H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment

  1. C Jake Harris  Is a corresponding author
  2. Zhenhui Zhong
  3. Lucia Ichino
  4. Suhua Feng
  5. Steven E Jacobsen  Is a corresponding author
  1. Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, United States
  2. Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, United States
  3. Howard Hughes Medical Institute, University of California, Los Angeles, United States
6 figures and 4 additional files

Figures

Figure 1 with 1 supplement
NRPE1 accumulates in heterochromatin in an h1 mutant background.

(A) Genome browser image showing increased NRPE1 enrichment in h1 over heterochromatic (long, H3K9me2 enriched) and not euchromatic (short, not H3K9me2 enriched) transposable elements (TEs). (B) …

Figure 1—figure supplement 1
NRPE1 enrichment in wild-type (WT) vs h1 when mapped to either TAIR10 or Col-CEN genome assemblies (Naish et al., 2021).
Figure 2 with 2 supplements
RNA-directed DNA methylation (RdDM) does not reciprocally affect H1 localization.

(A) Scatter plot showing H1 enrichment in wild-type (WT) vs. nrpe1 at euchromatic vs heterochromatic transposable elements (TEs). (B) Metaplot showing H1 enrichment at NRPE1 peaks in WT vs. nrpe1 (C)…

Figure 2—figure supplement 1
Loss of H1 results in increased heterochromatic accessibility and NRPE1 redistribution.

(A) Metaplot of DNase I accessibility in wild-typee (WT) vs h1 over euchromatic vs heterochromatic transposable elements (TEs). Data is obtained from Choi et al., 2020. (B) Scatterplot showing …

Figure 2—figure supplement 2
Benchmarking of H1 ChIP-seq.

(A) Western blot of H1 and NRPE1, using same antibodies as used for ChIPseq. H1 is only detectable in the wild-type (WT) samples, not h1 mutant. (B) H1 ChIP-seq metaplots with over WT H1 peaks with …

Figure 3 with 2 supplements
Major CG and CHG methylation gains in h1 are independent of RNA-directed DNA methylation (RdDM).

(A) Chromosomal view of DNA methylation levels (average of 10 kb windows) in the genotypes indicated on chromosome 1. Y-axis indicates fraction methylation (0–1). (B) Methylation level over …

Figure 3—figure supplement 1
NRPE1 CRISPR knock outs.

(A) h1 /nrpe1 cKO_49 has a deletion spanning exons 1–6. (B) h1 /nrpe1 cKO_63 has an indel induced frameshift leading to a premature stop codon in exon 1. (C) Both knockouts display complete loss of …

Figure 3—figure supplement 2
Whole genome DNA methylation analysis in h1 and nrpe1 mutants showing individual biological replicates.

(A) Whole genome view of DNA methylation levels (average of 10 kb windows) in the genotypes indicated (as in Figure 3, including all five chromosomes). Y-axis indicates fraction methylation (0–1). (B

Figure 4 with 1 supplement
Overlap analysis of h1 hyper CHG differentially methylated regions (DMRs) with 96 methylation mutants.

(A) Number of hypo vs hyper DMRs in genotype comparisons indicated. (B) h1 hyper CHG DMR frequency density plot over Chromosomes 1–5. (C) Similarity matrix based on pairwise overlapping scores …

Figure 4—figure supplement 1
96 mutant genotype comparison, as shown in Figure 4, with differentially methylated region (DMR) genotype comparison labels shown for visual inspection.
Figure 5 with 2 supplements
Patterns of NRPE1 re-localization in h1 show corresponding methylation changes.

(A) Methylation metaplot in the genotypes indicated over regions of the genome that gain NRPE1 in h1. Arrow highlights the change in average CHH methylation in the h1/nrpe1 double mutant as compared …

Figure 5—figure supplement 1
Same data as shown in Figure 5, with individual biological replicates plotted separately.
Figure 5—figure supplement 2
Genome browser images of representative regions that lose both NRPE1 occupancy and DNA methylation in h1.

Regions are highlighted in gray.

SUVH1 and H3K27me3 encroaches heterochromatin in an h1 mutant background.

(A) Genome browser image showing SUVH1 re-localization in h1 mirrors that of NRPE1. (B–D) Boxplot inlaid violin plots (boxplot medians shown in blue) showing SUVH1 enrichment in wild-type (WT) vs h1

Additional files

Supplementary file 1

Differential expression analysis of RNA-seq data (from Choi et al., 2020 PMID:31732458) for genes involved in DNA methylation, comparing wild-type (WT) to h1 mutant genotypes.

https://cdn.elifesciences.org/articles/89353/elife-89353-supp1-v2.xlsx
Supplementary file 2

Table showing bisulfite sequencing conversion efficiency estimation for the WGBS libraries generated and analysed in this paper.

https://cdn.elifesciences.org/articles/89353/elife-89353-supp2-v2.xlsx
Supplementary file 3

List of .bed files used for analysis in this paper.

https://cdn.elifesciences.org/articles/89353/elife-89353-supp3-v2.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/89353/elife-89353-mdarchecklist1-v2.docx

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