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Menon DU, Chakraborty P, Murcia N, Magnuson T. ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.25.542290. [PMID: 37292940 PMCID: PMC10245947 DOI: 10.1101/2023.05.25.542290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I. Those germ cells showing a Cre-induced loss of ARID1A were arrested in pachynema and failed to repress sex-linked genes, indicating a defective MSCI. Consistent with this defect, mutant sex chromosomes displayed an abnormal presence of elongating RNA polymerase II coupled with an overall increase in chromatin accessibility detectable by ATAC-seq. By investigating potential mechanisms underlying these anomalies, we identified a role for ARID1A in promoting the preferential enrichment of the histone variant, H3.3, on the sex chromosomes, a known hallmark of MSCI. Without ARID1A, the sex chromosomes appeared depleted of H3.3 at levels resembling autosomes. Higher resolution analyses by CUT&RUN revealed shifts in sex-linked H3.3 associations from discrete intergenic sites and broader gene-body domains to promoters in response to the loss of ARID1A. Several sex-linked sites displayed ectopic H3.3 occupancy that did not co-localize with DMC1 (DNA Meiotic Recombinase 1). This observation suggests a requirement for ARID1A in DMC1 localization to the asynapsed sex chromatids. We conclude that ARID1A-directed H3.3 localization influences meiotic sex chromosome gene regulation and DNA repair.
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2
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Kitamura Y, Namekawa SH. Epigenetic priming in the male germline. Curr Opin Genet Dev 2024; 86:102190. [PMID: 38608568 PMCID: PMC11162906 DOI: 10.1016/j.gde.2024.102190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Epigenetic priming presets chromatin states that allow the rapid induction of gene expression programs in response to differentiation cues. In the germline, it provides the blueprint for sexually dimorphic unidirectional differentiation. In this review, we focus on epigenetic priming in the mammalian male germline and discuss how cellular memories are regulated and inherited to the next generation. During spermatogenesis, epigenetic priming predetermines cellular memories that ensure the lifelong maintenance of spermatogonial stem cells and their subsequent commitment to meiosis and to the production of haploid sperm. The paternal chromatin state is also essential for the recovery of totipotency after fertilization and contributes to paternal epigenetic inheritance. Thus, epigenetic priming establishes stable but reversible chromatin states during spermatogenesis and enables epigenetic inheritance and reprogramming in the next generation.
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Affiliation(s)
- Yuka Kitamura
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
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3
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Han C. Gene expression programs in mammalian spermatogenesis. Development 2024; 151:dev202033. [PMID: 38691389 DOI: 10.1242/dev.202033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Mammalian spermatogenesis, probably the most complex of all cellular developmental processes, is an ideal model both for studying the specific mechanism of gametogenesis and for understanding the basic rules governing all developmental processes, as it entails both cell type-specific and housekeeping molecular processes. Spermatogenesis can be viewed as a mission with many tasks to accomplish, and its success is genetically programmed and ensured by the collaboration of a large number of genes. Here, I present an overview of mammalian spermatogenesis and the mechanisms underlying each step in the process, covering the cellular and molecular activities that occur at each developmental stage and emphasizing their gene regulation in light of recent studies.
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Affiliation(s)
- Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101 Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, 100101 Beijing, China
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4
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Nitahara K, Kawamura A, Kitamura Y, Kato K, Namekawa SH, Nishiyama M. Chromatin remodeler CHD8 is required for spermatogonial proliferation and early meiotic progression. Nucleic Acids Res 2024; 52:2995-3010. [PMID: 38224953 PMCID: PMC11014243 DOI: 10.1093/nar/gkad1256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Meiosis is a key step during germ cell differentiation, accompanied by the activation of thousands of genes through germline-specific chromatin reorganization. The chromatin remodeling mechanisms underpinning early meiotic stages remain poorly understood. Here we focus on the function of one of the major autism genes, CHD8, in spermatogenesis, based on the epidemiological association between autism and low fertility rates. Specific ablation of Chd8 in germ cells results in gradual depletion of undifferentiated spermatogonia and the failure of meiotic double-strand break (DSB) formation, leading to meiotic prophase I arrest and cell death. Transcriptional analyses demonstrate that CHD8 is required for extensive activation of spermatogenic genes in spermatogonia, necessary for spermatogonial proliferation and meiosis. CHD8 directly binds and regulates genes crucial for meiosis, including H3K4me3 histone methyltransferase genes, meiotic cohesin genes, HORMA domain-containing genes, synaptonemal complex genes, and DNA damage response genes. We infer that CHD8 contributes to meiotic DSB formation and subsequent meiotic progression through combined regulation of these meiosis-related genes. Our study uncovers an essential role of CHD8 in the proliferation of undifferentiated spermatogonia and the successful progression of meiotic prophase I.
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Affiliation(s)
- Kenta Nitahara
- Department of Histology and Cellular Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Atsuki Kawamura
- Department of Histology and Cellular Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Yuka Kitamura
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - Kiyoko Kato
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - Masaaki Nishiyama
- Department of Histology and Cellular Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
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5
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Kaku Y, Isono Y, Tanaka H, Kobayashi T, Kanemori Y, Kashiwabara SI. Intronless Pabpc6 encodes a testis-specific, cytoplasmic poly(A)-binding protein but is dispensable for spermatogenesis in the mouse†. Biol Reprod 2024; 110:834-847. [PMID: 38281153 DOI: 10.1093/biolre/ioae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/25/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024] Open
Abstract
Besides ubiquitous poly(A)-binding protein, cytoplasmic 1 (PABPC1), testis-specific PABPC2/PABPt (in humans, referred to as PABPC3), and female and male germline-specific PABPC1L/ePAB, have been reported in the mouse testis. Recent in silico analysis additionally identified testis-specific Pabpc6 in the mouse. In this study, we characterized PABPC6 and its mutant mice. PABPC6 was initially detectable in the cytoplasm of pachytene spermatocytes, increased in abundance in round spermatids, and decreased in elongating spermatids. PABPC6 was capable of binding to poly(A) tails of various mRNAs and interacting with translation-associated factors, including EIF4G, PAIP1, and PAIP2. Noteworthy was that PABPC6, unlike PABPC1, was barely associated with translationally active polysomes and enriched in chromatoid bodies of round spermatids. Despite these unique characteristics, neither synthesis of testicular proteins nor spermatogenesis was affected in the mutant mice lacking PABPC6, suggesting that PABPC6 is functionally redundant with other co-existing PABPC proteins during spermatogenesis.
