), worms can survive to a median of 145–190 days at 20 degrees and a maximal lifespan of approximately 260 days, with nearly 10-fold extension of both median and maximum adult lifespan relative to control animals (Ayyadevara et al., 2008).

Therefore, we concluded that a number of set genes limit the lifespan and stress resistance of daf-2 animals in C. elegans.

Lifespan-limiting SET proteins regulate DAF-16 Class I genes in daf-2 animals

The longevity phenotype of daf-2 animals depends on the downstream DAF-16 transcription factor (Kenyon et al., 1993). DAF-16 localizes in the cytoplasm in N2 worms but accumulates in the nucleus upon daf-2 mutation (Henderson and Johnson, 2001; Lin et al., 2001). To determine whether the expression pattern and subcellular localization of DAF-16 are altered upon the mutation of these lifespan-limiting HMTs, we crossed a widely used high-copied DAF-16::GFP transgene with daf-2, set-21, set-25, daf-2;set-21, and daf-2;set-25 animals. As reported, the mutation of daf-2 resulted in a pronounced nuclear accumulation of DAF-16::GFP (Figure 5—figure supplement 1A). In N2 background, the mutation of set-21 or set-25 did not detectably change the cytoplasmic localization of DAF-16::GFP (Figure 5—figure supplement 1A). In daf-2 background worms, the mutation of set-21 or set-25 did not further induce detectable changes in the expression pattern and subcellular localization of DAF-16::GFP.

We generated a single-copied DAF-16::GFP transgene by inserting a GFP tag onto the C-terminal of DAF-16 via CRISPR/Cas9 technology (Figure 5A). Then, we crossed the single-copied DAF-16::GFP transgene with daf-2, set-21, set-25, daf-2;set-21, and daf-2;set-25 animals. DAF-16::GFP accumulated in the cytoplasm in N2 background animals. Unlike in the high-copied DAF-16::GFP transgenic animal, daf-2 mutation only modestly enriched DAF-16::GFP to the nucleus in the single-copied DAF-16::GFP transgenic strain (Figure 5B and Figure 5—figure supplement 1B). Strikingly, in daf-2;set-21 and daf-2;set-25 double mutant animals, DAF-16::GFP was strongly enriched in the nucleus in the single-copied transgenic animals. The reason for the subcellular localization difference between the high-copied and single-copied DAF-16::GFP transgenic animals is unclear. However, the single-copied DAF-16::GFP may be used to re-visit the mechanism of lifespan regulation pathways. In addition, the mechanism of enhanced nuclear accumulation of DAF-16::GFP in daf-2;set-21 and daf-2;set-25 animals is unknown. Given that daf-2;set-21 exhibited extended lifespan but daf-2;set-25 did not, and both of them revealed strong nuclear localization of DAF-16::GFP, it is quite possible that there is an additional level of regulation downstream of the nuclear localization of DAF-16.

Figure 5 with 2 supplements see all
The lifespan-limiting SET proteins regulate DAF-16 Class I genes in daf-2 mutants.

(A) Construction of an in situ GFP-tagged DAF-16 transgene by CRISPR/Cas9 technology. The subcellular localization of DAF-16::GFP was scored at the pharynx in young adult animals. (B) (Left) Fluorescent images of the single-copied DAF-16::GFP transgene in indicated animals at 20°C. (Right) The subcellular localization of the single-copied DAF-16::GFP transgene was scored in indicated animals. (C, D) (Left) Survival curves of indicated animals. (Right) Histogram displaying the average lifespan of the indicated animals. Mean ± s.e.m. of three independent experiments. Asterisks indicate significant differences using log rank tests. ****p<0.0001. Lifespan data were summarized in Supplementary file 1. (E) Heatmap of the standardized fragments per kilobase of transcript per million mapped reads (FPKM) of reported top 50 DAF-16 Class I and Class II genes by mRNA-seq in the indicated animals. Statistical analysis was performed to obtain the expression levels of each gene in each strain and the average of the expression levels in the five strains. The gene expression levels in a single strain were compared with the average of the five strains, and the ratio obtained was processed by log2. The resulting value>0 means the expression level of the gene in the indicated strain is higher than the average expression levels of this gene in the five strains, as shown from yellow to red. The resulting value<0 means the expression level of the gene in the indicated strain is lower than the average expression levels of this gene in the five strains, as shown in blue. The expression levels are indicated by the color bar. The mRNA-seq was conducted in single replicate and validated by quantitative real-time PCR in Figure 7A. The 50 most significant positive (Class I) and negative (Class II) targets of DAF-16 were selected according to their responsiveness to DAF-16 (Tepper et al., 2013).

To further test the role of DAF-16 in the daf-2;set-21-induced synergistic longevity, we constructed a daf-2(e1370);daf-16(mu86);set-21(ust68) triple mutant. The daf-16 mutation reverted the prolonged longevity phenotype of daf-2;set-21 to an average lifespan of 23 days, which is similar to that of set-21 or N2 alone (Figure 5C). In N2 background, daf-16 and daf-16;set-21 mutant worms lived shorter than wild-type N2 and set-21 animals (Figure 5D).

The depletion of DAF-2 reduces the insulin signaling pathway and leads to both upregulation and downregulation of large sets of genes, referred to as DAF-16 Class I and II genes, respectively (Murphy et al., 2003). Class I genes are induced in daf-2 mutants but are repressed in daf-2;daf-16 double mutants. Class II genes are not induced in daf-2 mutants but are induced in daf-2; daf-16 double mutants; 1663 genes are classified as positive (Class I) DAF-16 targets and 1733 genes are classified as negative (Class II) DAF-16 targets of DAF-16 (Tepper et al., 2013). Class I genes are enriched for the Gene Ontology categories including oxidation, reduction, and energy metabolism, whereas Class II genes are enriched for genes involved in biosynthesis, growth, reproduction, and development. We performed mRNA-seq and analyzed Class I and II DAF-16 genes to identify the mis-regulated genes in daf-2;set mutants. Interestingly, the mRNA levels of DAF-16 Class I, but not Class II, genes are consistently activated in long-lived daf-2;set-19, daf-2;set-21, and daf-2;set-32 worms, than in control daf-2 and daf-2;set-25 animals (Figure 5E, Figure 5—figure supplement 2).

Identification of the lifespan-limiting SET targeted genes in daf-2 animals

To identify target genes in this group of lifespan extension daf-2;set mutants, we re-analyzed the mRNA expression profile in the double mutants (Figure 6, Figure 6—figure supplement 1). We identified 49 co-upregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived daf-2;set-19, daf-2,set-21, daf-2;set-32 double mutants, but not in short-lived control daf-2 and daf-2;daf-25 animals (Figure 6A–B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (Figure 6—figure supplement 1B). Twenty-two co-upregulated genes are not DAF-16 Class I genes, suggesting the existence of additional regulations.

Figure 6 with 1 supplement see all
mRNA-seq identified differentially expressed genes co-regulated by the lifespan-limiting SET proteins in daf-2 animals.

(A) Venn diagrams showing the overlapped genes upregulated or downregulated between daf-2(e1370);set-25(n5021), daf-2(e1370);set-19(ok1813), daf-2(e1370);set-21(ust068), daf-2(e1370);set-32(ok1387) compared with daf-2(e1370). Upregulated genes were defined as fold change ≥ 2and p<0.05. Downregulated genes were defined as fold change ≤ 0.5and p<0.05. (B) Heatmap of the standardized fragments per kilobase of transcript per million mapped reads (FPKM) for the 49 co-upregulated genes and 11 co-downregulated genes in the indicated animals. The expression levels are indicated by the color bar. (C, D) Profile plots showing the chromatin immunoprecipitation sequencing (ChIP-seq) signals of seven transcription factors around transcription start sites (TSSs) of (C) 49 co-upregulated genes and (D) 11 co-downregulated genes. The ChIP-seq datasets were downloaded from the ENCODE or NCBI GEO databases (Supplementary file 6).

We then analyzed a number of known transcription factors for their binding to the co-regulated targeted genes (Figure 6C–D, Figure 6—figure supplement 1C-E). Among them, DAF-16 and NHR-80 were specifically enriched at the transcription start sites (TSSs) of the 49 co-upregulated genes. NHR-80 is a homolog of mammalian hepatocyte nuclear factor 4 and is an important nuclear hormone receptor involved in the control of fat consumption and fatty acid composition in C. elegans (Goudeau et al., 2011; Pathare et al., 2012). Among the genes targeted by DAF-16 and NHR-80, 12 of them are co-regulated by both factors, which is consistent with previous report that daf-16 and nhr-80 function in parallel pathway for lipid metabolism (Wan et al., 2022).

To confirm the change in target gene expression, we chose 10 genes from the 49 co-upregulated genes. Among them, nhr-62, dao-3, and tts-1 are direct binding targets of both DAF-16 and NHR-80. sod-3 is a DAF-16 direct binding target. lys-7 and asm-2 are NHR-80 direct binding targets. All of the 10 genes have been shown to be upregulated in daf-2 compared to daf-2;daf-16 animals (Tepper et al., 2013; Essers et al., 2015). We quantified the mRNA levels by quantitative real-time PCR (qRT-PCR) in daf-2, daf-2;set-21 and daf-2;set-25 animals (Figure 7A). Consistently, all the 10 genes were upregulated in daf-2;set-21 double mutants than in daf-2 and daf-2;set-25 animals (Figure 7A).

Figure 7 with 1 supplement see all
Class I DAF-16 genes are required for the synergistic lifespan extension in daf-2;set-21 animals.

(A) Quantitative real-time PCR analysis of the indicated mRNAs. Levels of ama-1 mRNA were used as an internal control for sample normalization. Data were expressed as fold changes relative to those of daf-2 (e1370) animals. Data are presented as the mean ± s.e.m. of three independent experiments. Asterisks indicate significant differences using two-tailed t tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05. (B) Survival curves of indicated animals. Asterisks indicate significant differences using log rank tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05. Lifespan data were summarized in Supplementary file 1.

We generated deletion mutants of these genes by CRISPR/Cas9 technology (Figure 7—figure supplement 1) and crossed the mutants into daf-2;set-21 background. Seven of these mutants, tts-1, nhr-62, ins-35, sod-3, asm-2, F35E8.7, and Y39G8B.7, could partially shorten the lifespan extension phenotype of daf-2;set-21 double mutant animals, but not shorten the lifespan of daf-2 mutants (Figure 7B). Among them, tts-1 is a ribosome-associated long noncoding RNA in daf-2 mutant. Depleting tts-1 in daf-2 mutants has been reported to increase ribosome levels and shorten the extended lifespan (Tepper et al., 2013; Essers et al., 2015). NHR-62 is a nuclear hormone receptor with DNA binding activity, which is required for DR-induced longevity in C. elegans (Heestand et al., 2013). INS-35 is an insulin-like peptides and may act on DAF-2 to regulate UPRmt and mitochondrial dynamics (Chen et al., 2021). SOD-3 is a superoxide dismutase that is involved in the removal of superoxide radicals and required for lifespan extension in isp-1 mutant worms (Dues et al., 2017). ASM-2 is an ortholog of human SMPD1 (sphingomyelin phosphodiesterase 1) and is involved in ceramide biosynthetic processes and sphingomyelin catabolic processes (Lin et al., 1998; Deng et al., 2008). Strikingly, both F35E8.7 and Y39G8B.7 are predicted to encode proteins with ShK domain-like or ShKT domains, yet their functions are unknown.

Therefore, we concluded that the deletion of lifespan-limiting set genes in daf-2 mutants leads to a synergistically extended lifespan by increasing DAF-16 activity.

Lifespan-limiting SET proteins are required for H3K9me1/2 modification in daf-2 animals

To further investigate the mechanism by which these SET proteins limit daf-2 mutants’ lifespan, we used Western blotting assay to examine the levels of a number of histone 3 methylation marks in L4 animals and embryos. Previous work have reported that SET-6 is required for H3K9me2/3 methylation (Yuan et al., 2020), SET-25 is required for H3K9me3 methylation (Figure 2A; Towbin et al., 2012), and SET-32 is required for H3K23 methylation (Schwartz-Orbach et al., 2020).

The mutation of daf-2 did not significantly change the levels of H3K9me1/2/3 (Figure 8—figure supplement 1A). Similarly, the mutations of the set genes also did not significantly change the levels of tested histone modifications compared to those in wild-type N2 animals, except that set-19 was required for the accumulation of H3K23me3 in both embryos and L4 staged animals (Figure 8—figure supplement 1B-C). Interestingly, in the daf-2 mutant background, the long-lived daf-2;set-6, daf-2;set-19, daf-2;set-20, daf-2;set-21, daf-2;set-32, and daf-2;set-33 mutants, but not the short-lived daf-2;set-13, daf-2;set-15, and daf-2;set-25 animals, decreased global H3K9me1/2 levels at the L4 larval stage (Figure 8A). We used another anti-H3K9me2 antibody #ab176882 and confirmed that daf-2;set-6, daf-2;set-19, daf-2;set-20, daf-2;set-21, daf-2;set-32, and daf-2;set-33 mutants, but not daf-2;set-13, daf-2;set-15 and daf-2;set-25 animals, decreased global H3K9me1/2 levels at the L4 larval stage (Figure 8—figure supplement 2A). In embryos, daf-2;set-15, daf-2;set-20, and daf-2;set-32 mutants reduced H3K9me1/2 levels (Figure 8—figure supplement 2B). The daf-2;set-19 mutant also showed decreased H3K23me3 levels (Figure 8—figure supplement 2B). Although H3K4me has been shown to be involved in lifespan regulation, none of the long-lived daf-2;set-6, daf-2;set-19, daf-2;set-20, daf-2;set-21, daf-2;set-32, and daf-2;set-33 mutants revealed significant changes in H3K4 methylation levels (Figure 8A, Figure 8—figure supplement 2B). Chromatin immunoprecipitation (ChIP) followed by qRT-PCR further revealed a modest reduction in H3K9me1/2 levels of the 10 target genes in daf-2;set-21 mutants (Figure 8—figure supplement 3).

