Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline

Maezawa, So; Hasegawa, Kazuteru; Yukawa, Masashi; Kubo, Naoki; Sakashita, Akihiko; Alavattam, Kris G.; Sin, Ho Su; Kartashov, Andrey V.; Sasaki, Hidetada; Barski, Artem; Namekawa, Satoshi H.

doi:10.1073/pnas.1804512115

Cited by 64 publications

(112 citation statements)

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“…These observations are consistent with the down-regulation of late-spermatogenesis genes in PS and RS Scml2 -KO mice 3 . SCML2 is required for the establishment of H3K27me3 during meiosis, forming two major classes of bivalent genomic domains comprised of H3K27me3 and H3K4me2/3: Class I domains, which are associated with developmental regulator genes; and Class II domains, which are associated with somatic/progenitor genes 40 . We observed an increase in H3K27ac signal intensity at both classes of bivalent domains in Scml2 -KO mice (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…ChIP-seq data for A-MYB and RNA-seq data from A-MYB mutant and control testes were downloaded from the Gene Expression Omnibus (accession number: GSE44690) 21 . ChIP-seq data for H3K4me3, and H3K4me2, and RNA-seq data from KIT + spermatogonia, were downloaded from Gene Expression Omnibus (accession number: GSE89502) 40 . While generated for and analyzed in this study, our H3K27ac ChIP-seq data for wild-type PS and RS were initially introduced in another study that analyzed active enhancers on the sex chromosomes 23 ; ChIP-seq data for H3K27ac from PS and RS, were downloaded from Gene Expression Omnibus (accession number: GSE107398) 23 .…”

Section: Methodsmentioning

confidence: 99%

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

Maezawa

Yukawa

Rothenberg

et al. 2020

Preprint

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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...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Maezawa

Yukawa

Rothenberg

et al. 2020

Preprint

Self Cite

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“…However, it remains possible that some differences between mammalian and Drosophila PcG targeting are not intrinsic, but arise from differences in the experimental systems used for their study. For example, scml1, one of four mouse Scm paralogues, promotes H3K27me3 enrichment on CGIs in the male germline, raising the possibility the Scm is a conserved PRC2 targeting factor (Maezawa et al, 2018). Previously, Drosophila Pcl was found in a small fraction of embryonic PRC2 complexes, and Pcl was proposed to promote PRC2 and H3K27me3 enrichment near PREs (Nekrasov et al, 2007;O'Connell et al, 2001;Savla et al, 2008;Tie et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Differentiating Drosophila female germ cells initiate Polycomb silencing by altering PRC2 sampling

DeLuca

Ghildiyal

Niu

et al. 2020

Preprint

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Polycomb silencing represses gene expression and provides a molecular memory of chromatin state that is essential for animal development. We show that Drosophila female germline stem cells (GSCs) provide a powerful system for studying Polycomb silencing and how it is established. GSCs resemble pluripotent mammalian embryonic cells in lacking silenced chromatin, but most GSC daughters, like typical somatic cells, induce Polycomb silencing as they differentiate into nurse cells. Developmentally controlled changes in the levels of two Polycomb repressive complex 2 (PRC2)-interacting proteins, Pcl and Scm, initiate differentiation. In germline stem cells, abundant Pcl inhibits silencing by slowing PRC2 and diverting it from PRE sequences. During differentiation, core PRC2 represses inactive loci while Scm and residual Pcl cooperate to enrich PRC2 and silence traditional Polycomb domains. We propose that PRC2-interacting proteins regulate the transition from a variable to stable transcription state during differentiation by altering the rate that PRC2 samples regulatory sequences.

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“…The second factor that we investigated in detail was Klhl13, a substrate-adaptor protein of the Cul3 E3 ubiquitin ligase complex (Sumara et al, 2007) . Although Klhl13 (Bonasio et al, 2014;Hasegawa et al, 2015;Maezawa et al, 2018) .…”

Section: Discussionmentioning

confidence: 99%

“…Among the other candidates, Scml2 is a chromatin regulator, which might contribute to transcriptional changes downstream of Klhl13. Scml2 is associated with the polycomb repressive complexes 1 and 2 (PRC1/2) and promotes deposition of the repressive histone marks H2AK119ub and H3K27me3 (Bonasio et al, 2014;Hasegawa et al, 2015;Maezawa et al, 2018) . To our knowledge, Scml2 has so far not been implicated in pluripotency maintenance in mESCs or MAPK signaling.…”

Section: Identification Of Klhl13 Target Proteins That Mediate Its Efmentioning

confidence: 99%

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells

Genolet

Dunkel

et al. 2020

Preprint

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X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Here, double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signalling pathway and delaying differentiation. To identify the genetic basis of these sex differences, we have performed a series of CRISPR knockout screens in murine embryonic stem cells to comprehensively identify X-linked genes that cause the female pluripotency phenotype. We found multiple genes that act in concert, among which Klhl13 plays a central role. We show that this E3 ubiquitin ligase substrate adaptor protein promotes pluripotency factor expression, delays differentiation and represses MAPK target genes, and we identify putative substrates. We thus elucidate the mechanisms that drive sex-induced differences in pluripotent cells with implications for gender medicine in the context of induced pluripotent stem cell based therapies.

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Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline

Cited by 64 publications

References 48 publications

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

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

Differentiating Drosophila female germ cells initiate Polycomb silencing by altering PRC2 sampling

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells

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