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Affiliation(s)
- Yuko Kaku
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuka Isono
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideto Tanaka
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tomohiro Kobayashi
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshinori Kanemori
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shin-Ichi Kashiwabara
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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6
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Yue B, Wang HY, Huang Y, Li S, Ma W, Liu Q, Shao C. Molecular functional characterization of the setdb1 and its potential target gene sox5 illuminate the histone modification-mediated orchestration of gonadal development in Chinese tongue sole (Cynoglossus semilaevis). Gene 2024; 901:148199. [PMID: 38253299 DOI: 10.1016/j.gene.2024.148199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/31/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024]
Abstract
SET (SuVar3-9, Enhancer of Zeste, Trithorax) domain bifurcated histone lysine methyltransferase 1, setdb1, is the predominant histone lysine methyltransferase catalyzing H3K9me3. Prior studies have illustrated that setdb1 and H3K9me3 critically regulate sex differentiation and gametogenesis. However, the molecular details by which setdb1 is involved in these processes in fish have been poorly reported. Here, we cloned and characterized the setdb1 ORF (open reading frame) sequence from Chinese tongue sole (Cynoglossus semilaevis). The setdb1 ORF sequence was 3,669 bp, encoding a 1,222-amino-acid protein. Phylogenetic analysis showed that setdb1 was structurally conserved. qRT-PCR revealed that setdb1 had a high expression level in the testes at 12 mpf (months post fertilization). Single-cell RNA-seq data at 24 mpf indicated that setdb1 was generally expressed in spermatogenic cells at each stage except for sperm and was centrally expressed in oogonia. H3K9me3 modification was observed in gonads with the immunofluorescence technique. Furthermore, the overexpression experiment suggested that sox5 was a candidate target of setdb1. sox5 was abundantly expressed in male and pseudomale gonads at 24 mpf. Single-cell RNA-seq data showed that sox5 was mainly expressed in spermatogonia and its expression gradually declined with differentiation. Taken together, our findings imply that setdb1 regulates sox5 transcription in gonads, which provides molecular clues into histone modification-mediated orchestration of sex differentiation and gametogenesis.
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Affiliation(s)
- Bowen Yue
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Yingyi Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Shuo Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Wenxiu Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Qian Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China.
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7
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Gao J, Qin Y, Schimenti JC. Gene regulation during meiosis. Trends Genet 2024; 40:326-336. [PMID: 38177041 PMCID: PMC11003842 DOI: 10.1016/j.tig.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Meiosis is essential for gamete production in all sexually reproducing organisms. It entails two successive cell divisions without DNA replication, producing haploid cells from diploid ones. This process involves complex morphological and molecular differentiation that varies across species and between sexes. Specialized genomic events like meiotic recombination and chromosome segregation are tightly regulated, including preparation for post-meiotic development. Research in model organisms, notably yeast, has shed light on the genetic and molecular aspects of meiosis and its regulation. Although mammalian meiosis research faces challenges, particularly in replicating gametogenesis in vitro, advances in genetic and genomic technologies are providing mechanistic insights. Here we review the genetics and molecular biology of meiotic gene expression control, focusing on mammals.
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Affiliation(s)
- Jingyi Gao
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - Yiwen Qin
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - John C Schimenti
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA.
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8
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Uneme Y, Maeda R, Nakayama G, Narita H, Takeda N, Hiramatsu R, Nishihara H, Nakato R, Kanai Y, Araki K, Siomi MC, Yamanaka S. Morc1 reestablishes H3K9me3 heterochromatin on piRNA-targeted transposons in gonocytes. Proc Natl Acad Sci U S A 2024; 121:e2317095121. [PMID: 38502704 PMCID: PMC10990106 DOI: 10.1073/pnas.2317095121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 03/21/2024] Open
Abstract
To maintain fertility, male mice re-repress transposable elements (TEs) that were de-silenced in the early gonocytes before their differentiation into spermatogonia. However, the mechanism of TE silencing re-establishment remains unknown. Here, we found that the DNA-binding protein Morc1, in cooperation with the methyltransferase SetDB1, deposits the repressive histone mark H3K9me3 on a large fraction of activated TEs, leading to heterochromatin. Morc1 also triggers DNA methylation, but TEs targeted by Morc1-driven DNA methylation only slightly overlapped with those repressed by Morc1/SetDB1-dependent heterochromatin formation, suggesting that Morc1 silences TEs in two different manners. In contrast, TEs regulated by Morc1 and Miwi2, the nuclear PIWI-family protein, almost overlapped. Miwi2 binds to PIWI-interacting RNAs (piRNAs) that base-pair with TE mRNAs via sequence complementarity, while Morc1 DNA binding is not sequence specific, suggesting that Miwi2 selects its targets, and then, Morc1 acts to repress them with cofactors. A high-ordered mechanism of TE repression in gonocytes has been identified.
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Affiliation(s)
- Yuta Uneme
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Ryu Maeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Gen Nakayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Haruka Narita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Naoki Takeda
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
| | - Ryuji Hiramatsu
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara631-8505, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo113-0032, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
- Faculty of Life Sciences, Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Honjo, Kumamoto860-8556, Japan
| | - Mikiko C. Siomi
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
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Chakraborty P, Magnuson T. INO80 regulates chromatin accessibility to facilitate suppression of sex-linked gene expression during mouse spermatogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.04.522761. [PMID: 36711658 PMCID: PMC9881943 DOI: 10.1101/2023.01.04.522761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The INO80 protein is the main catalytic subunit of the INO80-chromatin remodeling complex, which is critical for DNA repair and transcription regulation in murine spermatocytes. In this study, we explored the role of INO80 in silencing genes on meiotic sex chromosomes in male mice. INO80 immunolocalization at the XY body in pachytene spermatocytes suggested a role for INO80 in the meiotic sex body. Subsequent deletion of Ino80 resulted in high expression of sex-linked genes. Furthermore, the active form of RNA polymerase II at the sex body of Ino80 -null pachytene spermatocytes indicates incomplete inactivation of sex-linked genes. A reduction in the recruitment of initiators of meiotic sex chromosome inhibition (MSCI) argues for INO80-facilitated recruitment of DNA repair factors required for silencing sex-linked genes. This role of INO80 is independent of a common INO80 target H2A.Z. Instead, in the absence of INO80, a reduction in chromatin accessibility at DNA repair sites occurs on the sex chromosomes. These data suggest a role for INO80 in DNA repair factor localization, thereby facilitating the silencing of sex-linked genes during the onset of pachynema. Summary Statement Chromatin accessibility and DNA repair factor localization at the sex chromosomes are facilitated by INO80, which regulates sex-linked gene silencing during meiotic progression in spermatocytes.
