Extended Data Figure 2: H3.3 and H3K9me3 co‐occupy class I and II ERVs.

Related to Fig. 1. a, Direct comparison of H3.3 enrichment at genic and repetitive sites. Box plot (top) showing enrichment of H3.3 over sets of intervals either representing genic or repetitive elements⁵ annotated in the reference genome, using inclusive read mapping. H3.3 ChIP was performed using an H3.3 antibody and formaldehyde (FA) crosslinking in H3.3 wild‐type (WT) cell line. H3.3 enrichment is shown as standardized ChIP‐seq read density divided by the standardized input read density on a per‐interval basis. The width of the box is proportional to the number of intervals in each group. TSS, transcription start sites of highly active genes; K27pro, bivalent promoters¹⁶. Box plot (bottom) shows the input read density (standardized by scaling to a genome‐wide mean of 1), confirming the even representation of unique and repetitive sequences resulting from the inclusive mapping procedure (see Methods for details). Result of one‐sided Wilcoxon rank sum test against a set of randomly selected genomic intervals (shuffled) is indicated (****P < 0.0001). b, H3K9me3 enrichment at genic and repetitive sites. H3K9me3 ChIP was performed using MNase digestion under native conditions. Box plot (top) showing enrichment of H3K9me3 over sets of intervals either representing genic or repetitive elements analogous to a. Box plot (bottom) shows the input read density analogous to a. Result of one‐sided Wilcoxon rank sum test against a set of randomly selected genomic intervals (shuffled) is indicated (****P < 0.0001). c, Sequential H3.3 and H3K9me3 (re)‐ChIP at genic and repetitive sites. Boxplots showing enrichment of Re‐ChIP inclusive read mapping relative to an input control. Result of one‐sided Wilcoxon rank sum test against a set of randomly selected genomic intervals (shuffled) is indicated (****P < 0.0001). d, Co‐occupancy of H3.3 and H3K9me3 at specific classes of ERVs. H3.3 and H3K9me3 peak intervals were independently intersected with annotated ERVs⁵ and their co‐occurrences within the same ERV were evaluated. L1Md_F (full) is a subset of L1Md_F, comprising only full length repeats (>5 kb). All pie charts include total number of intervals for each family that had none, (at least) one H3.3 peak (H3.3 only), or H3K9me3 peak(s) (H3K9me3 only), or at least one of each (H3.3+H3K9me3).