Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion
- Waksman Institute, Department of Genetics, Rutgers University, United States
- ModOmics Ltd, United Kingdom
- Department of Biology, Queens College, CUNY, United States
- Department of Molecular Biology and Genetics, Cornell University, United States
- PhD Program in Biology, The Graduate Center, CUNY, United States
Figures
Figure 1
Transcription factors SMA-3 and SMA-9 bind both overlapping and distinct genomic sites.
(a) Cumulative probability distribution graph of the distances between the centroids (base pair position located centrally within each peak) of nearest neighbor SMA-3 and SMA-9 Chromatin immunoprecipitation sequencing (ChIP-seq) peaks. The black line represents actual inter-peak distances, whereas the green line represents a hypothetical randomized dataset. The horizontal dotted line indicates the point in the curve at which half of the peak pairs fall. (b) Same cumulative probability distribution as in (a), but focused on distances less than 500 bps. The centroids of nearly half of all SMA-3/SMA-9 neighboring pairs fall within 500 bps of each other. (c) Histogram of the interpeak distances (actual data in black, randomized data in green), as well as the ChIP-seq peak widths (SMA-3 in red, SMA-9 in blue). Most peaks are larger in size than most interpeak centroid distances, indicating substantial peak overlap. (d) Size-proportional Venn diagram showing the number of SMA-3 and SMA-9 peaks that either overlap with one another or remain independent. Although most SMA-3 peaks overlap with SMA-9 peaks, more than half of SMA-9 peaks are located independently of SMA-3 peaks.
Figure 2
Identification of direct transcriptional targets of SMA-3 and SMA-9.
(a) Principal component analysis (PCA) over two dimensions (PC1 and PC2) for RNA-seq datasets for wild-type (in black), sma-3(wk30) (in red), and sma-9(ok1628) (in blue). The percent of variance for each component is indicated. The three biological replicates for each genotype are well clustered. (b) Volcano plot of RNA-seq false discovery rate (FDR) values versus log2 fold change (FC) expression for individual genes (squares) in sma-3 mutants relative to wild-type. The direct targets identified by BETA are indicated with red squares; the negative log2 FC values demonstrate that SMA-3 promotes the expression of these genes. Non-direct target genes nevertheless showing differential expression are indicated with green squares. (c) Strategy for integrating SMA-3 Chromatin immunoprecipitation sequencing (ChIP-seq) and mutant RNA-seq data to identify directly regulated targets. (d) Volcano plot of RNA-seq FDR values versus log2 fold change expression for individual genes (squares) in sma-9 mutants relative to wild-type. The direct targets identified by BETA are indicated with blue squares; the combination of positive and negative log2FC values demonstrates that SMA-9 promotes the expression of some of these genes and inhibits the expression of others. Non-direct target genes nevertheless showing differential expression are indicated with green squares. (e) Strategy for integrating SMA-9 ChIP-seq and mutant RNA-seq data to identify directly regulated targets.
Figure 3 with 2 supplements
Significant overlap in directly regulated differentially expressed genes (DEGs) of SMA-3 and SMA-9.
(a) Strategy for integrating SMA-3 and SMA-9 ChIP-seq and mutant RNA-seq data to identify common versus unique directly regulated targets. (b–f) Cartoon representations of the different types of direct target genes, their neighboring SMA-3 and/or SMA-9 binding sites, and the effect of those sites on that gene’s expression. The red circle labeled ‘3’ represents SMA-3 binding sites, whereas the blue circle labeled ‘9’ represents SMA-9 binding sites. Arrows represent that the wild-type transcription factor promotes the expression of the neighboring DEG (gray), whereas T-bars indicate that it inhibits the expression of the DEG. Types of regulation include (b) SMA-3 alone promoting DEG expression, (c) SMA-3 and SMA-9 combined promoting expression, (d) SMA-3 and SMA-9 showing antagonistic regulation of expression, (e) SMA-9 alone promoting DEG expression, and (f) SMA-9 alone inhibiting DEG expression. Example DEGs and tables of annotation clusters for gene ontology terms for those DEGs (via DAVID, with accompanying statistical EASE score) are shown under the cartoon demonstrating each type of regulation.
Figure 3—figure supplement 1
DAVID annotation clusters of gene ontology terms for identified SMA-3 and SMA-9 targets.
Tables of annotation clusters for gene ontology terms for direct target differentially expressed genes (DEGs) (via DAVID, with accompanying statistical EASE score) are shown for (a) SMA-3 and (b) SMA-9.