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Liu H, Tang Y, Sun L, Li S, Luo L, Chen Z, Li G. Involvement of Histone Acetyltransferase 1 (HAT1) in the Spermatogenesis of Non-Condensed Nuclear Sperm in Chinese Mitten Crab, Eriocheir sinensis. Biochem Genet 2024:10.1007/s10528-024-10700-0. [PMID: 38416273 DOI: 10.1007/s10528-024-10700-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/15/2024] [Indexed: 02/29/2024]
Abstract
Chinese mitten crab, Eriocheir sinensis, is a decapod crustacean with a special, non-condensated nucleus in the sperm. Studies have shown that the nuclear compact state of male germ cells during the spermatogenesis is closely related to histone modification. To explore the possible role of histone acetyltransferase 1 (HAT1) in the chromatin organization during the E. sinensis spermatogenesis, we took the testis tissues of both adult and juvenile crabs as the materials of study and analyzed the biological functions of HAT1 by whole transcriptome sequencing and bioinformatics, then further analyzed the expression and distribution of HAT1 using the methods of RT-qRCR, western blotting, and immunofluorescence location. The results showed that HAT1 is an alkaline-unstable hydrophilic protein. It was predicted to interact with a variety of histones and chromosome assembly proteins, including Asf1b, Chaf1b, and Hist1h3f, and is involved in many biological functions pertaining to chromatin dynamics such as chromatin organization, DNA dependent nucleosome assembly, DNA conformational changes, and so on. HAT1 was up-regulated in the adult testes compared to the juvenile (n = 3, P < 0.05). HAT1 was mainly located in the nuclei of male germ cells of E. sinensis. As spermatogenesis proceeded, the expression of HAT1 decreased and even disappeared in the nuclei (n = 3, P < 0.05). HAT1 is an important player in histone acetylation, which facilitates chromatin alteration in a three-dimensional conformation. The expression of HAT1 in different male germ cells might indicate the chromatin dynamics at the diversity stages of spermatogenesis. The high expression of HAT1 at the early stages of E. sinensis spermatogenesis hints the active involvement in chromatin organization, while its progressively reduced expression accompanied by the progression of spermatogenesis suggests a relatively gradual stabilization and stereotyping of chromatin. As for the disappearance of HAT1 in mature sperm with non-condensed nuclei, the reduction in histones targeted by HAT1 or histone acetylation may be an important initiator.
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Affiliation(s)
- Huiting Liu
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Yulian Tang
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Lishuang Sun
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Shu Li
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Lvjing Luo
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Zhengyu Chen
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Genliang Li
- Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
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11
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Du X, Yang D, Yu X, Wei Y, Chen W, Zhai Y, Ma F, Zhang M, Wan S, Li Y, Yang X, Aierken A, Zhang N, Xu W, Meng Y, Li N, Liao M, Yuan X, Zhu H, Qu L, Zhou N, Bai X, Peng S, Yang F, Hua J. PLZF protein forms a complex with protein TET1 to target TCF7L2 in undifferentiated spermatogonia. Theriogenology 2024; 215:321-333. [PMID: 38128225 DOI: 10.1016/j.theriogenology.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/18/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor promyelocytic leukemia zinc finger (PLZF, also known as ZBTB16) is critical for the self-renewal of spermatogonial stem cells (SSCs). However, the function of PLZF in SSCs is not clear. Here, we found that PLZF acted as an epigenetic regulator of stem cell maintenance and self-renewal of germ cells. The PLZF protein interacts with the ten-eleven translocation 1 (TET1) protein and subsequently acts as a modulator to regulate the expression of self-renewal-related genes. Furthermore, Transcription Factor 7-like 2 (TCF7L2) is promoted by the coordination of PLZF and Tri-methylation of lysine 4 on histone H3 (H3K4me3). In addition, testicular single-cell sequencing indicated that TCF7L2 is commonly expressed in the PLZF cluster. We demonstrated that PLZF directly targets TCF7L2 and alters the landscape of histone methylation in the SSCs nucleus. Meanwhile, the RD domain and Zn finger domain of PLZF synergize with H3K4me3 and directly upregulate TCF7L2 expression at the transcriptional level. Additionally, we identified a new association between PLZF and the histone methyltransferase EZH2 at the genomic level. Our study identified a new association between PLZF and H3K4me3, established the novel PLZF&TET1-H3K4me3-TCF7L2 axis at the genomic level which regulates undifferentiated spermatogonia, and provided a platform for studying germ cell development in male domestic animals.
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Affiliation(s)
- Xiaomin Du
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Donghui Yang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Xiuwei Yu
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China; Department of Histo-embryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yudong Wei
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Wenbo Chen
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Yuanxin Zhai
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Fanglin Ma
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Mengfei Zhang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Shicheng Wan
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Yunxiang Li
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Xinchun Yang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Aili Aierken
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Ning Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenjing Xu
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Yuan Meng
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Na Li
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaole Yuan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Na Zhou
- People's Hospital of Jingbian County, Ningxia Medical University, Yuling, Shaanxi, 718500, China
| | - Xue Bai
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, M13 9PL, UK
| | - Sha Peng
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China.
| | - Fan Yang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China.
| | - Jinlian Hua
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China.
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12
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Lismer A, Shao X, Dumargne MC, Lafleur C, Lambrot R, Chan D, Toft G, Bonde JP, MacFarlane AJ, Bornman R, Aneck-Hahn N, Patrick S, Bailey JM, de Jager C, Dumeaux V, Trasler JM, Kimmins S. The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:17008. [PMID: 38294233 PMCID: PMC10829569 DOI: 10.1289/ehp12013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND The organochlorine dichlorodiphenyltrichloroethane (DDT) is banned worldwide owing to its negative health effects. It is exceptionally used as an insecticide for malaria control. Exposure occurs in regions where DDT is applied, as well as in the Arctic, where its endocrine disrupting metabolite, p , p ' -dichlorodiphenyldichloroethylene (p , p ' -DDE) accumulates in marine mammals and fish. DDT and p , p ' -DDE exposures are linked to birth defects, infertility, cancer, and neurodevelopmental delays. Of particular concern is the potential of DDT use to impact the health of generations to come via the heritable sperm epigenome. OBJECTIVES The objective of this study was to assess the sperm epigenome in relation to p , p ' -DDE serum levels between geographically diverse populations. METHODS In the Limpopo Province of South Africa, we recruited 247 VhaVenda South African men and selected 50 paired blood serum and semen samples, and 47 Greenlandic Inuit blood and semen paired samples were selected from a total of 193 samples from the biobank of the INUENDO cohort, an EU Fifth Framework Programme Research and Development project. Sample selection was based on obtaining a range of p , p ' -DDE serum levels (mean = 870.734 ± 134.030 ng / mL ). We assessed the sperm epigenome in relation to serum p , p ' -DDE levels using MethylC-Capture-sequencing (MCC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq). We identified genomic regions with altered DNA methylation (DNAme) and differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3) in sperm. RESULTS Differences in DNAme and H3K4me3 enrichment were identified at transposable elements and regulatory regions involved in fertility, disease, development, and neurofunction. A subset of regions with sperm DNAme and H3K4me3 that differed between exposure groups was predicted to persist in the preimplantation embryo and to be associated with embryonic gene expression. DISCUSSION These findings suggest that DDT and p , p ' -DDE exposure impacts the sperm epigenome in a dose-response-like manner and may negatively impact the health of future generations through epigenetic mechanisms. Confounding factors, such as other environmental exposures, genetic diversity, and selection bias, cannot be ruled out. https://doi.org/10.1289/EHP12013.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Charlotte Dumargne
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Romain Lambrot
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gunnar Toft
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Peter Bonde
- Department of Occupational and Environmental Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Amanda J. MacFarlane
- Agriculture Food and Nutrition Evidence Center, Texas A&M University, Fort Worth, Texas, USA
| | - Riana Bornman
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Natalie Aneck-Hahn
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Sean Patrick
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Janice M. Bailey
- Research Centre on Reproduction and Intergenerational Health, Department of Animal Sciences, Université Laval, Quebec, Quebec, Canada
| | - Christiaan de Jager
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Jacquetta M. Trasler
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal, Quebec, Canada
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13
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Yin Q, Yang CH, Strelkova OS, Wu J, Sun Y, Gopalan S, Yang L, Dekker J, Fazzio TG, Li XZ, Gibcus J, Rando OJ. Revisiting chromatin packaging in mouse sperm. Genome Res 2023; 33:gr.277845.123. [PMID: 38129076 PMCID: PMC10760523 DOI: 10.1101/gr.277845.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023]
Abstract
Mammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, nucleosome localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis, we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, and appropriate lysis conditions, are together required to reveal a sperm chromatin state distinct from most previous reports. Using ATAC-seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with early development and transcriptional control. Histone modification and chromosome folding profiles also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies show that our knowledge of chromosome packaging in mammalian sperm remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.