Figure 8 with 4 supplements see all
H3K9me1/2 methylation limits the lifespan and stress resistance of daf-2 mutants.

(A) (Top) Western blotting of L4 stage animals with the indicated antibodies (also see Figure 8—figure supplement 1). (Bottom) The histogram displayed means + s.e.m. of scanned density by ImageJ from three independent experiments. (B) The G9a (EHMT2) inhibitor A-366 reduced H3K9me2 levels in daf-2 animals. (Left) Western blotting of L4 stage animals with the indicated antibodies. (Right) The histogram displayed means + s.e.m. of scanned density by ImageJ from three independent experiments. Data are expressed as fold changes relative to those of daf-2(e1370) animals without A-366. Asterisks indicate significant differences using two-tailed t tests. ***p<0.001. Also see Figure 8—figure supplement 4A-B for replicates. (C) (Top) Survival curves of indicated animals. (Bottom) Histogram displaying the average lifespan of the indicated animals. mean ± s.e.m. of three independent experiments. The percentage of change was compared to the average lifespan of the daf-2 mutant. Asterisks indicate significant differences using log rank tests. 0.001 < **p<0.01; ***p<0.001; ****p<0.0001. Lifespan data were summarized in Supplementary file 1. (D, E) Survival curves of G9a(EHMT2) inhibitor A-366-treated daf-2 animals upon (D) oxidative and (E) heat stress. Data are presented as the mean ± s.e.m. of five independent experiments (n=50 animals). Asterisks indicate significant differences using two-tailed t tests. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; n.s., not significant, p>0.05.

HMT G9a, also known as euchromatic histone lysine methyltransferase 2 (EHMT2), is the human homolog of SET-6 (Yuan et al., 2020) and mediates H3K9 dimethylation. Treating daf-2 animals with the G9a inhibitor A-366 reduced H3K9me2 levels (Figure 8B, Figure 8—figure supplement 4A-B). The A-366 treatment extended the lifespan of daf-2 worms by 15% (Figure 8C), but did not significantly change the lifespan of N2 worms (Figure 8—figure supplement 4C). Moreover, A-366 also increased nematode resistance to oxidative and heat stress of daf-2 animals (Figure 8D–E). Thus, we concluded that decreased H3K9me1/2 levels in daf-2 mutant by a G9a inhibitor may increase lifespan and resistance to oxidative stress and heat stress in C. elegans.

Discussion

Here, we identified a class of putative HMTs, as well as methyltransferases that have been suggested to indirectly regulate H3K9me, that limit the lifespan of daf-2 mutant in C. elegans. These putative HMTs are required for H3K9me1/2 modification and regulate DAF-16 Class I genes in daf-2 animals. In the absence of DAF-2 and H3K9me1/2, the DAF-16 accumulates in the nucleus and the expression of DAF-16 Class I genes increase, which promote the expression of longevity genes and anti-stress genes and extends lifespan of daf-2 animals (Figure 8—figure supplement 4D). Decreased H3K9me1/2 in daf-2 animals improved nematode tolerance to oxidative stress and heat stress. Notably, the inhibition of worm H3K9me1/2 methyltransferases by a human G9a inhibitor also extends the lifespan of daf-2 animals. Thus, targeting insulin pathway and H3K9me1/2 modification together may be a new means for the treatment of aging and aging-related diseases.

The depletion of SET proteins or the inhibition of worm H3K9me1/2 methyltransferases by G9a inhibitor significantly extended the lifespan only in daf-2 mutant worms, but has modest effects on N2 animals. Consistently, the long-lived set-6, set-19, set-20, set-21, set-32, and set-33 mutants only significantly decreased global H3K9me1/2 levels in daf-2 mutants but not in N2 animals. These results together suggested that DAF-2 limits the effects of these SET proteins.

It is unclear how and why these SET proteins only limit lifespan in daf-2 animals. There are three possibilities. First, DAF-2 may have profound effect on the chromatin accessibility. In daf-2 mutants, the chromatin may be more compact and prohibit the activity of the SET proteins to conduct H3K9me2 modification. Second, daf-2 mutation may sensitize the animals by increasing the nuclear accumulated DAF-16. Although it is unclear whether DAF-16 preferentially recognizes H3K9me2 or H3K9me3, we observed a much stronger enrichment of DAF-16 in the nucleus in daf-2;set-21 than in daf-2 animals, which suggested that H3K9me2 may prohibit the accumulation of DAF-16 in the nucleus. Third, DAF-2 may have other indirect effect on the SET proteins. Further ChIP experiments can be used to test whether daf-2 mutation could affect the association of the SET proteins with chromatin. The ATAC-seq technology may allow us to investigate whether daf-2 mutation have changed chromosome accessibility to facilitate the activity of SET proteins. In addition, identification of the substrate of SET proteins may help to elucidate their mechanism and functions.

In daf-2 animals, DAF-16 modestly accumulated in the nucleus, as shown by the newly generated single-copy GFP-tagged DAF-16 transgene. Yet in daf-2;set-21 double mutants, DAF-16 was strongly enriched in the nucleus. The depletion of DAF-16 completely blocked the synergistic lifespan extension in daf-2;set-21 animals. The mRNA-seq experiments revealed that the mRNA levels of DAF-16 Class I genes were elevated in the long-lived daf-2;set-19, daf-2;set-21, and daf-2;set-32 double mutants compared to those in control daf-2 and short-lived daf-2;set-25 mutants. Together, these data suggested that the activity to DAF-16 to Class I genes not only depends on the absence of insulin pathway, but also depends on the depletion of these SET proteins and H3K9me2. The single-copy GFP-tagged DAF-16 transgene may allow us to re-visit the mechanism of lifespan regulation pathways.

A trade-off has been proposed between fertility and lifespan, where increasing lifespan usually comes at the cost of reduced fertility (Kirkwood, 1977). In C. elegans, removing the germ cells extends lifespan, triggers the nuclear localization of the DAF-16/FOXO transcription factor, and activates target genes in the intestine (Berman and Kenyon, 2006). Some long-lived mutant worms, like daf-2 and rsks-1, show reduced brood size (Chen et al., 2013). Consistently, we found that the long-lived worms daf-2;met-2, daf-2;set-6, daf-2;set-19, daf-2;set-20, daf-2;set-21, daf-2;set-32, and daf-2;set-33 all have reduced brood size compared to that of daf-2 animals. However, additional investigations are necessary to examine whether removing the germline cells could further extend worm lifespan beyond the 100 days’ ceiling.

Lifespan is controlled by both genetic and epigenetic factors. The perturbation of insulin/insulin-like signaling, TOR pathway, and mitochondrial functions have been shown to extensively modulate the aging process and lifespan. Epigenetic marks, including histone acetylation and methylation, are altered during aging and regulate lifespan in a number of species (Lee et al., 2000; Lund et al., 2002; Bennett-Baker et al., 2003; Lu et al., 2004). In C. elegans, both H3K4 and H3K27 methylation are involved in lifespan limitation. Animals with reduced H3K4me, for example, in wdr-5, ash-2, and set-2 mutants, live longer than wild-type animals (Greer et al., 2010). Interestingly, perturbation of H3K27 methylation, via either a decrease in mes-2 mutants or an increase in utx-1 mutants, is associated with enhanced longevity, suggesting context-dependent lifespan regulation (Maures et al., 2011; Guillermo et al., 2021).

H3K9me3 is a hallmark of heterochromatin and is often enriched on repetitive sequences (Peters et al., 2003; Guenatri et al., 2004; Martens et al., 2005). In addition, H3K9me1/2/3 have all been shown enrichment on repeat sequences (Gerstein et al., 2010). H3K9 methylation and its association with the nuclear envelope help maintain silencing of repetitive sequences and may contribute to the maintenance and stability of heterochromatin-like regions in C. elegans (Liu et al., 2011), as observed in other organisms (Peng and Karpen, 2008). A hallmark of heterochromatin is the enrichment of HP1 (James and Elgin, 1986). The nematode C. elegans has two HP1 paralogous proteins: HPL-1 and HPL-2 (Couteau et al., 2002). Interestingly, HPL-2 may serve additional roles than HPL-1, as hpl-2 mutants display diverse defects while hpl-1 mutants generally lack obvious defects (Garrigues et al., 2015). The pattern of HPL-2 most closely resembles H3K9me1 and H3K9me2 but less closely resembles H3K9me3 (Garrigues et al., 2015). HPL-2-bound genes, especially those located on arms, possess significantly higher levels of H3K9me2, but show no significant difference in H3K9me3 levels when compared to genes not bound by HPL-2 (Garrigues et al., 2015). SET-25 is a putative H3K9me3 methyltransferase and is recruited to targeted genomic loci either by H3K9me2 which is deposited by MET-2 or by the somatic Argonaute protein NRDE-3 and small RNAs (Mao et al., 2015; Padeken et al., 2021). SET-25 colocalizes with both H3K9me3 and HPL-1, but does not colocalize with HPL-2 (Towbin et al., 2012).

H3K9me2 and H3K9me3 exhibit different patterns of repeat enrichment (McMurchy et al., 2017). H3K9me2 is more associated with DNA transposons and satellite repeats, similar to the heterochromatin factors HPL-2, LET-418, LIN-13, LIN-61, and MET-2, whereas H3K9me3 is particularly associated with retrotransposon families, especially LINE and SINE elements (McMurchy et al., 2017). Moreover, H3K9me2 and the five heterochromatin factors are enriched at telomeres, whereas H3K9me3 is not (McMurchy et al., 2017). Therefore, H3K9me2, rather than H3K9me3, may be more closely associated with canonical heterochromatin factors in C. elegans. It was postulated that losing repressive chromatin is detrimental to lifespan (Villeponteau, 1997; Tsurumi and Li, 2012). In humans, two premature aging diseases are caused by mutations in lamins that reduce heterochromatin and disrupt its nuclear localization (Shumaker et al., 2006). In C. elegans, Drosophila, and mammals, heterochromatin decreases as individuals grow older (Haithcock et al., 2005; Wood et al., 2010; Wood and Helfand, 2013). Additionally, mutations that increase repressive chromatin extend lifespan in eukaryotes (Kennedy et al., 1995; Jin et al., 2011; Maures et al., 2011; Larson et al., 2012). In N2 background animals, the depletion of hpl-2 was shown increased lifespan (Meister et al., 2011). However, we did not observe a further lifespan extension in daf-2;hpl-2 animals, comparing to the daf-2 mutant. Similarly, we did not observe a significant change in lifespan in daf-2;set-25 mutants. The depletion of the two heterochromatin factors HPL-1 and HPL-2 failed to further extend the lifespan in daf-2 mutant worms, suggesting that heterochromatin itself may not be sufficient to perturb lifespan in daf-2 mutant worms.

MET-2, a mammalian H3K9 methyltransferase SETDB1 homolog (Loyola et al., 2006), likely monomethylates and dimethylates H3K9 in C. elegans (Towbin et al., 2012). MET-2 is necessary both for a normal lifespan in N2 background (Tian et al., 2016) and for the lifespan extension of wdr-5 mutants (Lee et al., 2019). In met-2 mutants, the lifespan is shortened compared to that of N2 animals. However, the lifespan was significantly extended in daf-2;met-2 double mutants, suggesting context-dependent lifespan regulation by epigenetic machinery. SET-6 is a putative H3K9me2/3 methyltransferase that was postulated to prevent healthy aging rather than modulate the normal lifespan in N2 background (Yuan et al., 2020). SET-6 accelerates behavioral deterioration in C. elegans by reducing mitochondrial function and repressing the expression of nuclear-encoded mitochondrial proteins. Here, we found that the depletion of set-6 dramatically increased the lifespan of daf-2 animals, which further supports the context-dependent lifespan regulation model.

We noticed that the stress resistance is enhanced in both met-2 and daf-2;met-2 animals, yet met-2 single mutant shortens lifespan and daf-2;met-2 extends lifespan. In addition, daf-2;set-15 showed a modest increase of stress resistance, while daf-2;set-15 revealed no further lifespan extension. The reason is unknown yet. Previous research showed correlations between stress resistance and lifespan extension in many mutant worms, for example daf-2. However, since daf-2 mutation already twitched the homeostasis and increased the stress resistance of animals, it is unclear that to what extent this correlation can further increase lifespan and stress resistance. Alternatively, some of these putative lifespan-limiting HMTs may have additional functions. Further investigations are required to understand the mechanism of each putative lifespan-limiting HMT.

In this work, we examined the role of 10 putative H3K9 methyltransferases, most of which have not been directly characterized for their biochemical properties by in vitro experiments (Schwartz-Orbach et al., 2020). The presence of these many putative H3K9 methyltransferases, or methyltransferases that may indirectly regulate H3K9me, may lead to a complexity of the interaction network of histone modifications. In addition, some SET proteins may have multiple roles in mediating histone modification. For example, SET-19 is required for both H3K9me1/2 and H3K23me3 marks, further bringing up complexity of the regulation. Further investigations are necessary to reveal their enzymatic activities by in vitro experiments (Schwartz-Orbach et al., 2020). In addition, identifying the in vivo targeted genes will also be crucial to help understanding why and how these SET proteins are involved in lifespan regulation in daf-2 mutants.

Additionally, we identified seven genes required for H3K9me1/2-involved lifespan extension in daf-2;set-21 animals. Among them, tts-1 is a long noncoding RNA on ribosomes of the daf-2 mutant. Depleting tts-1 in daf-2 mutants increases ribosome levels (Tepper et al., 2013; Essers et al., 2015). NHR-62 is known to be required for longevity in C. elegans (Heestand et al., 2013). INS-35 is an insulin-like peptides and may act on DAF-2 to regulate UPRmt and mitochondrial dynamics (Chen et al., 2021). SOD-3 is a superoxide dismutase that is involved in the removal of superoxide radicals. ASM-2 is an ortholog of human acid sphingomyelinase (ASM) and is involved in ceramide biosynthetic processes and sphingomyelin catabolic processes (Lin et al., 1998; Deng et al., 2008). The C. elegans genome encodes three ASM homologs, asm-1, asm-2, and asm-3. Among them, ASM-3 is most closely related to human ASM. During development and aging, ceramide and sphingosine accumulate (Sacket et al., 2009). Interestingly, monounsaturated fatty acid (MUFA) accumulation is necessary for the lifespan extension of H3K4me3-methyltransferase-deficient worms, and dietary MUFAs are sufficient to extend lifespan (Han et al., 2017). However, when asm-1, asm-2, or asm-3 was inactivated by RNAi knockdown, a modest lifespan extension phenotype was observed (Kim and Sun, 2012). Further investigation is required to examine how and why these genes are involved in lifespan regulation in daf-2;set-21 animals.