Figure 3—figure supplement 2
SMA-3 and SMA-9 sites tend not to be at HOT sites.
(a, b) Cumulative probability distributions measuring the number of (a) SMA-3 or (b) SMA-9 Chromatin immunoprecipitation sequencing (ChIP-seq) peaks against the number of other transcription factors known from ModENCODE/ModERN analysis to bind to each site’s region of the genome (within 400 bps of each ChIP-seq peak center). The black line indicates all SMA-3 or SMA-9 ChIP-seq peaks, whereas the magenta line indicates functional SMA-3 or SMA-9 ChIP-seq peaks identified by BETA analysis. The cyan line indicates SMA-3 and SMA-9 sites that overlap near co-regulated genes. The orange line indicates SMA-3-exclusive or SMA-9-exclusive sites. The red dotted vertical line with the rightward arrow indicates the minimum cutoff for high occupancy target (HOT) sites, which bind to 15 or more different transcription factors as determined by modENCODE/modERN. The black dotted horizontal line indicates the cumulative probability distribution percentage at which the curve for all ChIP-seq peaks intersects the cutoff for HOT sites (i.e. 15 or more TFs binding within 400 bps).
Figure 4 with 1 supplement
Genetic interactions between SMA-3 and SMA-9.
(a) Mean body length of L4 animals (measured head to tail in microns). Dots indicate the size of individual animals. ****p<0.0001, **p<0.01 One-way ANOVA with Tukey’s multiple comparison test. (b) Mean mRNA levels for the indicated target gene (x-axis) for the indicated genotypes (sma-3, sma-9, or the double mutant combination) relative to the level in the wild-type. Expression values are in log2 fold change (FC). Individual genotype mRNA levels for each gene were first normalized to actin mRNA levels in that genotype. *p<0.05 Two-way ANOVA with Tukey’s multiple comparison test. Data was analyzed from three biological replicates.
Figure 4—figure supplement 1
Genes antagonistically regulated by SMA-3 and SMA-9.
(a) Mean mRNA levels for the indicated target gene (x-axis) for the indicated genotypes (sma-3, sma-9, or the double mutant combination) relative to the level in wild-type. Expression values are in log2 fold change (FC). Individual genotype mRNA levels for each gene were first normalized to actin mRNA levels in that genotype. ****p<0.0001, ***p<0.001, *p<0.05 Two-way ANOVA with Tukey’s multiple comparison test. Data was analyzed from three biological replicates. (b) Heat map showing hierarchical clustering of individual target gene expression (rows) in three replicates for each indicated genotype (columns). Z-scores are color-coded (yellow for elevated, cyan for repressed) and reflect the expression relative to the average across each row.
Figure 5 with 2 supplements
Multiple SMA-3 and SMA-9 target genes regulate body size.
(a,c) The adjusted p-value (plotted as -log10) for mean body size for genes either knocked down by RNAi or mutation compared to control (empty vector and wild-type, respectively) is shown for individual genes giving the indicated Glass’ effect size Δ for body size when knocked down. Larger Glass’ effect values indicate smaller bodies compared to the control. Genes regulated by SMA-9 exclusively, SMA-3 exclusively, or by both factors are indicated by blue, red, and gray circles, respectively. The horizontal dotted line indicates a p-value cutoff of 0.05. The vertical dotted line indicates an effect size cutoff of 1. The sma-3 and sma-9 controls are indicated by empty circles. (b,d) The BETA rank values for SMA-3 or SMA-9 (plotted as -log10 and acting as measures of Chromatin immunoprecipitation sequencing (ChIP-seq)/RNA-seq correlation demonstrating the direct target nature of those factors) are shown as circles for individual genes. Each circle gives the Glass’ effect size for body size (indicated by the area of each circle – larger circles indicate greater decreases in body size when the indicated gene is knocked down or mutated) and gene ontology group (indicated by circle color). Two genetic backgrounds are shown: (a, b) wild-type and (c, d) lon-2. The circle for dpy-11 is highlighted.
Figure 5—figure supplement 1
Target genes required for exaggerated growth.