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Affiliation(s)
- Qiangzong Yin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Chih-Hsiang Yang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Olga S Strelkova
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Jingyi Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yu Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Sneha Gopalan
- Department of Molecular Cellular and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Thomas G Fazzio
- Department of Molecular Cellular and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Johan Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA;
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14
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Kitamura Y, Takahashi K, Maezawa S, Munakata Y, Sakashita A, Kaplan N, Namekawa SH. CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569508. [PMID: 38076840 PMCID: PMC10705413 DOI: 10.1101/2023.11.30.569508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin contacts on autosomes pre-establish meiosis-specific super-enhancers (SE). These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.
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Affiliation(s)
- Yuka Kitamura
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
| | - Kazuki Takahashi
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, 281-8510, Japan
| | - Yasuhisa Munakata
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582 Japan
| | - Noam Kaplan
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Satoshi H. Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, USA
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
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15
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Cheng J, Li T, Zheng Z, Zhang X, Cao M, Tang W, Hong K, Zheng R, Shao J, Zhao X, Jiang H, Xu W, Lin H. Loss of histone reader Phf7 leads to immune pathways activation via endogenous retroviruses during spermiogenesis. iScience 2023; 26:108030. [PMID: 37920670 PMCID: PMC10618686 DOI: 10.1016/j.isci.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/12/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023] Open
Abstract
Genetic studies have elucidated the critical roles of Phf7 in germline development in animals; however, the exact etiology of Phf7 mutations leading to male infertility and the possibility of mechanism-based therapy are still unclear and warrant further investigation. Using the Phf7 knockout mouse model, we verified that genetic defects were responsible for male infertility by preventing histone-to-protamine exchange, as previously reported. The deficiency of spermatogenesis caused by Phf7 deletion through the endogenous retrovirus-mediated activation of the immune pathway is a common mechanism of infertility. Furthermore, we identified PPARα as a promising target of immunity and inflammation in the testis, where endogenous retroviruses are suppressed, and Phf7 as a crucial regulator of endogenous retrovirus-mediated immune regulation and revealed its role as an epigenetic reader. The loss of Phf7 activates immune pathways, which can be rescued by the PPARα agonist astaxanthin. These results showed that astaxanthin is a potential therapeutic agent for treating male infertility. The findings in our study provide insights into the molecular mechanisms underlying male infertility and suggest potential targets for future research and therapeutic development.
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Affiliation(s)
- Jianxing Cheng
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
| | - Tongtong Li
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhongjie Zheng
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
| | - Xueguang Zhang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Mengyang Cao
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
| | - Wenhao Tang
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
- Department of Human Sperm Bank, Peking University Third Hospital, Peking University, Beijing, China
| | - Kai Hong
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
| | - Rui Zheng
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jichun Shao
- Department of Urology, Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital), Chengdu, Sichuan, China
| | - Xiaomiao Zhao
- Department of Reproductive Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan 2nd Road, Guangzhou 510080, China
| | - Hui Jiang
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
| | - Wenming Xu
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
- Department of Reproductive Medicine Center, Peking University Third Hospital, Peking University, Beijing, China
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16
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Huang Y, Li L, An G, Yang X, Cui M, Song X, Lin J, Zhang X, Yao Z, Wan C, Zhou C, Zhao J, Song K, Ren S, Xia X, Fu X, Lan Y, Hu X, Wang W, Wang M, Zheng Y, Miao K, Bai X, Hutchins AP, Chang G, Gao S, Zhao XY. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination. Nat Cell Biol 2023; 25:1520-1534. [PMID: 37723297 DOI: 10.1038/s41556-023-01232-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
Human spermatogenesis is a highly ordered process; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes using the modified single-cell chromatin overall omic-scale landscape sequencing approach, we revealed that the transcriptional changes throughout human spermatogenesis were correlated with chromatin accessibility changes. In particular, we identified a set of transcription factors and cis elements with potential functions. A round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. Aberrant DNA hypermethylation could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination and fertility. Our work provides multi-omics landscapes of human spermatogenesis at single-cell resolution and offers insights into the association between DNA demethylation and male meiotic recombination.
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Affiliation(s)
- Yaping Huang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Geng An
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiuling Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jing Lin
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiaoling Zhang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Zhaokai Yao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cong Wan
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cai Zhou
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jiexiang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Ke Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Shaofang Ren
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xinyu Xia
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xin Fu
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Yu Lan
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xuesong Hu
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Wen Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Mei Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Kai Miao
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, P. R. China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P. R. China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, P. R. China.
| | - Shuai Gao
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China.
| | - Xiao-Yang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China.
- Guangdong Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, P. R. China.
- Key Laboratory of Mental Health of the Ministry of Education, Guangzhou, P. R. China.
- Department of Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China.
- National Clinical Research Center for Kidney Disease, Guangzhou, P. R. China.