Stichodactyla toxin (ShK, ShkT) is a 35-residue basic peptide from the sea anemone Stichodactyla helianthus that blocks a number of potassium channels with nanomolar to picomolar potency. We found that F35E8.7 and Y39G8B.7 are required for lifespan extension in daf-2;set-21 animals. Human proteins containing ShK-like domains are MMP-23 (matrix metalloprotease 23) and MFAP-2 (microfibril-associated glycoprotein 2). Whether modulating the expression of these two proteins or their downstream targets can improve longevity or healthy lifespan will stimulate much drug potential.

Materials and methods

Strains

Bristol strain N2 was used as the standard wild-type strain. All strains were grown at 20°C unless specified. The strains used in this study are listed in Supplementary file 2.

Lifespan assay

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Lifespan assays were performed at 20°C. Worm populations were synchronized by placing young adult worms on NGM plates seeded with the Escherichia coli strain OP50-1 (unless otherwise noted) for 4–6 hr and then removed. The hatching day was counted as day 1 for all lifespan measurements. Worms were transferred every other day to new plates to eliminate confounding progeny. Animals were scored as alive or dead every 2 (before 52 days) or 4 (after 52 days) days. Worms were scored as dead if they did not respond to repeated prods with a platinum pick. Worms were censored if they crawled off the plate or died from vulval bursting and bagging. Plates were censored if they were contaminated by fungi or mites. For each lifespan assay, 90 worms were used in 3 plates (30 worms/plate). All lifespan data were summarized in Supplementary file 1.

Brood size

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L4 hermaphrodites were singled onto plates and transferred daily as adults until embryo production ceased and the progeny numbers were scored.

Hydrogen peroxide assay

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Ten synchronized worms at day 1 of adulthood were transferred to each well, which contained 1 ml of worm S-basal buffer with various concentrations of H2O2 in a 12-well plate at 20°C. Four hours later, 100 μl of 1 mg/ml catalase (Sigma, C9322) was added to neutralize H2O2, and the mortality of worms was scored.

Heat-shock assay

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Ten synchronized hermaphrodites at day 1 of adulthood were transferred to new NGM plates and incubated at 35°C, and their mortality was checked every 2 or 4 hr until there were no living worm.

G9a inhibitor treatment

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Several P0 young adult worms were placed onto fresh NGM plates seeded with E. coli strain OP50 (with the same concentration of G9a inhibitors in both NGM plates and OP50 liquid). Four or five days later, F1 young adult worms were placed onto new NGM plates with OP50 and G9a inhibitor. Then, we singled out the F2 worms for other assays. For heat-shock assay, we placed worms on G9a plates until day 1 of adulthood, and then transferred the hermaphrodites to NGM plates without G9a inhibitor, and incubated the worms at 35°C.

Western blot

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Embryos or L4 stage worms were harvested and washed three times with M9 buffer. Samples were frozen in –80°C. Ten minutes at 95°C in ×1 protein dye (62.5 mM Tris pH 6.8, 10% glycerol, 2% SDS, 5% β-mercaptoethanol, 0.2% bromophenol blue) was sufficient to expose worm proteins. The next step was spin for 1 min at high speed to remove insoluble components, then quickly transfer supernatant into a new tube (on ice) and immediately run on gel or store aliquots at –80°C. Proteins were resolved by SDS-PAGE on gradient gels (10% separation gel, 5% spacer gel) and transferred to a Hybond-ECL membrane. After washing with ×1 TBST buffer (Sangon Biotech, Shanghai) and blocking with 5% milk-TBST, the membrane was incubated overnight at 4°C with antibodies (listed below). The membrane was washed three times for 10 min each with ×1 TBST and then incubated with secondary antibodies at room temperature for 2 hr. The membrane was washed three times for 10 min with ×1 TBST and then visualized.

The primary antibodies used were β-actin (Beyotime, AF5003), H3 (Abcam, ab1791), H3K4me1 (Abcam, ab176877), H3K4me2 (Abcam, ab32356), H3K4me3 (Abcam, ab8580), H3K9me1 (Abcam, ab9045), H3K9me2 #1 (Abcam, ab1220), H3K9me2 #2 (Abcam, ab176882), H3K9me3 (Millipore, 07-523), H3K27me1 (Abcam, ab194688), H3K27me2 (Abcam, ab24684), H3K27me3 (Millipore, 07-449), H3K36me1 (Abcam, ab9048), H3K36me2 (Abcam, ab9049), H3K36me3 (Abcam, ab9050), H3K23me2 (Active Motif, 39653), and H3K23me3 (Active Motif, 61499). The secondary antibodies used were goat anti-mouse (Beyotime, A0216) and goat anti-rabbit (Abcam, ab205718) antibodies.

Construction of deletion mutants

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For gene deletions, triple sgRNA-guided chromosome deletion was conducted as previously described (Chen et al., 2014). To construct sgRNA expression vectors, the 20 bp unc-119 sgRNA guide sequence in the pU6::unc-119 sgRNA(F+E) vector was replaced with different sgRNA guide sequences. Addgene plasmid #47549 was used to express Cas9 II protein. Plasmid mixtures containing 30 ng/µl of each of the three or four sgRNA expression vectors, 50 ng/µl Cas9 II-expressing plasmid, and 5 ng/µl pCFJ90 were coinjected into tofu-5::gfp::3xflag (ustIS026) animals. Deletion mutants were screened by PCR amplification and confirmed by sequencing. The sgRNA sequences are listed in Supplementary file 3.

Construction of plasmids and transgenic strains

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For SET-13::GFP, a SET-13 promoter and CDS region were PCR-amplified with the primers 5′-CTTATAATACGACTCACTAGTTTGGGAAATTCACCGAAAAGGTAAC-3′ and 5′-CTCCACCTCCACCTCCGCGTACATTCTCCTTACCATC-3′ from N2 genomic DNA. A GFP::3xFLAG region was PCR-amplified with the primers 5′-GGAGGTGGAGGTGGAGCTATG-3′ and 5′-CTTGTCATCGTCATCCTTGTAATCG-3′ from plasmid pSG085. A SET-13 3′ UTR (untranslated region) was PCR-amplified with the primers 5′-GGATGACGATGACAAGTAATAAGATTGATAATTGATAATTGATAATGATTAAC-3′ and 5′-AGGAATTCCTCGAGACGTACGCCTGAAAATCTCCAAAATGTCAG-3′ from N2 genomic DNA. The ClonExpress MultiS one-step cloning kit (Vazyme, C113-02) was used to insert the SET-13::GFP::3x FLAG fusion gene into the pCFJ151 vector. The transgene was integrated onto the C. elegans chromosome IV by the MosSCI method (Frøkjaer-Jensen et al., 2008).

For the in situ transgene expressing 3x FLAG::GFP::SET-21, a 1.5 kb left arm was PCR-amplified with primers 5′-GGGTAACGCCAGCACGTGTGTGACATCGACGAGAGCAACA-3' and 5′-GGCATCTACAGGCATTGGAG-3' from N2 genomic DNA. A 1.5 kb right arm was PCR-amplified with primers 5′-GGAGGTGGAGGTGGAGCTATGCCTGTAGATGCCGAGA-3′ and 5′-CAGCGGATAACAATTTCACACTTCTTGTGCGGCAATAACA-3′ from N2 genomic DNA. A 3xflag::gfp insertion was PCR-amplified with the primers 5′-ATGGACTACAAAGACCATGACG-3′ and 5′-ATAGCTCCACCTCCACCTC-3′ from YY178 genomic DNA. The sgRNA sequences were listed in Supplementary file 3. ClonExpress MultiS One Step Cloning Kit (Vazyme C113-02, Nanjing) was used to connect these fragments with vector which is amplified with 5′-TGTGAAATTGTTATCCGCTGG-3′ and 5′-CACACGTGCTGGCGTTACC-3′ from L4440. The injection mix contained PDD162 (50 ng/μl), SET-21 repair plasmid (50 ng/μl), pCFJ90 (5 ng/μl), and three sgRNAs (30 ng/μl). The mix was injected into young adult N2 animals. The transgenes were integrated onto the C. elegans’ chromosome IV by CRISPR/Cas9 system.

For the in situ transgene expressing 3x FLAG::GFP::SET-32, a 1.5 kb left arm was PCR-amplified with primers 5′-GGGTAACGCCAGCACGTGTCCATAATAGACGTCGTCG-3′ and 5′-CGATTTCGATGACATCTTA-3' from N2 genomic DNA. A 1.5 kb right arm was PCR-amplified with primers 5′-GAGGTGGAGGTGGAGCTATGTCATCGAAATCGAAGTC-3′ and 5′-CAGCGGATAACAATTTCACATGAAAACGAGATGTACGTGA-3′ from N2 genomic DNA. A 3xflag::gfp insertion was PCR-amplified with the primers 5′-ATGGACTACAAAGACCATGACG-3′ and 5′-ATAGCTCCACCTCCACCTC-3′ from YY178 genomic DNA. The sgRNA sequences were listed in Supplementary file 3. ClonExpress MultiS One Step Cloning Kit (Vazyme C113-02, Nanjing) was used to connect these fragments with vector which is amplified with 5′-TGTGAAATTGTTATCCGCTGG-3′ and 5′-CACACGTGCTGGCGTTACC-3′ from L4440. The injection mix contained PDD162 (50 ng/μl), SET-32 repair plasmid (50 ng/μl), pCFJ90 (5 ng/μl), and three sgRNAs (30 ng/μl). The mix was injected into young adult N2 animals. The transgenes were integrated onto the C. elegans’ chromosome I by CRISPR/Cas9 system.

For the in situ transgene expressing SET-25::GFP::3x FLAG, a 1.5 kb left arm was PCR-amplified with primers 5′-gggtaacgccagCACGTGtgATTTTTCTCGCAAAGACGTG-3' and 5′-ATAGCTCCACCTCCACCTCCGAATGCAGGAAGGGTTCC-3' from N2 genomic DNA. A 1.5 kb right arm was PCR-amplified with primers 5′-ACAAGGATGACGATGACAAGTGAAAGTTTCTCCCCTATAC-3′ and 5′-cagcggataacaatttcacaCTTATCGTGTCGAGACCGG-3′ from N2 genomic DNA. A GFP::3xFLAG region was PCR-amplified with the primers 5′-GGAGGTGGAGGTGGAGCTATGAGTAAAGG-3′ and 5′-CTTGTCATCGTCATCCTTGTAATCG-3′ from SHG326 genomic DNA. The sgRNA sequences were listed in Supplementary file 3. ClonExpress MultiS One Step Cloning Kit (Vazyme C113-02, Nanjing) was used to connect these fragments with vector which is amplified with 5′-TGTGAAATTGTTATCCGCTGG-3′ and 5′-CACACGTGCTGGCGTTACC-3′ from L4440. The injection mix contained PDD162 (50 ng/μl), SET-25 repair plasmid (50 ng/μl), pCFJ90 (5 ng/μl), and three sgRNAs (30 ng/μl). The mix was injected into young adult N2 animals. The transgenes were integrated onto the C. elegans’ chromosome III by CRISPR/Cas9 system.

For the in situ transgene expressing DAF-16::GFP::3x FLAG, a 1.5 kb left arm was PCR-amplified with primers 5′-gggtaacgccagCACGTGtgTCTCGATTCCTGGATCGTCG-3' and 5′-ATAGCTCCACCTCCACCTCCCAAATCAAAATGAATATGCTGC- 3' from N2 genomic DNA. A 1.5 kb right arm was PCR-amplified with primers 5′-AGGATGACGATGACAAGTAAATTCTCTTCATTTTGTTTCCC-3′ and 5′-cagcggataacaatttcacaGCCAGAAAGAATTGGAAGGA-3′ from N2 genomic DNA. A GFP::3xFLAG region was PCR-amplified with the primers 5′-GGAGGTGGAGGTGGAGCTATGAGTAAAGG-3′ and 5′-CTTGTCATCGTCATCCTTGTAATCG-3′ from SHG326 genomic DNA. The sgRNA sequences were listed in Supplementary file 3. ClonExpress MultiS One Step Cloning Kit (Vazyme C113-02, Nanjing) was used to connect these fragments with vector which is amplified with 5′-TGTGAAATTGTTATCCGCTGG-3′ and 5′-CACACGTGCTGGCGTTACC-3′ from L4440. The injection mix contained PDD162 (50 ng/μl), DAF-16 repair plasmid (50 ng/μl), pCFJ90 (5 ng/μl), and three sgRNAs (30 ng/μl). The mix was injected into young adult N2 animals. The transgenes were integrated onto the C. elegans’ chromosome I by CRISPR/Cas9 system.

RNA isolation

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Synchronized L4 worms were sonicated in sonication buffer (20 mM Tris-HCl [pH 7.5], 200 mM NaCl, 2.5 mM MgCl2, and 0.5% NP40). The eluates were incubated with TRIzol reagent followed by isopropanol precipitation and DNase I digestion. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing was performed with a HiSeqTen instrument reading 150 base paired-end reads.