(a) Mean body length of L4 animals (normalized to wild-type) for the indicated mutants. Dots indicate the size of individual animals. Asterisks above each column indicate one-way ANOVA with Dunnett’s multiple comparison test against wild-type (****p<0.0001, ***p<0.001, **p<0.01, *p<0.05). Asterisks over pairwise comparison bars indicate one-way ANOVA with Sídák’s multiple comparison test. The dotted line indicates the size value falling two standard deviations below the mean of the wild-type. (b) Glass’ effect size (the difference between the mean of the mutant and the mean for the wild-type, divided by the standard deviation of wild-type) for the indicated mutants. The dotted line indicates an effect size of one. (c, d) Mean body size and Glass’ effect size for RNAi knockdowns of the indicated gene in the rrf-3 RNAi sensitive strain. ’EV’ indicates the empty RNAi vector as a negative control. Asterisks above each column indicate one-way ANOVA with Dunnett’s multiple comparison test against EV (****p<0.0001, ***p<0.001, **p<0.01, *p<0.05). For all graphs, red, blue, and purple columns indicate values for sma-3 (mutant or RNAi knockdown), sma-9 (mutant or RNAi knockdown), and their double mutant combination, respectively. Green bars indicate genotypes for which the mutant or RNAi knockdown resulted in a statistically significant reduction (p<0.05) with a Glass’ effect size of one or greater.
Figure 5—figure supplement 2
Target genes required for exaggerated growth in lon-2 mutants.
(a) Mean body length of L4 animals (normalized to EV) for the indicated RNAi knockdowns in the rrf-3; lon-2 double mutant. ‘EV’ indicates the empty RNAi vector as a negative control. Dots indicate the size of individual animals. Asterisks above each column indicate one-way ANOVA with Dunnett’s multiple comparison test against EV (****p<0.0001, ***p<0.001, **p<0.01, *p<0.05). The dotted line indicates the size value falling two standard deviations below the mean of EV (b) Glass’ effect size (the difference between the mean of the RNAi knockdown and the mean for EV, divided by the standard deviation for EV) for the indicated gene undergoing knockdown. The dotted line indicates an effect size of one. Green bars indicate genotypes for which the RNAi knockdown resulted in a statistically significant reduction (p<0.05) with a Glass effect size of one or greater. (c) The average of the Glass’ effect size between the rrf-3 wild-type background and the rrf-3 lon-2 mutant background (individual dots for each is shown). For (c), yellow bars indicate genotypes for which the RNAi knockdown resulted in a statistically significant reduction (p<0.05) with a Glass’ effect size of one or greater in both the wild-type and the lon-2 mutant background. For all graphs, red and blue columns indicate values for sma-3 and sma-9 RNAi knockdown, respectively.
Figure 6 with 1 supplement
DBL-1 signaling promotes body size through collagen secretion.
(a) Cartoon illustrating a cross-section through the nematode body (dorsal oriented up). Rings of cuticular collagen annuli (magenta), secreted by the underlying hypodermal cell layer (tan) surround the body. Lateral alae containing collagen, secreted by the underlying seam cells (gray), run orthogonal along the length of the body. (b) Cartoon illustrating a cross-section through a portion of the nematode body (lateral oriented up) underneath a microscope cover glass. Horizontal green bars indicate the cuticular versus hypodermal plates captured by confocal microscopy in panels c-e. (c) ROL-6::wrmScarlet fluorescence detected in annuli and alae in the cuticular layer, as well as in nuclear envelopes in the underlying hypodermal layer in wild-type animals. The horizontal red line indicates the specific xz cross section shown below the cuticular and hypodermal plane panels. The bar indicates 5 microns. (d) ROL-6::wrmScarlet in sma-3 mutants, visualized as per wild-type. Patches of cuticular surface show diminished levels of ROL-6::wrmScarlet, whereas the protein is detected in the hypodermal layer just under these patches (yellow arrowheads), suggesting a failure to deliver collagen to the surface cuticle (easily visualized in the xz panel). (e) Mutants for sma-9 show the same phenotype as sma-3. (f,g) Quantification of ROL-6::wrmScarlet fluorescence in the (f) hypodermal layer or (g) cuticular layer of indicated mutants. Dots indicate the fluorescence of individual animals. Asterisks over pairwise comparison bars indicate one-way ANOVA with (f) Sídák’s multiple comparison test or (g) the Kruskall-Wallis comparison test (***p<0.001, **p<0.01). (h) A similar analysis for RNAi knockdowns of the SMA-3 target gene dpy-11, as well as four known ER secretion factors as comparative controls. Asterisks above each column indicate one-way ANOVA with Dunnett’s multiple comparison test against wild-type (***p<0.001, **p<0.01, *p<0.05). The bar indicates 5 microns.