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17
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Maezawa S, Yukawa M, Hasegawa K, Sugiyama R, Iizuka M, Hu M, Sakashita A, Vidal M, Koseki H, Barski A, DeFalco T, Namekawa SH. PRC1 suppresses a female gene regulatory network to ensure testicular differentiation. Cell Death Dis 2023; 14:501. [PMID: 37542070 PMCID: PMC10403552 DOI: 10.1038/s41419-023-05996-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 08/06/2023]
Abstract
Gonadal sex determination and differentiation are controlled by somatic support cells of testes (Sertoli cells) and ovaries (granulosa cells). In testes, the epigenetic mechanism that maintains chromatin states responsible for suppressing female sexual differentiation remains unclear. Here, we show that Polycomb repressive complex 1 (PRC1) suppresses a female gene regulatory network in postnatal Sertoli cells. We genetically disrupted PRC1 function in embryonic Sertoli cells after sex determination, and we found that PRC1-depleted postnatal Sertoli cells exhibited defective proliferation and cell death, leading to the degeneration of adult testes. In adult Sertoli cells, PRC1 suppressed specific genes required for granulosa cells, thereby inactivating the female gene regulatory network. Chromatin regions associated with female-specific genes were marked by Polycomb-mediated repressive modifications: PRC1-mediated H2AK119ub and PRC2-mediated H3K27me3. Taken together, this study identifies a critical Polycomb-based mechanism that suppresses ovarian differentiation and maintains Sertoli cell fate in adult testes.
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Affiliation(s)
- So Maezawa
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan.
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, 278-8510, Japan.
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Sha Tin, New Territories, Hong Kong
| | - Kazuteru Hasegawa
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Ryo Sugiyama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Mizuho Iizuka
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Mengwen Hu
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Akihiko Sakashita
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas, Department of Cellular and Molecular Biology, Madrid, 28040, Spain
| | - Haruhiko Koseki
- Developmental Genetics Laboratory, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tony DeFalco
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Satoshi H Namekawa
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA.
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18
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Sakashita A, Ooga M, Otsuka K, Maezawa S, Takeuchi C, Wakayama S, Wakayama T, Namekawa S. Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin. Nucleic Acids Res 2023; 51:6668-6683. [PMID: 37283086 PMCID: PMC10359620 DOI: 10.1093/nar/gkad479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/03/2023] [Accepted: 05/20/2023] [Indexed: 06/08/2023] Open
Abstract
Sperm chromatin retains small amounts of histones, and chromatin states of sperm mirror gene expression programs of the next generation. However, it remains largely unknown how paternal epigenetic information is transmitted through sperm chromatin. Here, we present a novel mouse model of paternal epigenetic inheritance, in which deposition of Polycomb repressive complex 2 (PRC2) mediated-repressive H3K27me3 is attenuated in the paternal germline. By applying modified methods of assisted reproductive technology using testicular sperm, we rescued infertility of mice missing Polycomb protein SCML2, which regulates germline gene expression by establishing H3K27me3 on bivalent promoters with other active marks H3K4me2/3. We profiled epigenomic states (H3K27me3 and H3K4me3) of testicular sperm and epididymal sperm, demonstrating that the epididymal pattern of the sperm epigenome is already established in testicular sperm and that SCML2 is required for this process. In F1 males of X-linked Scml2-knockout mice, which have a wild-type genotype, gene expression is dysregulated in the male germline during spermiogenesis. These dysregulated genes are targets of SCML2-mediated H3K27me3 in F0 sperm. Further, dysregulation of gene expression was observed in the mutant-derived wild-type F1 preimplantation embryos. Together, we present functional evidence that the classic epigenetic regulator Polycomb mediates paternal epigenetic inheritance through sperm chromatin.
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Affiliation(s)
- Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
- Department of Molecular Biology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Masatoshi Ooga
- Faculty of Life and Environmental Science, University of Yamanashi, Kofu400-8510, Japan
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA95616, USA
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa252-5201, Japan
| | - Kai Otsuka
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA95616, USA
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa252-5201, Japan
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Chiba278-8510, Japan
| | - Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Sayaka Wakayama
- Advanced Biotechnology Center, University of Yamanashi, Kofu400-8510, Japan
| | - Teruhiko Wakayama
- Faculty of Life and Environmental Science, University of Yamanashi, Kofu400-8510, Japan
- Advanced Biotechnology Center, University of Yamanashi, Kofu400-8510, Japan
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH45229, USA
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA95616, USA
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19
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Otsuka K, Sakashita A, Maezawa S, Schultz RM, Namekawa SH. KRAB-zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.24.546405. [PMID: 37720031 PMCID: PMC10503828 DOI: 10.1101/2023.06.24.546405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
As transposable elements (TEs) coevolved with the host genome, the host genome exploited TEs as functional regulatory elements. What remains largely unknown are how the activity of TEs, namely, endogenous retroviruses (ERVs), are regulated and how TEs evolved in the germline. Here we show that KRAB domain-containing zinc-finger proteins (KZFPs), which are highly expressed in mitotically dividing spermatogonia, bind to suppressed ERVs that function following entry into meiosis as active enhancers. These features are observed for independently evolved KZFPs and ERVs in mice and humans, i.e., are evolutionarily conserved in mammals. Further, we show that meiotic sex chromosome inactivation (MSCI) antagonizes the coevolution of KZFPs and ERVs in mammals. Our study uncovers a mechanism by which KZFPs regulate ERVs to sculpt germline transcriptomes. We propose that epigenetic programming in the mammalian germline during the mitosis-to-meiosis transition facilitates coevolution of KZFPs and TEs on autosomes and is antagonized by MSCI.
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Affiliation(s)
- Kai Otsuka
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, 95616, USA
| | - Akihiko Sakashita
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - So Maezawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Richard M. Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California 95616, USA
| | - Satoshi H. Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, 95616, USA
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, 45229, USA
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20
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Lismer A, Kimmins S. Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. Nat Commun 2023; 14:2142. [PMID: 37059740 PMCID: PMC10104880 DOI: 10.1038/s41467-023-37820-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Although more studies are demonstrating that a father's environment can influence child health and disease, the molecular mechanisms underlying non-genetic inheritance remain unclear. It was previously thought that sperm exclusively contributed its genome to the egg. More recently, association studies have shown that various environmental exposures including poor diet, toxicants, and stress, perturbed epigenetic marks in sperm at important reproductive and developmental loci that were associated with offspring phenotypes. The molecular and cellular routes that underlie how epigenetic marks are transmitted at fertilization, to resist epigenetic reprogramming in the embryo, and drive phenotypic changes are only now beginning to be unraveled. Here, we provide an overview of the state of the field of intergenerational paternal epigenetic inheritance in mammals and present new insights into the relationship between embryo development and the three pillars of epigenetic inheritance: chromatin, DNA methylation, and non-coding RNAs. We evaluate compelling evidence of sperm-mediated transmission and retention of paternal epigenetic marks in the embryo. Using landmark examples, we discuss how sperm-inherited regions may escape reprogramming to impact development via mechanisms that implicate transcription factors, chromatin organization, and transposable elements. Finally, we link paternally transmitted epigenetic marks to functional changes in the pre- and post-implantation embryo. Understanding how sperm-inherited epigenetic factors influence embryo development will permit a greater understanding related to the developmental origins of health and disease.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal Hospital Research Centre, Montreal, QC, H2X 0A9, Canada.
