Fig. 2: Chromatin environment at H3K79me2 regions in male germ cells.

a The 18 chromatin states model obtained with ChromHMM. TSSA Active Transcription start site, TSSFlnk flanking TSS, and TSSFlnkD flanking TSS downstream (which were pooled in the state named TSSFlnk), Tx strong transcription, TxWk weak transcription, EnhG1 and EnhG2 genic enhancers (which were pooled in one state named EnhG), EnhA active enhancer, EnhWk weak enhancer, ZNF/Rpts ZNF genes and repeats, Het Heterochromatin, TSSBiv bivalent/poised TSS, EnhBiv bivalent enhancer, ReprPC repressed PolyComb and ReprPCWk weak repressed polycomb (which were pooled in one state named ReprPC), Quies1, Quies2, and Quies3 Quiescent/Low (which were pooled in one state called Quies). b Distribution of chromatin states among H3K79me2 enriched regions (H3K79me2+) and H3K79me2 devoid regions (H3K79me2−). c Alluvial plot showing the dynamic of H3K79me2+ chromatin states (as defined with ChromHMM) throughout spermatogenesis. Only groups containing more than 100 regions are shown. d Mean gene expression level (log(cpm)) of genes associated with enhancers enriched (+) or not (−) in H3K79me2, in RS. Stars indicate p-values calculated using the Wilcoxon test (*p < 0.05). e and f Heatmaps obtained by regioneR (multicomparison) displaying correlations between H3K79me2 in SCI (e) and in RS (f) and TAD boundaries, A and B compartments, compartment switch (from A to B and vice versa), CpG islands, CTCF, cohesins (RAD21L and REC8), ATAC-Seq, transcription start sites (TSS) and the 18 chromatin states defined in Fig. 2a (and indicated as SC1–SC18 for primary spermatocytes and RS1–RS18 for round spermatids). SCI comparison also included PRDM9 sites (Type I and II) and DMC1 sites. RS included post-meiotic DSBs.