Figure 6—figure supplement 1
DPY-11 promotes body size through collagen secretion.
(a) ROL-6::wrmScarlet fluorescence detected in annuli and alae in the cuticular layer, as well as in nuclear envelopes in the underlying hypodermal layer in wild-type animals exposed to an empty vector for RNAi knockdown. (b–f) ROL-6::wrmScarlet in animals exposed to RNAi knockdown for the indicated gene. (b) In animals knocked down for dpy-11, little ROL-6::wrmScarlet makes it to the cuticle, instead accumulating intracellularly in the hypodermis. (c–f) In animals knocked down for known ER secretory factors, patches of cuticular surface show diminished levels of ROL-6::wrmScarlet, whereas the protein is detected in the hypodermal layer just under these patches (yellow arrowheads), similar to what is observed in sma-3 and sma-9 mutants, and consistent with a failure to deliver collagen to the surface cuticle. The bar indicates 5 microns.
Figure 7 with 1 supplement
ROL-6::wrmScarlet accumulates in the endoplasmic reticulum (ER) of sma-3 mutants.
ROL-6::wrmScarlet (magenta) and VIT2ss::oxGFP::KDEL (an ER marker, shown here in yellow) shown separately (a–d, g–j) or merged (e–f, k–l) in either (a–f) wild-type or (g–l) a sma-3 mutant. (a,c,e,g,i,k) shows the interface between the cuticle and the hypodermis, as visualized by SIM super-resolution microscopy. (b, d, f, h, j, l) shows the hypodermal layer at a focal plane centered around the nuclear envelope. In wild-type, most ROL-6::wrmScarlet is delivered into the cuticle. In sma-3 mutants, lower levels of ROL-6::wrmScarlet are present in the cuticle and rapidly bleached under the SIM laser even under low power, whereas abundant ROL-6::wrmScarlet colocalized with the ER VIT2ss::oxGFP::KDEL marker (yellow). We noted that ER reticulation in sma-3 was thinner and skeletonized compared to the wild-type, perhaps suggesting reduced secretory throughput. (m) Quantification of ROL-6::wrmScarlet fluorescence in the hypodermal layer of tunicamycin-treated versus untreated nematodes. (n) Mean body length of L4 animals (normalized to untreated) of tunicamycin treated versus untreated nematodes. (m, n) Dots indicate the values for individual animals. Asterisks over pairwise comparison bars indicate a student t-test (****p<0.0001). The bar indicates 5 microns.
Figure 7—figure supplement 1
Tunicamycin treatment mimics the effect of sma-3 and sma-9 mutations on collagen secretion.
(a) ROL-6::wrmScarlet fluorescence detected in annuli and alae in the cuticular layer, as well as in nuclear envelopes in the underlying hypodermal layer in untreated wild-type animals. (b) ROL-6::wrmScarlet in animals exposed to tunicamycin. Patches of cuticular surface show diminished levels of ROL-6::wrmScarlet, whereas the protein is detected in the hypodermal layer just under these patches (yellow arrowheads), similar to what is observed in sma-3 and sma-9 mutants, and consistent with a failure to deliver collagen to the surface cuticle. In addition, collagen in the lateral alae is disorganized, suggesting secretion is impaired in the seam cells. The bar indicates 5 microns.
Figure 8
A model for the regulation of growth by DBL-1/BMP Signaling.