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21
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Zhang GW, Wang L, Wu J, Ye Y, Zhao J, Du Y, Tu Y, Luo Z, Fu S, Zuo F. Evaluation of MYBL1 as the master regulator for pachytene spermatocyte genes dysregulated in interspecific hybrid dzo. J Dairy Sci 2023; 106:4366-4379. [PMID: 37059660 DOI: 10.3168/jds.2022-22963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/08/2022] [Indexed: 04/16/2023]
Abstract
Misregulation of spermatogenesis transcription factors (TF) in hybrids can lead to misexpression, which is a mechanism for hybrid male sterility (HMS). We used dzo (male offspring of Bos taurus ♂ × Bos grunniens ♀) in bovines to investigate the relationship of the key TF with HMS via RNA sequencing and assay for transposase-accessible chromatin with high-throughput sequencing analyses. RNA sequencing showed that the widespread misexpression in dzo was associated with spermatogenesis-related genes and somatic or progenitor genes. The transition from leptotene or zygotene spermatocytes to pachytene spermatocytes may be the key stage for meiosis arrest in dzo. The analysis of TF-binding motif enrichment revealed that the male meiosis-specific master TF MYB proto-oncogene like 1 (MYBL1, known as A-MYB) motif was enriched on the promoters of downregulated pachytene spermatocyte genes in dzo. Assay for transposase-accessible chromatin with high-throughput sequencing revealed that TF-binding sites for MYBL1, nuclear transcription factor Y, and regulatory factor X were enriched in the low-chromatin accessibility region of dzo. The target genes of the MYBL1-binding motif were associated with meiosis-specific genes and significantly downregulated in dzo testis. The transcription factor MYBL1 may be the candidate master regulator for pachytene spermatocyte genes dysregulated in interspecific HMS dzo. This study reported that a few upstream TF regulation changes might exert a cascading effect downstream in a regulatory network as a mechanism for HMS.
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Affiliation(s)
- Gong-Wei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China.
| | - Ling Wang
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China
| | - Jingjing Wu
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Yiru Ye
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Jianjun Zhao
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Yanan Du
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Yun Tu
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Zonggang Luo
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Shubing Fu
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China.
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22
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Alexander AK, Rice EJ, Lujic J, Simon LE, Tanis S, Barshad G, Zhu L, Lama J, Cohen PE, Danko CG. A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis. Nat Commun 2023; 14:1753. [PMID: 36990976 PMCID: PMC10060231 DOI: 10.1038/s41467-023-37408-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
During meiotic prophase I, spermatocytes must balance transcriptional activation with homologous recombination and chromosome synapsis, biological processes requiring extensive changes to chromatin state. We explored the interplay between chromatin accessibility and transcription through prophase I of mammalian meiosis by measuring genome-wide patterns of chromatin accessibility, nascent transcription, and processed mRNA. We find that Pol II is loaded on chromatin and maintained in a paused state early during prophase I. In later stages, paused Pol II is released in a coordinated transcriptional burst mediated by the transcription factors A-MYB and BRDT, resulting in ~3-fold increase in transcription. Transcriptional activity is temporally and spatially segregated from key steps of meiotic recombination: double strand breaks show evidence of chromatin accessibility earlier during prophase I and at distinct loci from those undergoing transcriptional activation, despite shared chromatin marks. Our findings reveal mechanisms underlying chromatin specialization in either transcription or recombination in meiotic cells.
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Affiliation(s)
- Adriana K Alexander
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Jelena Lujic
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Leah E Simon
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Stephanie Tanis
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Lina Zhu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Jyoti Lama
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Paula E Cohen
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, 14853, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, 14853, USA.
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23
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Tatara M, Ikeda T, Namekawa SH, Maezawa S. ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis. Methods Mol Biol 2023; 2577:65-81. [PMID: 36173566 DOI: 10.1007/978-1-0716-2724-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Accessible chromatin often represents gene regulatory elements, including promoters and enhancers, essential for gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is one of the most popular techniques to investigate chromatin accessibility across the genome. Here we describe, step by step, a series of optimized experimental methods and bioinformatics pipelines for ATAC-seq analysis. As an example, we present an analysis of murine spermatogenic cells: a method to isolate germ cells, a reaction step using Tn5 transposase to insert sequencing adapters into accessible DNA, a library preparation method for high-throughput sequencing, and bioinformatics analysis of sequencing data. Overall, we introduce a framework of ATAC-seq analysis that can be applied to any cell population to identify cell-type-specific gene regulatory elements and their cis-regulatory networks.
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Affiliation(s)
- Mayu Tatara
- Department of Applied Biological Science, Tokyo University of Science, Chiba, Japan
| | - Taiyo Ikeda
- Department of Applied Biological Science, Tokyo University of Science, Chiba, Japan
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA, USA.
| | - So Maezawa
- Department of Applied Biological Science, Tokyo University of Science, Chiba, Japan.
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24
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Sakashita A, Takeuchi C, Maezawa S, Namekawa SH. Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts. Methods Mol Biol 2023; 2577:123-146. [PMID: 36173570 DOI: 10.1007/978-1-0716-2724-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Precise regulation of gene expression is integral in development. Emerging studies have highlighted that super-enhancers (SEs), which are clusters of multiple enhancers, play critical roles in regulating cell type-specific gene expression via 3D chromatin, thereby defining the cellular identities of given cells. Here we provide optimized bioinformatics pipelines to identify SEs and 3D chromatin contacts. Our pipelines encompass the processing of chromatin immunoprecipitation sequencing (ChIP-seq) data to identify SEs and the processing of genome-wide chromosome conformation capture (Hi-C) data. We can then infer long-range chromatin contacts between SEs and other genomic regions. This integrative computational approach, which can be applied to CUT&RUN and CUT&Tag, alternative technologies to ChIP-seq, allows us to identify genomic locations of SEs and their 3D genome configuration, whereby multiple SEs act in concert. We show an analysis of mouse spermatogenesis as an example of this application.
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Affiliation(s)
- Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.
| | - Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - So Maezawa
- Department of Applied Biological Science, Tokyo University of Science, Chiba, Japan
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA, USA.
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25
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Zhao T, Lu J, Zhang H, Xue M, Pan J, Ma L, Berger F, Jiang D. Histone H3.3 deposition in seed is essential for the post-embryonic developmental competence in Arabidopsis. Nat Commun 2022; 13:7728. [PMID: 36513677 PMCID: PMC9747979 DOI: 10.1038/s41467-022-35509-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in endowing seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5' gene end distribution and facilitates chromatin opening at regulatory regions in seeds. During germination, H3.3 is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3' gene end, correlating with gene body DNA methylation and the restriction of chromatin accessibility and cryptic transcription at this region. Our results suggest a fundamental role of H3.3 in initiating chromatin accessibility at regulatory regions in seed and licensing the embryonic to post-embryonic transition.
