Fig. 1: Establishment of a comprehensive chromatin epigenomic atlas during mouse spermatogenesis.

a Schematic workflow showing the 11 subtypes of synchronized mouse spermatogenic cells isolated. These include mitotic stages (Undiff: undifferentiated spermatogonia, A1: type A1 spermatogonia, B: type B spermatogonia), meiotic stages (pL: preleptotene spermatocytes, L: leptotene spermatocytes, Z: zygotene spermatocytes, D: diplotene spermatocytes) and spermiogenesis stages (RS2: steps 1–2 round spermatids, RS4: steps 3–4 round spermatids, RS8: steps 7–8 round spermatids). Genome-wide landscapes of seven histone marks, nucleosome positioning and DNAme were profiled in the 11 subtypes by ChIP-seq and NOMe-seq, respectively. The transcriptome was established by RNA-seq. b Snapshots of UCSC genome browser showing RNA-seq, histone marks, DNA methylation, and chromatin accessibility at B (upper panels) and RS4 (middle panels) stages, and H3K4me3 at 11 different stages (lower panels) during mouse spermatogenesis at the Sohlh2 and Ttll4 gene loci. c Quantification representation of ChIP-seq peak numbers for seven histone modifications in 11 stages during mouse spermatogenesis. d Western blot analyses showing the global levels of histone marks during mouse spermatogenesis. H3 was used as the internal control. e Emission probabilities for histone modifications in 15 ChromHMM chromatin states, with a descriptive title of each chromatin state shown on the right. Active promoters are proximal to TSS, marked by hyper H3K4me3 and H3K27ac. Active enhancers, enriched in H3K27ac and H3K4me1, are distal from the TSS. Transcriptional elongation signatures were decorated with H3K36me3. Heterochromatin regions are typically associated with H3K9me2, H3K9me3, or H3K27me3 but lack active marks. The no signal (Ns) state is characterized by the absence of any histone modification. f Average chromatin accessibility on different chromatin states (Promoter and Enhancer) at RS4 stage. g Chromatin state profiles at the gene loci of Zbtb16, Sohlh1, Dmc1 and Acr across 11 different stages. Pr, promoter; En, enhancer; Tr, transcription; Hc, heterochromatin. h Stacked chart showing the genomic coverage of 4 promoter-related chromatin states. i Radar charts showing the fraction of variable bases across different stages (left panel) and distinct chromatin states (right panel). Points on the lines in both radar charts represent the median values of the fraction of variable bases.