RNA-seq analysis

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The Illumina-generated raw reads were first filtered to remove adaptors, low-quality tags, and contaminants to obtain clean reads at Novogene. The clean reads were mapped to the reference genome of ce10 via TopHat software (version 2.1.1). Gene expression levels were determined by the fragments per kilobase of transcript per million mapped reads (FPKM).

qRT-PCR for mRNA

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Total RNA was reverse-transcribed into cDNA using the GoScript Reverse Transcription System (Promega) and quantified by qPCR using SYBR GREEN mix (Vazyme Q111-02, Nanjing) with a MyIQ2 real-time PCR system. Levels of ama-1 mRNA were used as internal controls for sample normalization. Data are expressed as fold changes relative to those of daf-2(e1370) animals. The data analysis was performed using a ΔΔCT approach. The primers used for qRT-PCR are listed in Supplementary file 4.

ChIP-qPCR

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ChIP experiments were performed as previously described with L4 staged animals. After crosslinking, samples were resuspended in 1 ml FA buffer (50 mM Tris/HCl [pH 7.5], 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with a proteinase inhibitor tablet (Roche no. 05056489001) and sonicated for 20 cycles at high output (each cycle: 30 s on and 30 s off) with a Bioruptor plus. Lysates were precleared and then immunoprecipitated with 2 μl anti-histone H3 (monomethyl K9) antibody (Abcam no. ab9045), 2 μl anti-histone H3 (dimethyl K9) antibody (Abcam no. mAbcam1220) or 2 μl anti-trimethylated H3K9 antibody (Millipore no. 07-523). ChIP signals were normalized to coimmunoprecipitated ama-1 and then expressed as fold changes relative to that of daf-2 (e1370) animals. qRT-PCR primers for ChIP assays are listed in Supplementary file 5.

ChIP-seq data analysis

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ChIP-seq reads were aligned to the WBcel235 assembly of the C. elegans genome using Bowtie2 version 2.3.5.1 (Langmead and Salzberg, 2012) by Ben Langmead with the default settings. The SAMtools version 0.1.19 (Li et al., 2009) ‘view’ utility was used to convert the alignments to BAM format, and the ‘sort’ utility was used to sort the alignment files. ChIP-seq peaks were called using MACs2 with default parameters against the ChIP-seq input sample. Custom Shell scripts were used to convert BAM files to BigWig format. Finally, deepTools version 3.4.3 (Ramírez et al., 2014) were used to generate profile plots showing the ChIP-seq signals of transcription factors around TSSs of indicated genes. The ChIP-seq datasets were downloaded from the ENCODE or NCBI GEO databases (Supplementary file 6).

Statistics

Bar graphs with error bars are presented as the mean and standard deviation. All of the experiments were conducted with independent C. elegans animals for the indicated N times. Statistical analysis was performed with a two-tailed Student’s t-test.

Data availability

Sequencing data have been deposited in GSA under accession codes CRA005256. Figure 2 - Source Data 1 and Figure 8 - Source Data 2 contain the original files and figures of the blots used to generate the figures. Source Code Files 1 is used to convert BAM files to BigWig format in ChIP-seq data analysis.

The following data sets were generated
    1. Guang S
    2. Huang M
    3. Hong M
    (2021) GSA
    ID CRA005256. H3K9me1/2 methylation limits the lifespan of C. elegans.

References

Decision letter

  1. Scott F Leiser
    Reviewing Editor; University of Michigan, United States
  2. Carlos Isales
    Senior Editor; Medical College of Georgia at Augusta University, United States
  3. David Katz
    Reviewer

Our editorial process produces two outputs: (i) public reviews designed to be posted alongside the preprint for the benefit of readers; (ii) feedback on the manuscript for the authors, including requests for revisions, shown below. We also include an acceptance summary that explains what the editors found interesting or important about the work.

Decision letter after peer review:

Thank you for submitting your article "H3K9me1/2 methylation limits the lifespan of C. elegans" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Carlos Isales as the Senior Editor. The following individual involved in review of your submission has agreed to reveal their identity: David Katz (Reviewer #3).

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.

Summary of reviewer discussion:

The reviewers were all very positive about the central idea of the manuscript, that putative HMTs act synergistically with daf-2 to extend lifespan. During review and subsequent discussion, several key weaknesses of the manuscript were identified that will need to be addressed before the manuscript is suitable for publication at eLife. While many of these weaknesses can be addressed by modifying the text and including additional supplementary information likely on hand, they also include a limited number of experiments that are necessary to support the key findings of the manuscript. Of highest importance, revisions must address the lack of wild-type and mutant only controls in methylation studies and the assumption of the enzymes studied as being bona fide H3K9 methyltransferases. A revision should focus on what is being shown (changes in H3K9me1/2 that correspond with lifespan in daf-2 mutants), while either addressing or taking into account the remaining unknowns. Additionally, all the reviewer comments are included, from which the essential revisions were identified, that should be addressed before publication.

Essential revisions:

1. The 6 genes being studied are putative methyltransferases, but are frequently described in the text as though they are validated and bona fide H3K9 methyltransferases. While the data presented support that they affect H3K9 methylation status, there are both direct and indirect ways this could occur. Some evidence that these putative HMTs are actual H3K9me1/me2 MTs (not acting indirectly, as observed in Schwartz-Orbach L et al., eLife 2020) and that they and daf-2 affect H3K9 methylation (ChIP seq) would greatly strengthen the manuscript. Barring this, the circumstantial data using inhibition would need to be strengthened and the text modified to clarify the lack of evidence (e.g., the introduction currently states that MET-2 and SET-25 are responsible for the methylation of H3K9, rather than saying the genes are required for the presence of H3K9me in vivo) on the direct nature of the observed effects.

2. To properly interpret the data, wild-type and mutant controls in methylation assays must be included. Presumably, based on the lifespan results, daf-2 changes methylation status in such a way that these genes are now limiting lifespan. Without control data, it is very difficult to interpret how this may work.

3. An explanation for why 6 different H3K9me1/me2 methylases would have such similar phenotypes. This explanation could come out of #1 and/or could involve other experiments and insights, including a better discussion of the individual HMTs and how they are similar/different. For example, addressing the H3K23me2/3 data in light of the Gu lab paper referenced in #1 may help in emphasizing the complexity of the interaction network and will also highlight the biological relevance of these findings.

4. Better discussion and clarity on the relationship between brood size and fertility tradeoffs in these animals, including inclusion of daf-2 single mutant brood sizes.

5. Better clarity on replication, blinding, and inclusion of summary survival data including conditions examined per assay, N, animals censored, median lifespan (along with average lifespan), and comparison used for determination of significance. If replicates are lacking, additional replicates may be necessary (see reviewer comments).

6. A significantly more detailed transcriptomic analysis and clarity about the analysis and it's methods: e.g., unbiased analysis to identify other pathways, differentiation between DAF-16 class I/II genes, better evidence to claim class I.

7. Tempered statements on generality, or more experiments to show generality, and clarified writing to more accurately report findings.

8. Use of the data to clarify the relationship between heterochromatin, H3K9me1/2, and H3K9me3.1.

Reviewer #1 (Recommendations for the authors):

1) The C. elegans enzymes described in the intro are still only putative methyltransferases. Most of them, outside of SET-2 have not been shown by in vitro methylation assays so should be referred to as putative methyltransferases (unless the authors wish to perform in vitro methylation assays to complement the in vivo findings of others which could still be indirect). Since so much of the manuscript is focused on H3K9 methylation it would be good to show that some of these enzymes (maybe just SET-21 if it is too much to show for them all) are indeed H3K9 methyltransferases.

2) It's important to see how H3K9 methylation changes in daf-2 worms relative to WT worms, both by WB at gross level and genome wide by ChIPseq. This change in H3K9me1/me2 genome wide should then be compared to daf-16 target gene lists to see if there is an enrichment.

3) For 6b you have to present all 4 conditions for epistasis experiments. The reader needs to see what the effect of lys-7 deletion is in the daf-2 background by itself. And then 2-way anova needs to be done to test whether the effect of lys-7 in the daf-2 background is different from in the daf-2;set-21 background.

4) Some attempt should be made to explain why there are 6 redundant H3K9me1/me2 methylases (again I'm not convinced yet that there are because of point 1) that all affect lifespan in the same manner. Are these enzymes expressed in the same tissue? Do they affect H3K9me1/me2 on the same genes? At the same time? Usually it is believed that different enzymes that modify the same mark have some sort of specificity but here they are not seeing that. I don't think it's necessary to perform tissue specific experiments for this initial manuscript but some experimental justification should be provided. Do they believe that it's the amount of heterochromatin DNA in general which is regulating this? Or is it a gene specific effect?

Reviewer #2 (Recommendations for the authors):

1. As the authors mentioned in the discussion, H3K9me2 is the histone modification in C. elegans that corresponds best with canonical heterochromatin factors like HPL-2 (McMurchy et al., 2017). However, in their results, they focus on the lack of effect on lifespan seen for H3K9me3 modifiers like SET-25 to rule out any effect with heterochromatin. In fact, despite corresponding highly with H3K9me2, one of the marks implicated in further extending the lifespan of their HMT; daf-2 double mutants, hpl-1 and hpl-2 mutations had no effect in a daf-2 background (although they do seem to slightly decrease lifespan, and it would be interesting to see the statistical comparison of a log-rank test). The authors should clarify the relationship between heterochromatin, H3K9me1/2, and H3K9me3.

2. I was confused by the statements describing Figure 4C on lines 176-178. Both double and triple mutants were much longer-lived than daf-2 single mutants, rather than having similar lifespan extensions as the daf-2 single mutants. There was even a distinction between the daf-2; set-21 double mutant and the daf-2; set-21; set-2 triple mutant – the presence of a set-2 mutation represses the slight lifespan extension difference seen in the daf-2; set-21 double mutant when compared to the daf-2; set-2 double mutant. The authors should rephrase their description of their results to more accurately convey their findings.

3. My major concerns with the approach to transcriptomic analysis were conveyed in the public review, but I include more specific concerns here. Given that Class I genes are an important downstream consequence of DAF-16, it isn't clear why these are primarily unaffected in the daf-2 control condition shown in Figure 5A. Furthermore, the authors focus primarily on the top 50 Class I genes, but there are interesting effects seen in the top 50 Class II genes as well, especially given that mutations in the HMTs seem to suppress some of the upregulation observed in daf-2 control – why exclude these from their interpretations? Additionally, the brevity of the methods makes it hard to tell exactly what comparisons are being drawn – in the heatmaps shown in in Figure 5C, D, does the color refer upreglation in comparison to a wild-type control? Why not compare misregulation to a daf-2 single mutant instead? What does "Top 50" refer to – are these the fifty most-affected in these specific data sets, or are they a gene set identified by an independent metric? Why limit the analysis to only fifty genes? Finally, this analysis would be further strengthened by comparing locus-specific effects to the known locations of H3K9me1/2/3 peaks in wild-type genomes in previously published datasets (like in Li et al., 2021 or McMurchy et al., 2017) or even to H3K9me1/2/3 localization in datasets of relevant HMT mutants like set-32.

4. How were the 10 Class I DAF-16 target genes chosen? It doesn't seem like they were in the top 50 (or not that I could easily see). Furthermore, why were no Class II genes chosen? The authors should clarify how they chose to examine these specific candidates, and if necessary, extend the analysis for other targets to see whether the effects are specific to Class I targets only (as they argue in their model). Furthermore, each of these candidate genes needs to be examined in a daf-2 mutant background to fully interpret the meaning of the suppression of long-lived daf-2; set-21 mutants.

5. The authors claim that loss of H3K9me1/2 increases binding of DAF-16 at its target genes (line 282). There is no evidence to support this claim (and a lack of evidence for this claim, if we take the DAF-16 localization data in Figure S3 at complete face value). This could be part of their proposed model (outlined in Figure S7), but as written, it reads as if it were a summary of work presented in the paper. The authors should clarify their writing to ensure full accuracy for what their data can support.

6. Throughout the manuscript, it's difficult to build a cohesive understanding of the functional effects of the HMT mutants. In part, this is because the paper investigates several HMTs without discussing their specific effects (in certain tissues or cell types, or at specific stages). The analyses are sometimes too broad (immunoblots of total histone modifications) and at other times too narrow (focusing only on 50 Class I DAF-16 target genes). Given that H3K9me1/2 will likely have locus specificity, it is unsatisfying to leave the analysis at the global level of immunoblots (although it is very compelling to see global effects in their mutants). Including a deeper, and unbiased, analysis of their transcriptomic data will help to bridge the gap between the global and the locus-specific, and may even point out other interesting avenues that will further bolster their claims about potential mechanism (or open new avenues of study).

[Editors’ note: further revisions were suggested prior to acceptance, as described below.]

Thank you for resubmitting your work entitled "H3K9me1/2 methylation limits the lifespan of C. elegans" for further consideration by eLife. Your revised article has been evaluated by Carlos Isales (Senior Editor) and a Reviewing Editor.

The manuscript has been improved but there are some remaining issues that need to be addressed, as outlined below:

Primarily, the three areas that remain an issue before submission are (1) a second replicate needs to be included (and ideally, performed blinded) for experiments such as Figures 1B, 4A, and 4B, (2) the appropriate epistasis controls should be included as requested by reviewer 1 to properly interpret the experiments (e.g., Figure 7), and (3) the text needs to be modified where precision remains an issue, as described by reviewer 1. There should be no technical issues with completing these experiments, and they're relatively straightforward, although I appreciate that it can take some time to complete longevity assays for these long-lived mutants. However, these experiments are necessary to experimentally validate the claims within the manuscript, along with responses to the reviewer comments below.

Reviewer #1 (Recommendations for the authors):

In the revised manuscript "H3K9me1/2 methylation limits the lifespan of C. elegans" Huang M, Hong M et al., performed additional experiments to examine the role of putative H3K9 methyltransferases in the lifespan regulation of daf-2 mutant worms. While the new experiments do bolster some portions of the manuscript I felt that the critical questions which I had asked in my initial review weren't addressed and are still important. I understand that COVID has made it difficult to perform certain experiments but with those restrictions in mind then the paper needs to be reworked to reflect what the experiments actually show rather than the model the authors wish to be true. Most importantly the role of H3K9 methylation in daf-2 mutants is still not really clear. These genes seem to have virtually no effect in WT background so the text needs to really be rewritten to reflect that. Starting with the title of the manuscript and then from the intro on it should be written from the perspective of "we wanted to examine how chromatin modifying enzymes were important in insulin receptor mutant worms".