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Affiliation(s)
- Ting Zhao
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jingyun Lu
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Huairen Zhang
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Mande Xue
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Jie Pan
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Lijun Ma
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Frédéric Berger
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Danhua Jiang
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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26
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scATAC-Seq reveals heterogeneity associated with spermatogonial differentiation in cultured male germline stem cells. Sci Rep 2022; 12:21482. [PMID: 36509798 PMCID: PMC9744833 DOI: 10.1038/s41598-022-25729-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Spermatogonial stem cells are the most primitive spermatogonia in testis, which can self-renew to maintain the stem cell pool or differentiate to give rise to germ cells including haploid spermatids. All-trans-retinoic acid (RA), a bioactive metabolite of vitamin A, plays a fundamental role in initiating spermatogonial differentiation. In this study, single-cell ATAC-seq (scATAC-seq) was used to obtain genome-wide chromatin maps of cultured germline stem cells (GSCs) that were in control and RA-induced differentiation states. We showed that different subsets of GSCs can be distinguished based on chromatin accessibility of self-renewal and differentiation signature genes. Importantly, both progenitors and a subset of stem cells are able to respond to RA and give rise to differentiating cell subsets with distinct chromatin accessibility profiles. In this study, we identified regulatory regions that undergo chromatin remodeling and are associated with the retinoic signaling pathway. Moreover, we reconstructed the differentiation trajectory and identified novel transcription factor candidates enriched in different spermatogonia subsets. Collectively, our work provides a valuable resource for understanding the heterogeneity associated with differentiation and RA response in GSCs.
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27
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Shi K, Wang B, Dou L, Wang S, Fu X, Yu H. Integrated bioinformatics analysis of the transcription factor-mediated gene regulatory networks in the formation of spermatogonial stem cells. Front Physiol 2022; 13:949486. [PMID: 36569748 PMCID: PMC9773208 DOI: 10.3389/fphys.2022.949486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background: In vitro induction of spermatogonial stem cells (SSCs) from embryonic stem cells (ESCs) provides a promising tool for the treatment of male infertility. A variety of molecules are involved in this complex process, which needs to be further clarified. Undoubtedly, the increased knowledge of SSC formation will be beneficial to facilitate the currently complex induction process. Methods: Based on ATAC-seq, DNase-seq, RNA-seq, and microarray data from GEO datasets, chromatin property data (ATAC-seq, DNase-seq) and gene expression data (RNA-seq, microarray data) were combined to search for SSC-specific transcription factors (TFs) and hub SSC-specific genes by using the WGCNA method. Then, we applied RNA-seq and microarray data screening for key SSC-specific TFs and constructed key SSC-specific TF-mediated gene regulatory networks (GRNs) using ChIP-seq data. Results: First, after analysis of the ATAC-seq and DNase-seq data of mouse ESCs, primordial germ cells (PGCs), and SSCs, 33 SSC-specific TFs and 958 targeting genes were obtained. RNA-seq and WGCNA revealed that the key modules (turquoise and red) were the most significantly related to 958 SSC-specific genes, and a total of 10 hub SSC-specific genes were identified. Next, when compared with the cell-specific TFs in human ESCs, PGCs, and SSCs, we obtained five overlapping SSC-specific TF motifs, including the NF1 family TF motifs (NFIA, NFIB, NFIC, and NFIX), GRE, Fox:Ebox, PGR, and ARE. Among these, Nfib and Nfix exhibited abnormally high expression levels relative to mouse ESCs and PGCs. Moreover, Nfib and Nfix were upregulated in the testis sample with impaired spermatogenesis when compared with the normal group. Finally, the ChIP-seq data results showed that NFIB most likely targeted the hub SSC-specific genes of the turquoise module (Rpl36al, Rps27, Rps21, Nedd8, and Sec61b) and the red module (Vcam1 and Ccl2). Conclusion: Our findings preliminarily revealed cell-specific TFs and cell-specific TF-mediated GRNs in the process of SSC formation. The hub SSC-specific genes and the key SSC-specific TFs were identified and suggested complex network regulation, which may play key roles in optimizing the induction efficiency of the differentiation of ESCs into SSCs in vitro.
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28
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Lehtiniemi T, Bourgery M, Ma L, Ahmedani A, Mäkelä M, Asteljoki J, Olotu O, Laasanen S, Zhang FP, Tan K, Chousal JN, Burow D, Koskinen S, Laiho A, Elo L, Chalmel F, Wilkinson M, Kotaja N. SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis. Nucleic Acids Res 2022; 50:11470-11491. [PMID: 36259644 PMCID: PMC9723633 DOI: 10.1093/nar/gkac900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 12/24/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA turnover pathway that depends on the endonuclease SMG6. Here, we show that SMG6 is essential for male germ cell differentiation in mice. Germ-cell conditional knockout (cKO) of Smg6 induces extensive transcriptome misregulation, including a failure to eliminate meiotically expressed transcripts in early haploid cells, and accumulation of NMD target mRNAs with long 3' untranslated regions (UTRs). Loss of SMG6 in the male germline results in complete arrest of spermatogenesis at the early haploid cell stage. We find that SMG6 is strikingly enriched in the chromatoid body (CB), a specialized cytoplasmic granule in male germ cells also harboring PIWI-interacting RNAs (piRNAs) and the piRNA-binding protein PIWIL1. This raises the possibility that SMG6 and the piRNA pathway function together, which is supported by several findings, including that Piwil1-KO mice phenocopy Smg6-cKO mice and that SMG6 and PIWIL1 co-regulate many genes in round spermatids. Together, our results demonstrate that SMG6 is an essential regulator of the male germline transcriptome, and highlight the CB as a molecular platform coordinating RNA regulatory pathways to control sperm production and fertility.
