Super-enhancer switching drives a burst in germline gene expression at the mitosis-to-meiosis transition

Abstract

26The testis has the most diverse and complex transcriptome of all organs due to bursts in 27 expression of thousands of germline-specific genes. Much of this unique gene expression takes 28 place when mitotic germ cells differentiate and enter into meiotic prophase. Here, we 29 demonstrate that the genome-wide reorganization of super-enhancers (SEs) drives bursts of 30 germline genes after the mitosis-to-meiosis transition. At the mitosis-to-meiosis transition, 31 mitotic SEs dissolve while meiotic SEs are established. Meiotic SEs are associated with the 32 activation of key germline genes, defining the cellular identity of germ cells. This SE switching 33 is regulated by the establishment of meiotic SEs via A-MYB (MYBL1), a key transcription 34 factor for germline genes, and by the resolution of mitotic SEs via SCML2, a germline-specific 35 Polycomb protein required for spermatogenesis-specific gene expression. Prior to the entry 36 into meiosis, meiotic SEs are preprogrammed in mitotic spermatogonia, serving to direct the 37 unidirectional differentiation of spermatogenesis. We identify key regulatory factors for both 38 mitotic and meiotic enhancers, revealing a molecular logic for the concurrent activation of 39 mitotic enhancers and suppression of meiotic enhancers in the somatic and/or mitotically 40 proliferating phase.41replicates ( Fig. 1b, Supplementary Fig. 1). (While generated for and analyzed in this study, our 93 H3K27ac ChIP-seq data for wild-type PS and RS was initially introduced in another study that 94 analyzed active enhancers on the sex chromosomes 23 .) Consistent with the massive, dynamic 95 transcriptional change occurring at the mitosis-to-meiosis transition, we observed H3K27ac peaks 96 in mitotically proliferating spermatogonia (blue shadow), H3K27ac peaks unique to meiotic 97 spermatocytes (red shadow), and constitutive peaks (gray shadow: Fig. 1b). 99For the quantitative comparison of active enhancers during spermatogenesis, we analyzed 100 H3K27ac ChIP-seq peaks ±1 kb outside transcription start sites (TSSs); hereafter, we refer to such 101 peaks as 'distal peaks' and peaks within ±1 kb as 'proximal peaks.' Through the use of MACS2 24 , 102 a program that identifies the significant enrichment of ChIP-seq signals, we detected 11,433 distal 103 H3K27ac ChIP-seq peaks that were present in at least one stage of spermatogenesis (for these 104 analyses, we permitted only distal peaks with a normalized enrichment value of ≥4; see Methods;105 Supplementary Table 1). The distal peaks were categorized into 9 clusters through k-means 106 clustering; we further organized these into three classes as follows (Fig. 1c). The first class (705 107 peaks, comprising clusters 1-3) represents constitutive active enhancers, i.e., those observed 108 throughout spermatogenesis. The second class (2,524 peaks, comprising clusters 4 and 5) represents 109 enhancers that are active in the mitotic proliferation phase of spermatogenesis (i.e., the 'mitotic 110 phase') but are inactive in meiotic and postmeiotic p...

ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse

“…SMARCC1 promotes XCI by increasing promoter accessibility of the inactive X chromosome (Xi). Interestingly, during MSCI, sex-linked chromatin displays enhanced accessibility (Maezawa et al, 2018b). In contrast, our studies showed that BAF-A limits rather than enhances sex-linked chromatin accessibility.…”

Endogenous retroviruses drive species-specific germline transcriptomes in mammals

“…Therefore, we postulate that retrotransposition of ERVs provides new binding sites for key transcription factors, which, in turn, function as newly evolved cis regulatory elements for many genes. Importantly, we have also shown that A-MYB is associated with super-enhancers to drive the expression of key germline genes (Maezawa et al) 30 . Therefore, an A-MYB-dependent mechanism appears to lie at the heart of two distinct enhancer types: (1) super-enhancers, which drive robust activation of germline genes; and (2) ERV-driven, rapidly evolving enhancers, which fine-tune the expression of species-specific germline genes.…”

“…Given that ERVs are interspersed throughout the genome, we hypothesized that ERVs function as enhancers that drive the expression of spermatogenesis-specific genes. To test this hypothesis, we analyzed the ChIP-seq (chromatin immunoprecipitation sequencing) signal enrichment for H3K27 acetylation (H3K27ac), a marker of active enhancers, in PS 29 (Maezawa et al) 30 . Through the thresholding of H3K27ac enrichment and accessible chromatin at individual ERV loci (see Methods ), we defined a category of ERVs said to be “enhancer-like” in PS (ERV1: 116 enhancer-like loci; ERVK: 970 enhancer-like loci; ERVL: 36 enhancer-like loci; Fig.…”

“… Data availability H3K27ac ChIP-seq data reported in this study are described in the accompanying study (Maezawa et al) 30 and deposited to the Gene Expression Omnibus (GEO) under the accession number GSE130652. H3K27ac native ChIP-seq data in WT and A-myb mutant PS are deposited under the accession number GSE142173.…”