1) As stated last review (major point #3), in epistasis experiments (such as WT and eat-2 +/- set-21 and WT and daf-2 +/- met-2, and Figure 3C +D, 7B) you need to include all 4 conditions in the experiment to make any conclusions. For example, you can't do the set-21 vs WT at a different time and assume that the set-21 is still going to have no effect in that particular experiment. There might be some unknown factor (food, temperature, etc) that makes set-21 actually have an effect in the WT worms in that experiment which would mean a very different conclusion. Then after the experiment is done you perform a 2 way ANOVA analysis to reveal whether set-21 has a significantly different effect in the WT context or the mutant context. This comment still holds true for asm-2, Y39G8B.7, etc… that I had asked for last review. You do not need to perform all possible combinations of these 3 genes but at the very least daf-2, daf-2;set-21, daf-2;asm-2 and daf-2;set-21;asm-2 if you want to make any conclusion about asm-2 relative to set-21 in the daf-2 background), examining 3 lines in an epistasis experiment rather than 4 is not really informative.

2) The text needs to be rewritten to reflect that this is all only occurring in daf-2 mutant worms and not in WT worms. This rewriting needs to start with the title ("…limits the lifespan of daf-2 mutant C. elegans".) and work its way thru the intro, results and discussion (where the authors claim H3K9me regulators should be considered for lifespan regulation). Need to include explicit writing that deletion of all these putative enzymes has only modest effects on H3K9me and lifespan in the WT context and their role is only revealed in the daf-2 mutants. Need to speculate about what that is. What makes the daf-2 mutation special to reveal a regulatory role for these genes?

Reviewer #2 (Recommendations for the authors):

Upon resubmission, this paper is greatly improved – readers now have the evidence needed to evaluate the paper's main claim that H3K9 HMTs synergistically extend lifespan in daf-2 mutants, in part via DAF-16, but also via. The additional experiments, along with a more tempered approach to discussing their findings, significantly strengthen the paper.

However, several of our concerns were not addressed by these changes, nor in the rebuttal. For example, Reviewer 2 asked that some of the key lifespan experiments be replicated at least once and also performed blinded – there are several figures where only a single replicate is shown. Key controls are still missing, like in Figure 7, where Reviewer 1 had asked for appropriate controls to interpret the epistasis experiments for example, set-21 single mutants and daf-2; lys-7 double mutants. The authors' rebuttal mentioned generating new alleles for some genes, but providing appropriate single mutant and double mutant controls should require no new strains to be built (since the strains likely already exist if the authors generated the triple mutant).

The extended analysis of the mRNA-seq is better (and opens up an interesting line of questioning for future studies!). However, the authors failed to address most of Reviewer 2's Major Point 3 about their transcriptomic analysis, nor did they include further details about how the analysis was done. The methods for the mRNA-seq will need to be more detailed. What is their unbiased approach? What is the differential expression shown in the Figure 5? For example, I had previously asked: "Does the color refer to upregulation in comparison to a wild-type control? Why not compare misregulation to a daf-2 single mutant instead?" and the answer is still not clear. Furthermore, if Class I genes are defined as being induced in daf-2 mutants, why are they downregulated in Figure 5E? And if Class II genes are defined as being not induced in daf-2 mutants, why are they upregulated in Figure 5F? I may be misunderstanding the gene classifications, but it is a demonstration of how the text is unclear. Overall, I found the new transcriptomic analyses are compelling, but more care needs to be taken to fully explain what was done.

https://doi.org/10.7554/eLife.74812.sa1

Author response

Essential revisions:

1. The 6 genes being studied are putative methyltransferases, but are frequently described in the text as though they are validated and bona fide H3K9 methyltransferases. While the data presented support that they affect H3K9 methylation status, there are both direct and indirect ways this could occur. Some evidence that these putative HMTs are actual H3K9me1/me2 MTs (not acting indirectly, as observed in Schwartz-Orbach L et al., eLife 2020) and that they and daf-2 affect H3K9 methylation (ChIP seq) would greatly strengthen the manuscript. Barring this, the circumstantial data using inhibition would need to be strengthened and the text modified to clarify the lack of evidence (e.g., the introduction currently states that MET-2 and SET-25 are responsible for the methylation of H3K9, rather than saying the genes are required for the presence of H3K9me in vivo) on the direct nature of the observed effects.

Thanks very much for the comments.

We completely agree with the reviewers that we lack direct biochemical evidence showing that these SET proteins are bona fide H3K9 methyltransferases. We have tried very hard to conduct similar experiments as Schwartz-Orbach has done on SET-32. However, given the covid-19 pandemic and biosafety issue, we could not get access to [3H]-labeled S-adenosylmethionine (SAM). We are very sorry that we could not pursue further at this stage. Therefore, we have revised the manuscript saying that these SET proteins are putative histone methyltransferases and are required for the presence of H3K9me1/2 marks. The text of MET-2 and SET-25 has been revised similarly and saying that they are required for the presence of H3K9me in vivo.

We also added in the Discussion section that further investigations are required to reveal their enzymatic activities by in vitro experiments (lines 496-506).

2. To properly interpret the data, wild-type and mutant controls in methylation assays must be included. Presumably, based on the lifespan results, daf-2 changes methylation status in such a way that these genes are now limiting lifespan. Without control data, it is very difficult to interpret how this may work.

Thanks very much for the comments.

We have included new data comparing the global levels of H3K9me1/2/3 in N2 and daf-2 animals by Western blotting (new Figure 8—figure supplement 1A). The daf2 mutation itself did not significantly change the gross levels of H3K9me1/2/3 status.

We also compared the levels of H3K9me1/2/3, H3K4me1/2/3, H3K27me1/2/3, H3K36me1/2/3 and H3K23me2/3 in N2 and set mutants at L4 and embryonic stages (new Figure 8—figure supplement 1B-C). In N2 background, the mutation of these set genes did not significantly change gross levels of H3K9me1/2/3 either.

We speculated that the mutation of daf-2 sensitizes the animals, for example,

increases the cytoplasm-to-nuclear translocation of DAF-16. We have generated a

single-copy, in situ GFP-tagged DAF-16 transgene, crossed to daf-2, set-21, set-25

single mutants and their double mutants, and scored the nuclear localization of DAF16 at 20oC and 25oC, respectively (new Figure 5A-B, Figure 5—figure supplement 1B). The mutation of daf-2 increased the nuclear accumulation of DAF-16. The double mutants daf-2;set-21 and daf-2;set-25 further increased the nuclear accumulation of DAF-16.

Interestingly, DAF-16 was nearly 100% localized in the nucleus in both daf-2;set21 and daf-2;set-25 double mutants. Yet daf-2;set-21, but not daf-2;set-25, extended the lifespan of daf-2 animals, suggesting addition regulation required beyond the nuclear localization of DAF-16. Our work suggested that the transcription activity of DAF-16 may preferentially depend on H3K9me1/2, but not H3K9me3.

We have revised the text to include the information (lines 245-275, 357-361).

3. An explanation for why 6 different H3K9me1/me2 methylases would have such similar phenotypes. This explanation could come out of #1 and/or could involve other experiments and insights, including a better discussion of the individual HMTs and how they are similar/different. For example, addressing the H3K23me2/3 data in light of the Gu lab paper referenced in #1 may help in emphasizing the complexity of the interaction network and will also highlight the biological relevance of these findings.

Thanks very much for the comments. We are also eager to know why the 6 different H3K9me1/me2 methylases would have such similar phenotypes in this lifespan extension assay, yet have no clue at this stage.

We have generated in situ single-copy 3xFLAG-GFP tagged SET-21, SET-25 and SET-32 transgenes by CRISPR/Cas9 technology and single-copy GFP-3xFlAG-tagged SET-13 transgenic strains using the Mos1-mediated single-copy insertion (MosSCI) technology. These animals were imaged in N2 and daf-2 background at embryonic and larva stages respectively, to figure out the expression patterns and cellular localizations of SET proteins (new Figure 4—figure supplement 1). However, we failed to find a clear correlation between their expression pattern with the lifespan extension phenotype. The depletion of SET-21 and SET-32 extended the lifespan of daf-2 animals, but GFP::SET21 and GFP::SET-32 showed different expression patterns and subcellular localizations. GFP::SET-21 exclusively located in the nucleus but GFP::SET-32 located in both the nucleus and cytoplasm in embryos. At larval stage, GFP::SET-21 was expressed in soma but GFP::SET-32 was expressed in germline. Both set-13 and set-25 mutants did not show lifespan extension in N2 and daf-2 background worms. SET-13 and SET-25 were enriched in the nucleus. SET-13::GFP was expressed through 8-cell stage to lateembryonic stage, while SET-25::GFP was expressed in the whole embryonic stage and the germline in young adults.

To identify the target genes in this group of lifespan extension daf-2;set mutants, we re-analyzed the mRNA expression profile in the double mutants via an unbiased method (Figure 6, Figure 6—figure supplement 1). We have identified 49 co-upregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants daf-2;set-19, daf-2,set-21, daf-2;set-32, but not in daf-2 and daf-2;daf25 animals (Figure 6A-B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (Figure 6—figure supplement 1B). 22 co-upregulated genes are not DAF-16 Class I genes, suggesting the existence of additional regulations.

C. elegans’ genome encodes 10 putative H3K9 methyltransferases, most of which have not been directly characterized for their biochemical properties by in vitro experiments. The presence of these many putative H3K9 methyltransferases may lead to a complexity of the interaction network of histone modifications. In addition, some SET proteins may have multiple roles in mediating histone modifications. For example, SET-19 is required for both H3K9me1/2 and H3K23me3 marks, further bringing up complexity of the regulation. Further investigations are necessary to reveal their enzymatic activities by in vitro experiments. In addition, identifying the in vivo targeted genes will also be crucial to help understanding why and how these SET proteins are involved in lifespan regulation.

We have revised the text to include the information (lines 186-201, 301-320, 496506).

4. Better discussion and clarity on the relationship between brood size and fertility tradeoffs in these animals, including inclusion of daf-2 single mutant brood sizes.

Thanks very much for the suggestion.

We have included the brood size assay of N2, daf-2, set-21 and daf-2;set-21. Knocking out set-21 reduced the brood size of daf-2(e1370) mutant worms and significantly extended lifespan (Figure 1B, Figure1—figure supplement 1C). However, we did not find significant difference between the brood size of N2 and daf-2 (new Figure 1—figure supplement 1C and Figure 3—figure supplement 1B).

A trade-off has been proposed between fertility and lifespan, where increasing lifespan usually comes at the cost of reduced fertility. In C. elegans, removing the germ cells extends lifespan by triggering the nuclear localization of the DAF-16/FOXO transcription factor and activating target genes in the intestine. Some long-lived mutant worms, like daf-2 and rsks-1, show reduced brood size. Consistently, we found that the long-lived worms daf-2;met-2, daf-2;set-6, daf-2;set-19, daf-2;set-20, daf-2;set-21, daf-2;set-32, and daf-2;set-33 all have reduced brood size compared to that of daf-2 animals. However, additional investigations are necessary to examine whether removing the germline cells could further extend worm lifespan.

We revised the Discussion section to include this information (lines 115-117, 402411).

5. Better clarity on replication, blinding, and inclusion of summary survival data including conditions examined per assay, N, animals censored, median lifespan (along with average lifespan), and comparison used for determination of significance. If replicates are lacking, additional replicates may be necessary (see reviewer comments).

Thanks very much for the comments.

We have revised the Materials and methods section (lines 549-559) and figure legends to include the information of each life span assay. We also included a new Table S1 to summarize all lifespan experiments.

6. A significantly more detailed transcriptomic analysis and clarity about the analysis and it's methods: e.g., unbiased analysis to identify other pathways, differentiation between DAF-16 class I/II genes, better evidence to claim class I.

Thanks very much for the suggestions.

We used two approaches to analyze the mRNA-seq data.

First, the depletion of DAF-2 reduces the insulin signaling pathway, promotes DAF-16 nuclear translocation, and leads to both upregulation and downregulation of large sets of genes, referred to as Class I and II genes, respectively. Class I genes are induced in daf-2 mutants but are repressed in daf-2;daf-16 double mutants. Class II genes are not induced in daf-2 mutants but are induced in daf-2; daf-16 double mutants. 1663 genes are classified as positive (class I) DAF-16 targets and 1733 genes are classified as negative (class II) DAF-16 targets of DAF-16. Class I genes are enriched for the Gene Ontology categories including oxidation, reduction, and energy metabolism, whereas class II genes are enriched for genes involved in biosynthesis, growth, reproduction, and development. We performed mRNA-seq and analyzed Class I and II DAF-16 genes to identify the mis-regulated genes in the daf-2;set mutants. Interestingly, the mRNA levels of DAF-16 Class I, but not Class II, genes are consistently activated in long-lived daf-2;set-19, daf-2;set-21 and daf-2;set-32 worms, than in the control daf-2 and daf-2;set-25 animals (Figure 5E-F and new Figure 5figure supplement 2).

Second, to identify the target genes in the group of lifespan extension daf-2;set mutants, we re-analyzed the mRNA expression profile in the double mutants via an unbiased method (new Figure 6, Figure 6—figure supplement 1). We have identified 49 co-upregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants daf-2;set-19, daf-2,set-21, daf-2;set-32, but not in daf-2 and daf-2;daf-25 animals (Figure 6A-B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (new Figure 6—figure supplement 1B). 22 co-upregulated genes are not DAF-16 Class I genes, suggesting the existence of additional regulations.

We then analyzed a number of known transcription factors for their binding to the co-regulated targeted genes (new Figure 6C-D, Figure 6—figure supplement 1C-E). Among them, we found that DAF-16 and NHR-80 were specifically enriched at the transcription start sites (TSS) of the 49 co-upregulated genes. NHR-80 is a homolog of mammalian hepatocyte nuclear factor 4 and is an important nuclear hormone receptor involved in the control of fat consumption and fatty acid composition in C. elegans. Among the genes targeted by DAF-16 and NHR-80, twelve of them are co-regulated by both factors, which is consistent with previous report that daf-16 and nhr-80 function in parallel pathway for lipid metabolism.