During early larval development, the DBL-1 ligand binds to the BMP receptors SMA-6 and DAF-4, which activate the Smads SMA-2, SMA-3, and SMA-4. The resulting Smad complex binds to one category of sites along the genome either alongside or in complex with SMA-9, co-regulating neighboring genes (in purple). These co-regulated genes include several collagen genes, factors involved in one-carbon metabolism, innate immunity genes, and genes involved in lipid metabolism. The Smad complex also binds to another category of sites (in orange/red) which lack SMA-9, perhaps associating instead with other transcription factors or co-factors (gray question mark). These SMA-3-exclusive genes include chaperones and the disulfide reductase DPY-11, which in turn promote the secretion of collagen into the cuticular extracellular matrix, thereby remodeling the cuticle to allow for growth. In addition to binding either with or near Smad complex components, SMA-9 (in blue) also binds to sites along the genome lacking Smad (or at least SMA-3), perhaps associating instead with other transcription factors or co-factors (gray question mark). These SMA-9-exclusive genes, which can be either positively or negatively regulated by SMA-9, play a minimal role in body size growth, but rather are associated with innate immunity and lipid metabolism.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (C. elegans) | N2 | CGC | ||
| Genetic reagent (C. elegans) | CS24 | Savage-Dunn lab | sma-3(wk30) | |
| Genetic reagent (C. elegans) | VC1183 | CGC | sma-9(ok1628) | |
| Genetic reagent (C. elegans) | GFP::SMA-3 | Savage-Dunn lab | qcIs6[sma-3p::gfp::sma-3, rol-6(d)] | |
| Genetic reagent (C. elegans) | SMA-9::GFP | Liu lab | jjIs1253[sma-9p::sma-9C2::gfp +unc-119(+)] | |
| Genetic reagent (C. elegans) | ROL-6::wrmScarlet | Savage-Dunn lab | rol-6(syb2235[rol-6::wrmScarlet]) | |
| Genetic reagent (C. elegans) | ER marker | Barth Grant | pwSi82[hyp-7p::VIT2ss::oxGFP::KDEL, HygR]. | |
| Genetic reagent (C. elegans) | NL2099 | CGC | rrf-3(pk1426) | |
| Genetic reagent (C. elegans) | BX106 | CGC | fat-6(tm331) | |
| Genetic reagent (C. elegans) | BX153 | CGC | fat-7(wa36) | |
| Genetic reagent (C. elegans) | VC1760 | CGC | nhr-114(gk849) | |
| Genetic reagent (C. elegans) | CB7468 | CGC | acs-22(gk373989) | |
| Genetic reagent (C. elegans) | VC4077 | CGC | lbp-8(gk5151) | |
| Genetic reagent (C. elegans) | CB6734 | CGC | clec-60(tm2319) | |
| Genetic reagent (C. elegans) | VC2477 | CGC | sysm-1(ok3236) | |
| Genetic reagent (C. elegans) | RB1388 | CGC | ins-7(ok1573) | |
| Genetic reagent (C. elegans) | CB502 | CGC | sma-2(e502) | |
| Sequence-based reagent | act-1f | This paper | 5’-ATGTGTGACGACGAGGTTGCC-3’ | qRT-PCR primer |
| Sequence-based reagent | act-1r | This paper | 5’-GTCTCCGACGTACGAGTCCTT-3’ | qRT-PCR primer |
| Sequence-based reagent | fat-6f | This paper | 5’-GTGGATTCTTCTTCGCTCAT-3’ | qRT-PCR primer |
| Sequence-based reagent | fat-6r | This paper | 5’-CACAAGATGACAAGTGGGAA-3’ | qRT-PCR primer |
| Sequence-based reagent | nhr-114f | This paper | 5’-CATTCGATGTTTTTGAGGCG-3’ | qRT-PCR primer |
| Sequence-based reagent | nhr-114r | This paper | 5’-GATCGAAGTAGGCACCATCT-3’ | qRT-PCR primer |
| Sequence-based reagent | C54E4.5f | This paper | 5’-GGCAGGTCTAATCCACGACTTG-3’ | qRT-PCR primer |
| Sequence-based reagent | C54E4.5r | This paper | 5’-CTAATGTCCGGGTTCCCATCG-3’ | qRT-PCR primer |
| Sequence-based reagent | aard-19f | This paper | 5’-CGGAGGTTACGAGACCAGTACG-3’ | qRT-PCR primer |
| Sequence-based reagent | aard-19r | This paper | 5’-TGGAGTCACAGACGGAAGACG-3’ | qRT-PCR primer |
| Sequence-based reagent | nspe-7f | This paper | 5’-CTCCAAACCTTCTTTTCTCCTTCG-3’ | qRT-PCR primer |
| Sequence-based reagent | nspe-7r | This paper | 5’-GGACCGCCAGCCATATTGTC-3’ | qRT-PCR primer |
| Sequence-based reagent | nspc-16f | This paper | 5’-TGTTCTCCATGGTTGAGTTATGCT-3’ | qRT-PCR primer |
| Sequence-based reagent | nspc-16r | This paper | 5’-GTTTCTTTGCGGGGAATGTTGC-3’ | qRT-PCR primer |
| Sequence-based reagent | catp-3f | This paper | 5’-TTCGGTTGGAGGTGTCGTTG-3’ | qRT-PCR primer |
| Sequence-based reagent | catp-3r | This paper | 5’-GTTGCTCGGCATTCAGTACG-3’ | qRT-PCR primer |
| Sequence-based reagent | gdh-1f | This paper | 5’-TGCTCGTGGAGATTGCCTCATC-3’ | qRT-PCR primer |
| Sequence-based reagent | gdh-1r | This paper | 5’-GCATCTTGTTGGCTTCCTCGTC-3’ | qRT-PCR primer |
Additional files
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Supplementary file 1
SMA-3 and SMA-9 Chromatin immunoprecipitation sequencing (ChIP-seq) sites.
