Figures and data
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) TEs. B) metaplot showing ChIP-seq enrichment of NRPE1 in WT vs. h1, and H1 occupancy in WT for reference (data from GSE122394), at short vs. long TEs. C) boxplot showing association between NRPE1 and TE length in WT and h1. D) As in B) for drm12 vs. cmt2 hypo CHH DMRs. E) Violin plot inlaid with boxplot showing enrichment of NRPE1 at TEs that overlap with H3K9me2 peaks, vs. TEs that do not, in WT vs. h1. F) as in B) at euchromatic vs. heterochromatic TEs. G) Chromosomal plots showing NRPE1 enrichment in h1 as compared to WT, with pericentromeric regions denoted in grey.
RdDM does not reciprocally affect H1 localization:
A) Scatter plot showing H1 enrichment in WT vs. nrpe1 at euchromatic vs heterochromatic TEs. B) Metaplot showing H1 enrichment at NRPE1 peaks in WT vs. nrpe1 C) H1 and NRPE1 occupancy at ZF-DMS3 off target peaks. Upper panel: H1 occupancy in WT vs. ZF108-DMS3. Lower panel: NRPE1 occupancy in WT vs. ZF108-DMS3. Chromatin from the same sample was used for both H1 and NRPE1 ChIP-seq data, so the lower panel serves as a control showing that ZF108-DMS3 is recruited to these off-target regions in these samples, despite H1 localisation remaining unchanged. D) Same as C) at the subset of regions where CHH methylation is gained in ZF108-DMS3 (Liu et al 2018), indicating that the fully functioning RdDM pathway is recruited to these regions.
Major CG and CHG methylation gains in h1 are independent of RdDM:
A) Chromosomal view of DNA methylation levels (average of 10kb windows) in the genotypes indicated on chromosome 1. Y-axis indicates fraction methylation (0-1). B) Methylation level over heterochromatic TEs. Upper panel: metaplots, Lower panel - kernel density plots. x-axis indicates change in methylation fraction mutant minus WT. C) Methylation level over euchromatic TEs. Upper panel: metaplots, Lower panel - kernel density plots. Arrow highlights the gain in CHG methylation in the h1/nrpe1 double mutant, as compared to nrpe1 alone.
Overlap analysis of h1 hyper CHG DMRs with 96 methylation mutants:
A) hypo vs hyper DMR number for the comparisons indicated. B) h1 hyper CHG DMR density over chromosomes 1-5. C) heatmap showing pairwise comparisons of DMRs grouped by major methylation effects (individual genotypes are shown in Supplementary Figure 6). Colour scale represents observed / expected values. D) Zoomed in view of h1 hyper CHG cluster shown C) (see blue box and arrow).
Patterns of NRPE1 re-localisation 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 to the single mutants. B) Methylation metaplot of the genotypes indicated over regions of the genome that lose NRPE1 in h1.
SUVH1 encroaches heterochromatin in an h1 mutant background:
A) Genome browser image showing SUVH1 re-localisation in h1 mirrors that of NRPE1. B-D) Boxplot inlaid violin plots showing SUVH1 enrichment in WT vs h1 at short vs long TEs (B), at euchromatic vs heterochromatic TEs (C) and at drm12 vs cmt2 hypo CHH DMRs (D).