We revised the text to include this information (lines 284-320).

7. Tempered statements on generality, or more experiments to show generality, and clarified writing to more accurately report findings.

Thanks very much for the suggestion. We have revised the manuscript to tone down these SET proteins as putative H3K9me1/2 methyltransferases. And we also carefully revised the text to more accurately report our findings.

8. Use of the data to clarify the relationship between heterochromatin, H3K9me1/2, and H3K9me3.1.

Thanks very much for the suggestion. Actually, the relationship between heterochromatin, H3K9me1/2, and H3K9me3 is quite intriguing.

H3K9me3 is a hallmark of heterochromatin and is often enriched on repetitive sequences. In addition, H3K9me1/2/3 have all been shown enrichment on repeat sequences (GERSTEIN et al., 2010). H3K9 methylation and its association with the nuclear envelope help maintain silencing of repetitive sequences and may contribute to the maintenance and stability of heterochromatin-like regions in C. elegans, as observed in other organisms. A hallmark of heterochromatin is the enrichment of HP1. The nematode C. elegans has two HP1 paralogous proteins: HP1 Like 1 and 2 (HPL-1 and HPL-2). Interestingly, HPL-2 may serve additional roles than HPL-1, as hpl-2 mutants display diverse defects while hpl-1 mutants generally lack obvious defects. The pattern of HPL-2 most closely resembles H3K9me1 and H3K9me2 but less closely resembles H3K9me3. HPL-2-bound genes, especially those located on arms, possess significantly higher levels of H3K9me2, but show no significant difference in H3K9me3 levels when compared to genes not bound by HPL-2. SET-25 is a putative H3K9me3 methyltransferase and is recruited to targeted genomic loci either by H3K9me2 which is deposited by MET-2 or by the somatic Argonaute protein NRDE-3 and small RNAs. SET-25 colocalizes with both H3K9me3 and HPL-1, but does not colocalize with HPL-

2.

H3K9me2 and H3K9me3 exhibit different patterns of repeat enrichment. H3K9me2 is more associated with DNA transposons and satellite repeats, similar to the heterochromatin factors HPL-2, LET-418, LIN-13, LIN-61, and MET-2, whereas H3K9me3 is particularly associated with retrotransposon families, especially LINE and SINE elements. Moreover, H3K9me2 and the five heterochromatin factors are enriched at telomeres, whereas H3K9me3 is not. Therefore, H3K9me2, rather than H3K9me3, may be more closely associated with canonical heterochromatin factors in C. elegans. It was postulated that losing repressive chromatin is detrimental to lifespan. In humans, two premature aging diseases are caused by mutations in lamins that reduce heterochromatin and disrupt its nuclear localization. In C. elegans, Drosophila, and mammals, heterochromatin decreases as individuals grow older. Additionally, mutations that increase repressive chromatin extend lifespan in eukaryotes. In N2 background animals, the depletion of hpl-2 was shown increased lifespan. However, we did not observe a further lifespan extension in daf-2;hpl-2 animals, comparing to the daf-2 mutant. Similarly, we did not observe a significant change in lifespan in daf2;set-25 mutants. The depletion of the two heterochromatin factors HPL-1 and HPL-2 failed to further extend the lifespan, suggesting that heterochromatin itself may not be sufficient to perturb lifespan in daf-2 mutant worms.

We have revised the Discussion section to include the above information (lines 426-469).

Reviewer #1 (Recommendations for the authors):

1) The C. elegans enzymes described in the intro are still only putative methyltransferases. Most of them, outside of SET-2 have not been shown by in vitro methylation assays so should be referred to as putative methyltransferases (unless the authors wish to perform in vitro methylation assays to complement the in vivo findings of others which could still be indirect). Since so much of the manuscript is focused on H3K9 methylation it would be good to show that some of these enzymes (maybe just SET-21 if it is too much to show for them all) are indeed H3K9 methyltransferases.

Thanks very much for the suggestion.

We completely agree with the reviewer that we lack direct evidence showing that these SET proteins are bona fide H3K9 methyltransferases. We have tried very hard to conduct similar experiments as Schwartz-Orbach et al., has done on SET-32. However, given the covid-19 pandemic and biosafety issue, we could not get access to [3H]labeled S-adenosylmethionine (SAM). We are very sorry that we could not pursue further at this stage. Therefore, we have revised the manuscript saying that these SET proteins are putative histone methyltransferases and are required for the presence of H3K9me1/2.

C. elegans’ genome encodes 10 putative H3K9 methyltransferases, most of which have not been directly characterized for their biochemical properties by in vitro experiments (SCHWARTZ-ORBACH et al., 2020). The presence of these many putative H3K9 methyltransferases may lead to a complexity of the interaction network of histone modifications. In addition, some SET proteins may have multiple roles in mediating histone modification. For example, SET-19 is required for both H3K9me1/2 and H3K23me3 marks, further bringing up complexity of the regulation. Further investigations are necessary to reveal their enzymatic activities by in vitro experiments

(SCHWARTZ-ORBACH et al., 2020). In addition, identifying the in vivo targeted genes will also be crucial to help understanding why and how these SET proteins are involved in lifespan regulation.

We have revised the Discussion section to include the above information (lines 496-506).

2) It's important to see how H3K9 methylation changes in daf-2 worms relative to WT worms, both by WB at gross level and genome wide by ChIPseq. This change in H3K9me1/me2 genome wide should then be compared to daf-16 target gene lists to see if there is an enrichment.

Thanks very much for the comments.

We have included new data comparing the global levels of H3K9me1/2/3 in N2 and daf-2 animals by Western blotting (new Figure 8—figure supplement 1A). The daf2 mutation itself did not significantly change the gross levels of H3K9me1/2/3 status.

We also compared the levels of H3K9me1/2/3, H3K4me1/2/3, H3K27me1/2/3, H3K36me1/2/3 and H3K23me2/3 in N2 and set mutants at L4 and embryonic stages (new Figure 8—figure supplement 1B-C). In N2 background, the mutation of these set genes did not significantly change gross levels of H3K9me1/2/3 either.

However, for technical reasons, we could not successfully conduct ChIP-seq experiments on daf-2 and daf-2;set larva animals.

We speculated that the mutation of daf-2 sensitizes the animals, for example,

increases the cytoplasm-to-nuclear translocation of DAF-16. We have generated a

single-copy, in situ GFP-tagged DAF-16 transgene, crossed to daf-2, set-21, set-25

single mutants and their double mutants, and scored the nuclear localization of DAF16 at 20oC and 25oC, respectively (new Figure 5A-B, Figure 5—figure supplement 1B). The mutation of daf-2 increased the nuclear accumulation of DAF-16. The double mutants daf-2;set-21 and daf-2;set-25 further increased the nuclear accumulation of DAF-16.

Interestingly, DAF-16 was nearly 100% localized in the nucleus in both daf-2;set21 and daf-2;set-25 double mutants. Yet daf-2;set-21, but not daf-2;set-25, extended the lifespan of daf-2 animals, suggesting addition regulation required beyond the nuclear localization of DAF-16. Our work suggested that the transcription activity of DAF-16 may preferentially depend on H3K9me1/2, but not H3K9me3.

We have revised the text to include the information (lines 245-275, 357-361).

3) For 6b you have to present all 4 conditions for epistasis experiments. The reader needs to see what the effect of lys-7 deletion is in the daf-2 background by itself. And then 2-way anova needs to be done to test whether the effect of lys-7 in the daf-2 background is different from in the daf-2;set-21 background.

Thanks very much for the suggestions. These are really valuable experiments to understand the mechanism of each putative target gene. However, for the time issue, we are still at the stage to generate multiple alleles and transgenes of nhr-62, sod-3, asm-2, F35E8.7, and Y39G8B.7. Hopefully, we can carefully investigate how and why each gene is involved in lifespan regulation in daf-2;set double mutant animals in the near future.

4) Some attempt should be made to explain why there are 6 redundant H3K9me1/me2 methylases (again I'm not convinced yet that there are because of point 1) that all affect lifespan in the same manner. Are these enzymes expressed in the same tissue? Do they affect H3K9me1/me2 on the same genes? At the same time? Usually it is believed that different enzymes that modify the same mark have some sort of specificity but here they are not seeing that. I don't think it's necessary to perform tissue specific experiments for this initial manuscript but some experimental justification should be provided. Do they believe that it's the amount of heterochromatin DNA in general which is regulating this? Or is it a gene specific effect?

Thanks very much for the comments. We are also eager to know why the 6 different H3K9me1/me2 methylases would have such similar phenotypes in this lifespan extension assay, yet have no clue at this stage.

We have generated in situ single-copy 3xFLAG-GFP tagged SET-21, SET-25 and SET-32 transgenes by CRISPR/Cas9 technology and single-copy GFP-3xFlag-tagged SET-13 transgenic strains using the Mos1-mediated single-copy insertion (MosSCI) technology. These animals were imaged in N2 and daf-2 background at embryonic and larva stages respectively, to figure out the expression patterns and cellular localizations of SET proteins (new Figure 4—figure supplement 1). However, we failed to find a clear correlation between their expression pattern with the lifespan extension phenotype. The depletion of SET-21 and SET-32 extended the lifespan of daf-2 animals, but GFP::SET21 and GFP::SET-32 showed different expression pattern and subcellular localization. GFP::SET-21 exclusively located in the nucleus but GFP::SET-32 located in both the nucleus and cytoplasm in embryos. At larval stage, GFP::SET-21 was expressed in soma but GFP::SET-32 was expressed in germline. Both set-13 and set-25 mutants did not show lifespan extension in N2 and daf-2 background worms. SET-13 and SET-25 were enriched in the nucleus. SET-13::GFP was expressed through 8-cell stage to lateembryonic stage, while SET-25::GFP was expressed in the whole embryonic stage and the germline in young adults.

To identify the target genes in the group of lifespan extension daf-2;set mutants, we re-analyzed the mRNA expression profile in the double mutants via an unbiased method (new Figure 6, Figure 6—figure supplement 1). We have identified 49 coupregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants daf-2;set-19, daf-2,set-21, daf-2;set-32, but not in daf-2 and daf-2;daf-25 animals (new Figure 6A-B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (new Figure 6—figure supplement 1B). 22 co-upregulated genes are not DAF-16 Class I genes, suggesting the existence of additional regulations.

C. elegans’ genome encodes 10 putative H3K9 methyltransferases, most of which have not been directly characterized for their biochemical properties by in vitro experiments. The presence of these many putative H3K9 methyltransferases may lead to a complexity of the interaction network of histone modifications. In addition, some SET proteins may have multiple roles in mediating histone modifications. For example, SET-19 is required for both H3K9me1/2 and H3K23me3 marks, further bringing up complexity of the regulation. Further investigations are necessary to reveal their enzymatic activities by in vitro experiments. In addition, identifying the in vivo targeted genes will also be crucial to help understanding why and how these SET proteins are involved in lifespan regulation.

We have revised the text to include the information (lines 186-201, 301-320, 496-506).

Reviewer #2 (Recommendations for the authors):

1. As the authors mentioned in the discussion, H3K9me2 is the histone modification in C. elegans that corresponds best with canonical heterochromatin factors like HPL-2 (McMurchy et al., 2017). However, in their results, they focus on the lack of effect on lifespan seen for H3K9me3 modifiers like SET-25 to rule out any effect with heterochromatin. In fact, despite corresponding highly with H3K9me2, one of the marks implicated in further extending the lifespan of their HMT; daf-2 double mutants, hpl-1 and hpl-2 mutations had no effect in a daf-2 background (although they do seem to slightly decrease lifespan, and it would be interesting to see the statistical comparison of a log-rank test). The authors should clarify the relationship between heterochromatin, H3K9me1/2, and H3K9me3.

Thanks very much for the suggestion. Actually, the relationship between heterochromatin, H3K9me1/2, and H3K9me3 is quite intriguing.

H3K9me3 is a hallmark of heterochromatin and is often enriched on repetitive sequences. In addition, H3K9me1/2/3 have all been shown enrichment on repeat sequences. H3K9 methylation and its association with the nuclear envelope help maintain silencing of repetitive sequences and may contribute to the maintenance and stability of heterochromatin-like regions in C. elegans, as observed in other organisms. A hallmark of heterochromatin is the enrichment of HP1. The nematode C. elegans has two HP1 paralogous proteins: HP1 Like 1 and 2 (HPL-1 and HPL-2). Interestingly, HPL-2 may serve additional roles than HPL-1, as hpl-2 mutants display diverse defects while hpl-1 mutants generally lack obvious defects. The pattern of HPL-2 most closely resembles H3K9me1 and H3K9me2 but less closely resembles H3K9me3. HPL-2bound genes, especially those located on arms, possess significantly higher levels of H3K9me2, but show no significant difference in H3K9me3 levels when compared to genes not bound by HPL-2. SET-25 is a putative H3K9me3 methyltransferase and is recruited to targeted genomic loci either by H3K9me2 which is deposited by MET-2 or by the somatic Argonaute protein NRDE-3 and small RNAs. SET-25 colocalizes with both H3K9me3 and HPL-1, but does not colocalize with HPL-2.

H3K9me2 and H3K9me3 exhibit different patterns of repeat enrichment. H3K9me2 is more associated with DNA transposons and satellite repeats, similar to the heterochromatin factors HPL-2, LET-418, LIN-13, LIN-61, and MET-2, whereas H3K9me3 is particularly associated with retrotransposon families, especially LINE and SINE elements. Moreover, H3K9me2 and the five heterochromatin factors are enriched at telomeres, whereas H3K9me3 is not. Therefore, H3K9me2, rather than H3K9me3, may be more closely associated with canonical heterochromatin factors in C. elegans. It was postulated that losing repressive chromatin is detrimental to lifespan. In humans, two premature aging diseases are caused by mutations in lamins that reduce heterochromatin and disrupt its nuclear localization. In C. elegans, Drosophila, and mammals, heterochromatin decreases as individuals grow older. Additionally, mutations that increase repressive chromatin extend lifespan in eukaryotes. In N2 background animals, the depletion of hpl-2 was shown increased lifespan. However, we did not observe a further lifespan extension in daf-2;hpl-2 animals, comparing to the daf-2 mutant. Similarly, we did not observe a significant change in lifespan in daf2;set-25 mutants. The depletion of the two heterochromatin factors HPL-1 and HPL-2 failed to further extend the lifespan, suggesting that heterochromatin itself may not be sufficient to perturb lifespan in daf-2 mutant worms.