This file contains the chromosomal location of 4205 ChIP-seq peaks for SMA-3 and 7065 ChIP-seq peaks for SMA-9 in separate tabs labeled ‘SMA-3’ and ‘SMA-9,’ respectively. SMA-3 sites that overlap with a SMA-9 site are listed on the ‘Overlapping Sites_S3’ tab. SMA-9 sites that overlap with a SMA-3 site are listed on the ‘Overlapping Sites_S9’ tab. Non-overlapping SMA-3 and SMA-9 sites are listed on the ‘Non-overlapping_S3’ and ‘Non-overlapping_S9’ tabs, respectively. For all tabs, column A indicates chromosome location, column B indicates the start of the peak sequence, and column C indicates the end of the peak sequence. Column labels are in row 1.
- https://cdn.elifesciences.org/articles/99394/elife-99394-supp1-v1.xlsx
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Supplementary file 2
Differential gene expression from sma-3 and sma-9 mutants.
This file lists the differential gene expression from RNA-seq of sma-3 versus wild-type (the tab labeled ‘SMA3 versus N2’), as well as sma-9 versus wild-type (the tab labeled ‘SMA9 versus N2’). For each gene, WormBase GeneID, public gene name, log fold change, p-value, and false discovery rate (FDR) are listed. Column labels are in row 1.
- https://cdn.elifesciences.org/articles/99394/elife-99394-supp2-v1.xlsx
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Supplementary file 3
SMA-3 and SMA-9 direct targets.
This file lists the direct target genes identified by BETA analysis of RNA-seq and Chromatin immunoprecipitation sequencing (ChIP-seq) data. Direct targets of SMA-3 are in the tab labeled ‘SMA3 Direct Targets.’ Direct targets of SMA-9 are in the tab labeled ‘SMA9 Direct Targets.’ For each gene, chromosomal location, transcriptional start site, transcriptional end site, public gene name, rank product from BETA analysis, RNA-seq log fold change from corresponding mutant versus wild-type, and WormBase GeneID are listed. Column labels are in row 1.
- https://cdn.elifesciences.org/articles/99394/elife-99394-supp3-v1.xlsx
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Supplementary file 4
Differential gene expression shared between sma-3 and sma-9 mutants analyzed using LOA.
This file lists the differentially expressed genes identified by LOA analysis as being common to both the RNA-seq of sma-3 versus wild-type as well as the RNA-seq of sma-9 versus wild-type. For each gene, WormBase GeneID and public gene name are listed, followed by the log fold change, p-value, and false discovery rate (FDR) from the sma-3 versus wild-type RNA-seq, followed by the log fold change, p-value, and FDR from the sma-9 versus wild-type RNA-seq. Column labels are in row 1.
- https://cdn.elifesciences.org/articles/99394/elife-99394-supp4-v1.xlsx
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Supplementary file 5
Classes of direct targets for SMA-3 and SMA-9.
This file lists the direct target genes identified by combined LOA/BETA analysis of RNA-seq and Chromatin immunoprecipitation sequencing (ChIP-seq data), as described in Figure 3. Direct targets of SMA-3 alone are in the tab labeled ‘Figure 3b.’ Direct targets of SMA-3 and SMA-9 in which both factors promote the target’s expression are in the tab labeled ‘Figure 3c.’ Direct targets of SMA-3 and SMA-9 in which the two factors have opposite effects on the target’s expression are in the tab labeled ‘Figure 3d.’ Direct targets of SMA-9 alone in which the factor either promotes or inhibits the target’s expression are in the tabs labeled ‘Figure 3e’ and ‘Figure 3f,’ respectively. For each gene, WormBase GeneID and public gene name are listed, followed by the log fold change and false discovery rate (FDR) from the sma-3 versus wild-type RNA-seq, followed by the log fold change and FDR from the sma-9 versus wild-type RNA-seq. Column labels are in row 1.
- https://cdn.elifesciences.org/articles/99394/elife-99394-supp5-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/99394/elife-99394-mdarchecklist1-v1.docx
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Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion
eLife 13:RP99394.
https://doi.org/10.7554/eLife.99394.3
