Fig. 3: Dynamic changes in broad H3K4me3 and H3K27ac domains during spermiogenesis.

a Snapshots of the UCSC genome browser showing the normalized ChIP-seq read densities of H3K4me3 (red) and H3K27ac (blue) at the Crem gene locus during mouse spermatogenesis. Regions shaded in pink highlight two broad H3K4me3 and H3K27ac peaks at the distal (left) and promoter (right) regions of the Crem gene, emphasizing the broad enrichment pattern of H3K4me3 and H3K27ac at the RS stages. b Heatmaps showing the normalized ChIP-seq read densities of H3K4me3 (red, upper panel) or H3K27ac (blue, lower panel) during mouse spermatogenesis on all broad H3K4me3 or H3K27ac peaks identified at the RS stages. c Stacked chart showing the numbers of broad H3K4me3 peaks (upper panel) from undifferentiated spermatogonia (Undiff) to mature sperm and H3K27ac peaks (lower panel) from Undiff to RS8 on promoter and distal regions. The broad peaks are defined as ChIP-seq peaks exceeding 5 kb in length. The promoter regions are defined as ± 2 kb from the TSS, and the distal regions are defined as the genomic regions beyond ± 2 kb from the TSS. LS denotes elongating spermatid steps 10–12, and sperm denotes the mature sperm stage. d Stacked chart showing the number of broad H3K4me3 peaks in RS4 compared to a range of indicated cell types. These include diverse mouse and human cell lines, CD4⁺ T cells, and early embryonic cells. e Heatmaps showing the normalized ChIP-seq read densities of H3K4me3 (red, left panel) and H3K27ac (blue, right panel) in human pachytene/diplotene (P/D) and/or RS. The visualization encompasses all broad H3K4me3 or H3K27ac peaks identified in human RSs. f Venn diagrams showing the overlap between H3K4me3-based SEs (super H3K4me3) and H3K27ac-based SEs identified by ROSE in mouse RSs. g Venn diagrams showing the overlap among H3K4me3-based SEs, H3K27ac-based SEs and broad H3K4me3 peaks.