We have revised the Discussion section to include the above information (lines 426469).

We have revised the Materials and methods section (lines 549-559) and figure legends to include the information of each lifespan assay. We also included a new Table S1 to summarize all lifespan experiments.

2. I was confused by the statements describing Figure 4C on lines 176-178. Both double and triple mutants were much longer-lived than daf-2 single mutants, rather than having similar lifespan extensions as the daf-2 single mutants. There was even a distinction between the daf-2; set-21 double mutant and the daf-2; set-21; set-2 triple mutant – the presence of a set-2 mutation represses the slight lifespan extension difference seen in the daf-2; set-21 double mutant when compared to the daf-2; set-2 double mutant. The authors should rephrase their description of their results to more accurately convey their findings.

Sorry for the confusion.

We have revised the text as “the double mutants daf-2;set-2 and daf-2;set-21 and

the triple mutants daf-2;set-2;set-21 exhibited similar lifespan extensions relative to that of daf-2 animals (Figure 4C)” (lines 221-223).

3. My major concerns with the approach to transcriptomic analysis were conveyed in the public review, but I include more specific concerns here. Given that Class I genes are an important downstream consequence of DAF-16, it isn't clear why these are primarily unaffected in the daf-2 control condition shown in Figure 5A. Furthermore, the authors focus primarily on the top 50 Class I genes, but there are interesting effects seen in the top 50 Class II genes as well, especially given that mutations in the HMTs seem to suppress some of the upregulation observed in daf-2 control – why exclude these from their interpretations? Additionally, the brevity of the methods makes it hard to tell exactly what comparisons are being drawn – in the heatmaps shown in in Figure 5C, D, does the color refer upreglation in comparison to a wild-type control? Why not compare misregulation to a daf-2 single mutant instead? What does "Top 50" refer to – are these the fifty most-affected in these specific data sets, or are they a gene set identified by an independent metric? Why limit the analysis to only fifty genes? Finally, this analysis would be further strengthened by comparing locus-specific effects to the known locations of H3K9me1/2/3 peaks in wild-type genomes in previously published datasets (like in Li et al., 2021 or McMurchy et al., 2017) or even to H3K9me1/2/3 localization in datasets of relevant HMT mutants like set-32.

Thanks very much for the suggestions.

We used two approaches to analyze the mRNA-seq data.

First, the depletion of DAF-2 reduces the insulin signaling pathway, promotes DAF-16 nuclear translocation, and leads to both upregulation and downregulation of large sets of genes, referred to as Class I and II genes, respectively. Class I genes are induced in daf-2 mutants but are repressed in daf-2;daf-16 double mutants. Class II genes are not induced in daf-2 mutants but are induced in daf-2; daf-16 double mutants. 1663 genes are classified as positive (class I) DAF-16 targets and 1733 genes are classified as negative (class II) DAF-16 targets of DAF-16. Class I genes are enriched for the Gene Ontology categories including oxidation, reduction, and energy metabolism, whereas class II genes are enriched for genes involved in biosynthesis, growth, reproduction, and development. We performed mRNA-seq and analyzed Class I and II DAF-16 genes to identify the mis-regulated genes in the daf-2;set mutants. Interestingly, the mRNA levels of DAF-16 Class I, but not Class II, genes are consistently activated in long-lived daf-2;set-19, daf-2;set-21 and daf-2;set-32 worms, than in the control daf-2 and daf-2;set-25 animals (Figure 5E-F and new Figure 5—figure supplement 2).

Second, to identify the target genes in the group of lifespan extension daf-2;set mutants, we re-analyzed the mRNA expression profile in the double mutants via an unbiased method (new Figure 6, Figure 6—figure supplement 1). We have identified 49 co-upregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants daf-2;set-19, daf-2,set-21, daf-2;set-32, but not in daf-2 and daf-2;daf-25 animals (Figure 6A-B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (new Figure 6—figure supplement 1B). 22 co-upregulated genes are not DAF-16 Class I genes, suggesting the existence of additional regulations.

We then analyzed a number of known transcription factors for their binding to the co-regulated targeted genes (new Figure 6C-D, Figure 6—figure supplement 1C-E). Among them, we found that DAF-16 and NHR-80 were specifically enriched at the transcription start sites (TSS) of the 49 co-upregulated genes. NHR-80 is a homolog of mammalian hepatocyte nuclear factor 4 and is an important nuclear hormone receptor involved in the control of fat consumption and fatty acid composition in C. elegans. Among the genes targeted by DAF-16 and NHR-80, twelve of them are co-regulated by both factors, which is consistent with previous report that daf-16 and nhr-80 function in parallel pathway for lipid metabolism.

We revised the text to include this information (lines 284-320).

4. How were the 10 Class I DAF-16 target genes chosen? It doesn't seem like they were in the top 50 (or not that I could easily see). Furthermore, why were no Class II genes chosen? The authors should clarify how they chose to examine these specific candidates, and if necessary, extend the analysis for other targets to see whether the effects are specific to Class I targets only (as they argue in their model). Furthermore, each of these candidate genes needs to be examined in a daf-2 mutant background to fully interpret the meaning of the suppression of long-lived daf-2; set-21 mutants.

Thanks very much for the suggestion.

To identify the target genes in these group of lifespan extension daf-2;set mutants, we analyzed the mRNA expression profile in the double mutants via an unbiased method (new Figure 6, Figure 6—figure supplement 1). We have identified 49 coupregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants daf-2;set-19, daf-2,set-21, daf-2;set-32, but not in daf-2 and daf-2;daf-25 animals (Figure 6A-B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (new Figure 6—figure supplement 1B). 22 co-upregulated genes are not DAF-16 Class I genes, suggesting the existence of additional regulations.

To confirm the change in target gene expression, we chose 10 genes from the 49 co-upregulated genes. Among them, nhr-62, dao-3 and tts-1 are direct binding targets of both DAF-16 and NHR-80. sod-3 is a DAF-16 direct binding target. lys-7 and asm2 are NHR-80 direct binding targets. All of the 10 genes have been shown to be upregulated in daf-2 compared to daf-2;daf-16 animals. We quantified the mRNA levels by quantitative real-time PCR (qRT–PCR) in daf-2, daf-2;set-21 and daf-2;set-25 animals (Figure 7A). Consistently, all the 10 genes were up-regulated in daf-2;set-21 double mutants than in daf-2 and daf-2;set-25 animals (Figure 7A).

We are very interested in how and why each gene is involved in lifespan regulation in daf-2;set double mutant animals, we are trying to generate multiple alleles and transgenes for nhr-62, sod-3, asm-2, F35E8.7, and Y39G8B.7. However, for the time issue, we are still at the very early stage to generate more lines. Hopefully, we can answer this question in the near future.

5. The authors claim that loss of H3K9me1/2 increases binding of DAF-16 at its target genes (line 282). There is no evidence to support this claim (and a lack of evidence for this claim, if we take the DAF-16 localization data in Figure S3 at complete face value). This could be part of their proposed model (outlined in Figure S7), but as written, it reads as if it were a summary of work presented in the paper. The authors should clarify their writing to ensure full accuracy for what their data can support.

Thanks very much for the comments. We completely agree with the reviewer that we lack direct data showing that these set mutations increased the binding activity of DAF-16 to target genes by ChIP analysis.

We speculated that the mutation of daf-2 sensitizes the animals, for example, increases the cytoplasm-to-nuclear translocation of DAF-16. We have generated a single-copy, in situ GFP-tagged DAF-16 transgene, crossed to daf-2, set-21, set-25 single mutants and their double mutants, and scored the nuclear localization of DAF16 at 20oC and 25oC, respectively (new Figure 5A-B, Figure 5—figure supplement 1B). The mutation of daf-2 increased the nuclear accumulation of DAF-16. The double mutants daf-2;set-21 and daf-2;set-25 further increased the nuclear accumulation of DAF-16.

Interestingly, DAF-16 was nearly 100% localized in the nucleus in both daf-2;set21 and daf-2;set-25 double mutants. Yet daf-2;set-21, but not daf-2;set-25, extended the lifespan of daf-2 animals, suggesting addition regulation required beyond the nuclear localization of DAF-16. Our work suggested that the transcription activity of DAF-16 may preferentially depend on H3K9me1/2, but not H3K9me3.

This result is unlike a previous widely used multi-copied DAF-16::GFP transgene. In the multi-copied DAF-16::GFP transgene animals, DAF-16::GFP localized in the cytoplasm and a daf-2 mutation completely re-localizes DAF-16::GFP to the nucleus (Figure 5—figure supplement 1A). This result suggests further investigations are required to understand the mechanism of DAF-2/DAF-16 axis in lifespan regulation.

We have revised the text to include the information (lines 357-361).

We also revised the working model in the Discussion section (lines 391-396) as:

“These putative histone methyltransferases are required for H3K9me1/2 modification and regulate DAF-16 Class I genes. In the absence of H3K9me1/2, the DAF-16 accumulates in the nucleus and the expression of DAF-16 Class I genes increase, which promote the expression of longevity genes and anti-stress genes and extends lifespan of daf-2 animals (Figure 8—figure supplement 4D).”

6. Throughout the manuscript, it's difficult to build a cohesive understanding of the functional effects of the HMT mutants. In part, this is because the paper investigates several HMTs without discussing their specific effects (in certain tissues or cell types, or at specific stages). The analyses are sometimes too broad (immunoblots of total histone modifications) and at other times too narrow (focusing only on 50 Class I DAF-16 target genes). Given that H3K9me1/2 will likely have locus specificity, it is unsatisfying to leave the analysis at the global level of immunoblots (although it is very compelling to see global effects in their mutants). Including a deeper, and unbiased, analysis of their transcriptomic data will help to bridge the gap between the global and the locus-specific, and may even point out other interesting avenues that will further bolster their claims about potential mechanism (or open new avenues of study).

Thanks very much for the suggestions.

We have generated in situ single-copy 3xFLAG-GFP tagged SET-21, SET-25 and SET-32 transgenes by CRISPR/Cas9 technology and single-copy GFP-3xFLAG-tagged SET-13 transgenic strains using the Mos1-mediated single-copy insertion (MosSCI) technology. These animals were imaged in N2 and daf-2 background at embryonic and larva stages respectively, to figure out the expression patterns and cellular localizations of SET proteins (new Figure 4—figure supplement 1). However, we failed to find a clear correlation between their expression pattern with the lifespan extension phenotype. The depletion of SET-21 and SET-32 extended the lifespan of daf-2 animals, but GFP::SET21 and GFP::SET-32 showed different expression patterns and subcellular localizations. GFP::SET-21 exclusively located in the nucleus but GFP::SET-32 located in both the nucleus and cytoplasm in embryos. At larval stage, GFP::SET-21 was expressed in soma but GFP::SET-32 was expressed in germline. Both set-13 and set-25 mutants did not show lifespan extension in N2 and daf-2 background worms. SET-13 and SET-25 were enriched in the nucleus. SET-13::GFP was expressed through 8-cell stage to lateembryonic stage, while SET-25::GFP was expressed in the whole embryonic stage and the germline in young adults.

To identify the target genes in these group of lifespan extension daf-2;set mutants, we have analyzed the mRNA expression profile in the double mutants via an unbiased method (new Figure 6, Figure 6—figure supplement 1). We have identified 49 coupregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants daf-2;set-19, daf-2,set-21, daf-2;set-32, but not in daf-2 and daf-2;daf-25 animals (new Figure 6A-B and Figure 6—figure supplement 1A). Interestingly, among the 49 co-upregulated genes, 27 of them are also DAF-16 Class I genes (new Figure 6—figure supplement 1B). 22 co-upregulated genes are not DAF-16

Class I genes, suggesting the existence of additional regulations.

C. elegans’ genome encodes 10 putative H3K9 methyltransferases, most of which have not been directly characterized for their biochemical properties by in vitro experiments. The presence of these many putative H3K9 methyltransferases may lead to a complexity of the interaction network of histone modifications. In addition, some SET proteins may have multiple roles in mediating histone modification. For example, SET-19 is required for both H3K9me1/2 and H3K23me3 marks, further bringing up complexity of the regulation. Further investigations are necessary to reveal their enzymatic activities by in vitro experiments. In addition, identifying the in vivo targeted genes will also be crucial to help understanding why and how these SET proteins are involved in lifespan regulation.

We have revised the text to include the information (lines 186-201, 301-320, 496506).

[Editors’ note: what follows is the authors’ response to the second round of review.]

The manuscript has been improved but there are some remaining issues that need to be addressed, as outlined below:

Primarily, the three areas that remain an issue before submission are (1) a second replicate needs to be included (and ideally, performed blinded) for experiments such as Figures 1B, 4A, and 4B,

Thanks very much for the suggestions.

We have included a blinded replicate to compare the lifespan of daf-2 vs daf-2;set-21 mutants (new Figure 1A). We have also conducted new experiments to compare N2 vs all set-21 alleles (new Figure 1A). We did not found significant lifespan difference between N2 and all set-21 alleles, but daf-2;set-21 double mutants strongly extended the lifespan of daf-2 worms.

We have included blinded replicates for experiments in Figures 4A and 4B. The conclusions were unchanged.

2) the appropriate epistasis controls should be included as requested by reviewer 1 to properly interpret the experiments (e.g., Figure 7),

Thanks very much for the comments. We have included new epistasis control experiments and data analysis for Figures 1A, 1B, 3-S3, and 7B. The conclusions were unchanged.

and (3) the text needs to be modified where precision remains an issue, as described by reviewer 1.

