Extended Data Fig. 10: H3K9me3 heterochromatin.

a, Genome browser view showing a large region of chromosome 15 (chr15: 87,165,311–104,043,685; mm10). Signal tracks (fold enrichment over input) are shown for all marks. H3K9me3 looks relatively flat, unlike the other marks. We find very few regions of strong H3K9me3 enrichment outside repetitive elements, consistent with previous reports of H3K9me3 distribution in primary tissues²⁶. Data shown here and in d are from E15.5. b, The fraction of total sequencing reads that map to the reference genome (light green), and that map uniquely to the reference genome (mapq ≥30; dark green). y-axis is the mean for all ChIP libraries reported here separated by mark (n = 72 for all marks except for H3K4me2 and H3K9ac where n = 66), and error bars represent s.d. Control bars represent ChIP input libraries (no IP step). All marks and input have a high mapping rate (mean >90%), but H3K9me3 has a markedly low rate of unique mapping, suggesting that this modification is specifically enriched in non-unique (that is, repetitive) genomic regions. c, Stacked bar plots show the type of repetitive elements from which the non-uniquely mapping reads from b are likely to originate. H3K9me3 reads are highly enriched in satellite repeats relative to the input controls. d, Genome browser view of ChIP–seq fold enrichment tracks at Pchd (chr18: 36,720,767–38,058,585; mm10) and Zfp454 (chr11: 50,774,724–50,939,391; mm10) shows significant H3K9me3 enrichment (state 14) during development. The 3′ UTRs of Zfp genes marked by H3K9me3 (reported previously²⁸) are indicated by pink arrowheads. e, As in d, but showing chromatin states across these regions.