Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline

Abstract

Background: The male germline transcriptome changes dramatically during the mitosis-to-meiosis transition to activate late spermatogenesis genes and to transiently suppress genes commonly expressed in somatic lineages and spermatogenesis progenitor cells, termed somatic/progenitor genes.

Results: These changes reflect epigenetic regulation. Induction of late spermatogenesis genes during spermatogenesis is facilitated by poised chromatin established in the stem cell phases of spermatogonia, whereas silencing of somatic/progenitor genes during meiosis and postmeiosis is associated with formation of bivalent domains which also allows the recovery of the somatic/progenitor program after fertilization. Importantly, during spermatogenesis mechanisms of epigenetic regulation on sex chromosomes are different from autosomes: X-linked somatic/progenitor genes are suppressed by meiotic sex chromosome inactivation without deposition of H3K27me3.

Conclusions: Our results suggest that bivalent H3K27me3 and H3K4me2/3 domains are not limited to developmental promoters (which maintain bivalent domains that are silent throughout the reproductive cycle), but also underlie reversible silencing of somatic/progenitor genes during the mitosis-to-meiosis transition in late spermatogenesis.

Fig. 1

The global transcriptome changes during the late stages of male germline. a Schematic of spermatogenesis. In this study, germline stem (GS) cells were used as the representative stage of the stem cell phase. X chromosomes are depicted in green and the Y chromosomes are depicted in orange. Barred chromosomes represent suppressed transcription. b A heatmap showing gene expression patterns among several germ cells versus somatic cells. All 17,213 genes that showed more than 3 RPKM in at least one cell type are shown. RNA-seq data were obtained from published studies as described in the Methods section. c Flow chart of grouping of each class of spermatogenesis genes, degree of overlaps, and their expression heatmaps. d Gene ontology analysis of each class of spermatogenesis genes. e Summary table of each class of spermatogenesis genes. f Enrichment of RS active genes on the X chromosome. *P <2.2e-16, chi-square test. ES, embryonic stem cells; GS, germline stem cells; MEF, mouse embryonic fibroblasts; PS, pachytene spermatocytes; RPKM, reads per kilobase per million; RS, round spermatids; THY1+, THY1+ undifferentiated spermatogonia

Fig. 2

Distinct regulation between the X chromosome and autosomes during the late stages of male germline. a GS, b PS, and c RS are shown. Average tag density (ATD) of each histone mark was compared between all autosomal genes and all X-linked genes. ATD, average tag density; GS, germline stem cells; PS, pachytene spermatocytes; RS, round spermatids; ChIP-seq, chromatin immunoprecipitation sequencing

Fig. 3

Autosomal late spermatogenesis genes are poised in GS cells for activation at PS. a A heatmap showing distribution of histone marks in GS cells. Tag density around TSS (±5 kb) is shown. b ATD of active marks in representative groups in GS cells. c ATD of active marks at the genes activated in later stages. d ATD of silent marks in representative groups in GS cells. ATD, average tag density; GS, germline stem cells; PS, pachytene spermatocytes; TSS, transcription start site

Fig. 4

Active marks remain after the inactivation of autosomal somatic/progenitor genes in PS. a Distribution of histone marks around PS/RS inactive Vim gene locus and PS active Sycp3 gene locus in PS. b ATD of active marks at the active genes in PS. c ATD of active marks at the silent genes in PS. d ATD of active marks in PS. These genes are activated in RS. e ATD of each silent mark in representative groups in PS. ATD, average tag density; PS, pachytene spermatocytes; RS, round spermatids

Fig. 5

Epigenetic profiles for RS-specific activation and gene poising on autosomal somatic/progenitor genes in RS. a Distribution of histone marks on PS/RS inactive Vim gene locus and RS active Spata20 gene locus in RS. b A heatmap showing distribution of histone marks in RS. Density around TSS (±5 kb) is shown. c ATD of active marks at the active genes in RS. For H3K4me2, ATD on gene bodies from TSS to TES and ±5 kb regions were analyzed. d ATD of active marks at the silent genes in RS. e ATD of silent marks in representative groups in RS. f Expression of each gene set in GS, PS, RS, and ES. ATD, average tag density; ES, embryonic stem cells; GS, germline stem cells; PS, pachytene spermatocytes; RS, round spermatids; TSS, transcription start site

Fig. 6

Epigenetic profile of the X chromosome during the late stages of the male germline. a Binding peaks of histone marks on PS/RS inactive Timp1 gene locus in GS, PS, and RS. b Binding peaks of histone marks on RS active Akap4 gene locus in GS, PS, and RS. ATD of histone marks in representative groups in c GS, d PS, and e RS. For H3K4me2, ATD on gene bodies from TSS to TES and ±5 kb regions were analyzed. f Average RPKM of each group in GS, PS, RS, and ES. g, h ATD profiles of H3K4me2 on gene bodies and Kcr on TSS are compared between WT and Rnf8 KO. Wilcoxon rank sum test was performed for read counts in the highlighted area (H3K4me2: −1 kb from TSS to TES; Kcr: −500 bp to +500 bp from TSS, *P <0.05, **P <0.001). ATD, average tag density; ES, embryonic stem cells; GS, germline stem cells; Kcr, lysine crotonylation; KO, knockout; PS, pachytene spermatocytes; RS, round spermatids; RPKM, reads per kilobase per million; TES, transcription end site; TSS, transcription start site; WT, wild-type

Fig. 7

Summary: programmed gene poising for the male germline transcriptomes. See the Discussion section for detail