Thanks very much for the comments. We have revised the manuscript following reviewer #1’ s suggestions to state that the lifespan extension effect is likely more specific to daf-2(-) background animals.

Reviewer #1 (Recommendations for the authors):

1) As stated last review (major point #3), in epistasis experiments (such as WT and eat-2 +/- set-21 and WT and daf-2 +/- met-2, and Figure 3C +D, 7B) you need to include all 4 conditions in the experiment to make any conclusions. For example, you can't do the set-21 vs WT at a different time and assume that the set-21 is still going to have no effect in that particular experiment. There might be some unknown factor (food, temperature, etc) that makes set-21 actually have an effect in the WT worms in that experiment which would mean a very different conclusion. Then after the experiment is done you perform a 2 way ANOVA analysis to reveal whether set-21 has a significantly different effect in the WT context or the mutant context. This comment still holds true for asm-2, Y39G8B.7, etc… that I had asked for last review. You do not need to perform all possible combinations of these 3 genes but at the very least daf-2, daf-2;set-21, daf-2;asm-2 and daf-2;set-21;asm-2 if you want to make any conclusion about asm-2 relative to set-21 in the daf-2 background), examining 3 lines in an epistasis experiment rather than 4 is not really informative.

Thanks very much for the suggestions.

­

We have conducted new experiments to compare N2 vs all set-21 alleles (new Figure 1B). We did not found significant lifespan difference between N2 and all set-21 alleles, but daf-2;set-21 double mutants strongly extended the lifespan of daf-2 worms.

In new Figure 1C, we also included N2 vs set-21(ust68). We did not found significant lifespan difference between N2 and set-21(ust68) mutants, but eat-2;set-21 double mutants strongly extended the lifespan of eat-2 worms.

We conducted new experiments to compare the stress resistance of N2 vs set mutants (new Figure 3-S3A-B). We did not find strong difference of stress resistance between N2 vs set mutants, yet there are significant difference of stress resistance between daf-2 vs daf-2;set mutants (new Figure 3D-E).

We included new replicates for Figure 4A-B. The conclusions are not changed.

We conducted new experiments to compare the lifespan of daf-2, daf-2;y39g8b.7, daf-2;set-21 double mutants vs daf-2;set-21;y39g8b.7 triple mutant and etc… (new Figure 7B). Although we did not find significant lifespan difference between daf-2 vs daf-2;y39g8b.7, daf-2;asm-2, daf-2;nhr-62 double mutants, the mutations of y39g8b.7, asm-2 and nhr-62 could partially reverted the lifespan extension of daf-2;set-21 in triple mutants. Actually, none of the ten selected targeted genes could shorten the lifespan of daf-2 animals but seven of them specifically shorten the lifespan in triple mutants.

2) The text needs to be rewritten to reflect that this is all only occurring in daf-2 mutant worms and not in WT worms. This rewriting needs to start with the title ("…limits the lifespan of daf-2 mutant C. elegans". ) and work its way thru the intro, results and discussion (where the authors claim H3K9me regulators should be considered for lifespan regulation). Need to include explicit writing that deletion of all these putative enzymes has only modest effects on H3K9me and lifespan in the WT context and their role is only revealed in the daf-2 mutants. Need to speculate about what that is. What makes the daf-2 mutation special to reveal a regulatory role for these genes?

Thanks very much for the suggestions.

We have revised the manuscript as suggested, stating that these SET proteins and H3K9me2 may preferentially limit the lifespan of daf-2 mutant worms.

The depletion of SET proteins or the inhibition of worm H3K9me1/2 methyltransferases by G9a inhibitor significantly extended the lifespan only in daf-2 mutant worms, but has modest effects on N2 animals. Consistently, the long-lived set-6, set-19, set-20, set-21, set-32 and set-33 mutants only significantly decreased global H3K9me1/2 levels in daf-2 mutants but not in N2 animals. These results together suggested that DAF-2 limits the effects of these SET proteins.

It is unclear how and why these SET proteins only limit lifespan in daf-2 animals. There are three possibilities. First, DAF-2 may have profound effect on the chromatin accessibility. In daf-2 mutants, the chromatin may be more compact and prohibit the activity of the SET proteins to conduct H3K9me2 modification. Second, daf-2 mutation may sensitize the animals by increasing the nuclear accumulated DAF-16. Although it is unclear whether DAF-16 preferentially recognizes H3K9me2 or H3K9me3, we observed a much stronger enrichment of DAF-16 in the nucleus in daf-2;set-21 than in daf-2 animals, which suggested that H3K9me2 may prohibit the accumulation of DAF-16 in the nucleus. Third, DAF-2 may have other indirect effect on the SET proteins. Further chromatin-immunoprecipitation experiments can be used to test whether daf-2 mutation could affect the association of the SET proteins with chromatin. The ATAC-seq technology may allow us to investigate whether daf-2 mutation have changed chromosome accessibility to facilitate the activity of SET proteins. In addition, identification of the substrate of SET proteins may help to elucidate their mechanism and functions.

In daf-2 animals, DAF-16 modestly accumulated in the nucleus, as shown by the newly generated single-copy GFP-tagged DAF-16 transgene. Yet in daf-2;set-21 double mutants, DAF-16 was strongly enriched in the nucleus. The depletion of DAF-16 completely blocked the synergistic lifespan extension in daf-2;set-21 animals. The mRNA-seq experiments revealed that the mRNA levels of DAF-16 class I genes were elevated in the long-lived daf-2;set-19, daf-2;set-21, and daf-2;set-32 double mutants compared to those in control daf-2 and short-lived daf-2;set-25 mutants. Together, these data suggested that the activity to DAF-16 to class I genes not only depends on the absence of insulin pathway, but also depends on the depletion of these SET proteins and H3K9me2. The single-copy GFP-tagged DAF-16 transgene may allow us to re-visit the mechanism of lifespan regulation pathways.

We have revised the Discussion section to include the above information (lines 435-468).

Reviewer #2 (Recommendations for the authors):

Upon resubmission, this paper is greatly improved – readers now have the evidence needed to evaluate the paper's main claim that H3K9 HMTs synergistically extend lifespan in daf-2 mutants, in part via DAF-16, but also via. The additional experiments, along with a more tempered approach to discussing their findings, significantly strengthen the paper.

However, several of our concerns were not addressed by these changes, nor in the rebuttal. For example, Reviewer 2 asked that some of the key lifespan experiments be replicated at least once and also performed blinded – there are several figures where only a single replicate is shown. Key controls are still missing, like in Figure 7, where Reviewer 1 had asked for appropriate controls to interpret the epistasis experiments for example, set-21 single mutants and daf-2; lys-7 double mutants. The authors' rebuttal mentioned generating new alleles for some genes, but providing appropriate single mutant and double mutant controls should require no new strains to be built (since the strains likely already exist if the authors generated the triple mutant).

Thanks very much for the comments.

We conducted new experiments to compare the lifespan of daf-2, daf-2;y39g8b.7, daf-2;set-21 double mutants vs daf-2;set-21;y39g8b.7 triple mutant and etc… (new Figure 7B). Although we did not find significant lifespan difference between daf-2 vs daf-2;y39g8b.7, daf-2;asm-2, daf-2;nhr-62, the mutations of y39g8b.7, asm-2 and nhr-62 could partially reverted the lifespan extension of daf-2;set-21 in triple mutants. Actually, none of the ten selected targeted genes could shorten the lifespan of daf-2 animals but seven of them specifically shorten the lifespan in triple mutants.

We also included new blinded replicates for Figures 1A, 4A-B and 7B. The conclusions are not changed.

The extended analysis of the mRNA-seq is better (and opens up an interesting line of questioning for future studies!). However, the authors failed to address most of Reviewer 2's Major Point 3 about their transcriptomic analysis, nor did they include further details about how the analysis was done. The methods for the mRNA-seq will need to be more detailed. What is their unbiased approach? What is the differential expression shown in the Figure 5? For example, I had previously asked: "Does the color refer to upregulation in comparison to a wild-type control? Why not compare misregulation to a daf-2 single mutant instead?" and the answer is still not clear. Furthermore, if Class I genes are defined as being induced in daf-2 mutants, why are they downregulated in Figure 5E? And if Class II genes are defined as being not induced in daf-2 mutants, why are they upregulated in Figure 5F? I may be misunderstanding the gene classifications, but it is a demonstration of how the text is unclear. Overall, I found the new transcriptomic analyses are compelling, but more care needs to be taken to fully explain what was done.

Thanks very much for the comments.

We have analyzed the mRNA-seq data in two ways. The first one is comparing the expression levels of reported DAF-16 target genes in daf-2 and daf-2;daf-25 animals and in the long-lived daf-2;set-19, daf-2,set-21, daf-2;set-32 double mutants (Figure 5E and Figure 5—figure supplement 2A). The second method is directly comparing the gene expression in short-lived daf-2;daf-25 animals and the long-lived daf-2;set-19, daf-2,set-21, daf-2;set-32 double mutants to the gene expression in daf-2 animals (Figure 6A and Figure 6—figure supplement 1A). This method identified 49 co-upregulated genes and 11 co-downregulated genes that are specifically enriched in the long-lived double mutants but not in control daf-2 and daf-2;daf-25 animals. We then analyzed a number of known transcription factors for their binding to the co-regulated targeted genes.

Figure 5E showed heatmap of the standardized FPKM of reported top 50 DAF-16 Class I and Class II genes by mRNA-seq in the indicated animals. Figure 5—figure supplement 2A showed heatmap of the standardized FPKM for reported 1576 DAF-16 Class I and 1653 Class II genes by mRNA-seq in the indicated animals. Statistical analysis was performed to obtain the expression levels of each gene in each strain and the average of the expression levels in the five strains. The gene expression levels in a single strain were compared with the average of the five strains, and the ratio obtained was processed by log2. The resulting value > 0 means the expression level of the gene in the indicated strain is higher than the average expression levels of this gene in the five strains, as shown from yellow to red. The resulting value < 0 means the expression level of the gene in the indicated strain is lower than the average expression levels of this gene in the five strains, as shown in blue. The expression levels are indicated by the color bar. Most of the DAF-16 Class I genes are yellow and red in the long-lived daf-2;set-19, daf-2,set-21, daf-2;set-32 double mutants, but blue in daf-2 and daf-2;daf-25. The mRNA levels of DAF-16 Class I genes are consistently elevated in long-lived daf-2;set-19, daf-2;set-21 and daf-2;set-32 worms, but not in the control daf-2 and daf-2;set-25 animals.

We have revised the figure legends to describe our data analysis in more detail (lines 1118-1127, 1225-1234).

https://doi.org/10.7554/eLife.74812.sa2

Article and author information

Author details

  1. Meng Huang

    The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    Contribution
    Conceptualization, Formal analysis, Investigation, Visualization, Methodology, Writing - original draft, Project administration
    Contributed equally with
    Minjie Hong
    Competing interests
    No competing interests declared
  2. Minjie Hong

    The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    Contribution
    Formal analysis, Validation, Investigation, Visualization, Methodology
    Contributed equally with
    Meng Huang
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1510-6396
  3. Xinhao Hou

    The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    Contribution
    Software, Formal analysis, Visualization
    Competing interests
    No competing interests declared
  4. Chengming Zhu

    The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    Contribution
    Data curation, Supervision
    Competing interests
    No competing interests declared
  5. Di Chen

    State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Institute for Brain Sciences, Nanjing University, Nanjing, China
    Contribution
    Resources, Methodology
    For correspondence
    chendi@nju.edu.cn
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0514-7947
  6. Xiangyang Chen

    The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    Contribution
    Data curation, Supervision, Writing - review and editing
    For correspondence
    xychen91@ustc.edu.cn
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6530-7191
  7. Shouhong Guang

    1. The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    2. CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, China
    Contribution
    Conceptualization, Resources, Supervision, Funding acquisition, Methodology, Writing - original draft, Project administration, Writing - review and editing
    For correspondence
    sguang@ustc.edu.cn
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7700-9634
  8. Xuezhu Feng

    The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
    Contribution
    Supervision, Project administration, Writing - review and editing
    For correspondence
    fengxz@ustc.edu.cn
    Competing interests
    No competing interests declared

Funding

Fundamental Research Funds for the Central Universities

  • Shouhong Guang

National Key Research and Development Program of China (2019YFA0802600)

  • Shouhong Guang

National Natural Science Foundation of China (91940303)

  • Shouhong Guang

National Natural Science Foundation of China (31870812)

  • Shouhong Guang

National Natural Science Foundation of China (32070619)

  • Xuezhu Feng

National Natural Science Foundation of China (31871300)

  • Xuezhu Feng

National Natural Science Foundation of China (31900434)

  • Chengming Zhu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

We are grateful to the members of the Guang lab for their comments. We are grateful to the International C. elegans Gene Knockout Consortium, and the National Bioresource Project for providing the strains. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB39010600), the National Key R&D Program of China (2019YFA0802600), the National Natural Science Foundation of China (91940303, 31870812, 32070619, 31871300, and 31900434). This study was supported by the Fundamental Research Funds for the Central Universities.

Senior Editor

  1. Carlos Isales, Medical College of Georgia at Augusta University, United States

Reviewing Editor

  1. Scott F Leiser, University of Michigan, United States

Reviewer

  1. David Katz

Publication history

  1. Received: October 18, 2021
  2. Preprint posted: October 28, 2021 (view preprint)
  3. Accepted: September 16, 2022
  4. Accepted Manuscript published: September 20, 2022 (version 1)
  5. Version of Record published: September 27, 2022 (version 2)

Copyright

© 2022, Huang, Hong et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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  1. Meng Huang
  2. Minjie Hong
  3. Xinhao Hou
  4. Chengming Zhu
  5. Di Chen
  6. Xiangyang Chen
  7. Shouhong Guang
  8. Xuezhu Feng
(2022)
H3K9me1/2 methylation limits the lifespan of daf-2 mutants in C. elegans
eLife 11:e74812.
https://doi.org/10.7554/eLife.74812
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