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Affiliation(s)
- Tiina Lehtiniemi
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Matthieu Bourgery
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Lin Ma
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Ammar Ahmedani
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Margareeta Mäkelä
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Juho Asteljoki
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Opeyemi Olotu
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Samuli Laasanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Fu-Ping Zhang
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Turku Center for Disease Modeling, University of Turku, Turku, Finland
- GM-Unit, Helsinki Institute of Life Science, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Dana Burow
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Satu Koskinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Frédéric Chalmel
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine (IGM), University of California, San Diego, La Jolla, CA 92093, USA
| | - Noora Kotaja
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
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29
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Griffin KN, Walters BW, Li H, Wang H, Biancon G, Tebaldi T, Kaya CB, Kanyo J, Lam TT, Cox AL, Halene S, Chung JJ, Lesch BJ. Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction. Genome Res 2022; 32:gr.276578.122. [PMID: 36109149 PMCID: PMC9528986 DOI: 10.1101/gr.276578.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
Abstract
Argonaute 2 (AGO2) is a ubiquitously expressed protein critical for regulation of mRNA translation and vital to animal development. AGO2 protein is found in both cytoplasmic and nuclear compartments, and although its cytoplasmic role is well studied, the biological relevance of nuclear AGO2 is unclear. Here, we address this problem in vivo using spermatogenic cells as a model. We find that AGO2 transiently binds both chromatin and nucleus-specific mRNA transcripts of hundreds of genes required for sperm production during male meiosis in mice, and that germline conditional knockout (cKO) of Ago2 causes depletion of the encoded proteins. Correspondingly, Ago2 cKO males show abnormal sperm head morphology and reduced sperm count, along with reduced postnatal viability of offspring. Together, our data reveal an unexpected nuclear role for AGO2 in enhancing expression of developmentally important genes during mammalian male reproduction.
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Affiliation(s)
- Kimberly N Griffin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | | | - Haixin Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Huafeng Wang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Carolyn B Kaya
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - TuKiet T Lam
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Andy L Cox
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Pathology, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean-Ju Chung
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Bluma J Lesch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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30
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Sakamoto M, Ito D, Inoue R, Wakayama S, Kikuchi Y, Yang L, Hayashi E, Emura R, Shiura H, Kohda T, Namekawa SH, Ishiuchi T, Wakayama T, Ooga M. Paternally inherited H3K27me3 affects chromatin accessibility in mouse embryos produced by round spermatid injection. Development 2022; 149:276384. [DOI: 10.1242/dev.200696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/14/2022] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Round spermatid injection (ROSI) results in a lower birth rate than intracytoplasmic sperm injection, which has hampered its clinical application. Inefficient development of ROSI embryos has been attributed to epigenetic abnormalities. However, the chromatin-based mechanism that underpins the low birth rate in ROSI remains to be determined. Here, we show that a repressive histone mark, H3K27me3, persists from mouse round spermatids into zygotes in ROSI and that round spermatid-derived H3K27me3 is associated with less accessible chromatin and impaired gene expression in ROSI embryos. These loci are initially marked by H3K27me3 but undergo histone modification remodelling in spermiogenesis, resulting in reduced H3K27me3 in normal spermatozoa. Therefore, the absence of epigenetic remodelling, presumably mediated by histone turnover during spermiogenesis, leads to dysregulation of chromatin accessibility and transcription in ROSI embryos. Thus, our results unveil a molecular logic, in which chromatin states in round spermatids impinge on chromatin accessibility and transcription in ROSI embryos, highlighting the importance of epigenetic remodelling during spermiogenesis in successful reproduction.
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Affiliation(s)
- Mizuki Sakamoto
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Daiyu Ito
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Rei Inoue
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Sayaka Wakayama
- Advanced Biotechnology Center, University of Yamanashi 2 , Yamanashi, 400-8510 , Japan
| | - Yasuyuki Kikuchi
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Li Yang
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Erika Hayashi
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Rina Emura
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Hirosuke Shiura
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Takashi Kohda
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Satoshi H. Namekawa
- University of California Davis 3 Department of Microbiology and Molecular Genetics , , Davis, CA 95616 , USA
| | - Takashi Ishiuchi
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
| | - Teruhiko Wakayama
- Advanced Biotechnology Center, University of Yamanashi 2 , Yamanashi, 400-8510 , Japan
| | - Masatoshi Ooga
- University of Yamanashi 1 Faculty of Life and Environmental Sciences , , Yamanashi, 400-8510 , Japan
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31
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Zhao F, Grimm SA, Jia S, Yao HHC. Contribution of the Wolffian duct mesenchyme to the formation of the female reproductive tract. PNAS NEXUS 2022; 1:pgac182. [PMID: 36204418 PMCID: PMC9523451 DOI: 10.1093/pnasnexus/pgac182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 09/06/2022] [Indexed: 02/05/2023]
Abstract
The female reproductive tract develops from its embryonic precursor, the Müllerian duct. In close proximity to the Müllerian duct lies the precursor for the male reproductive tract, the Wolffian duct, which is eliminated in the female embryo during sexual differentiation. We discovered that a component of the Wolffian duct, its mesenchyme, is not eliminated after sexual differentiation. Instead, the Wolffian duct mesenchyme underwent changes in transcriptome and chromatin accessibility from male tract to female tract identity, and became a unique mesenchymal population in the female reproductive tract with localization and transcriptome distinct from the mesenchyme derived from the Müllerian duct. Partial ablation of the Wolffian duct mesenchyme stunted the growth of the fetal female reproductive tract in ex vivo organ culture. These findings reveal a new fetal origin of mesenchymal tissues for female reproductive tract formation and reshape our understanding of sexual differentiation of reproductive tracts.
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Affiliation(s)
- Fei Zhao
- Reproductive Developmental Biology Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sara A Grimm
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Shua Jia
- Present address: Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Humphrey Hung-Chang Yao
- Reproductive Developmental Biology Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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32
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Ki BS, Shim SH, Park C, Yoo H, La H, Lee OH, Kwon Y, Skalnik DG, Okada Y, Yoon HG, Kim JH, Hong K, Choi Y. Epigenetic regulator Cfp1 safeguards male meiotic progression by regulating meiotic gene expression. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1098-1108. [PMID: 35918532 PMCID: PMC9440128 DOI: 10.1038/s12276-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Meiosis occurs specifically in germ cells to produce sperm and oocytes that are competent for sexual reproduction. Multiple factors are required for successful meiotic entry, progression, and termination. Among them, trimethylation of histone H3 on lysine 4 (H3K4me3), a mark of active transcription, has been implicated in spermatogenesis by forming double-strand breaks (DSBs). However, the role of H3K4me in transcriptional regulation during meiosis remains poorly understood. Here, we reveal that mouse CXXC finger protein 1 (Cfp1), a component of the H3K4 methyltransferase Setd1a/b, is dynamically expressed in differentiating male germ cells and safeguards meiosis by controlling gene expression. Genetic ablation of mouse CFP1 in male germ cells caused complete infertility with failure in prophase I of the 1st meiosis. Mechanistically, CFP1 binds to genes essential for spermatogenesis, and its loss leads to a reduction in H3K4me3 levels and gene expression. Importantly, CFP1 is highly enriched within the promoter/TSS of target genes to elevate H3K4me3 levels and gene expression at the pachytene stage of meiotic prophase I. The most enriched genes were associated with meiosis and homologous recombination during the differentiation of spermatocytes to round spermatids. Therefore, our study establishes a mechanistic link between CFP1-mediated transcriptional control and meiotic progression and might provide an unprecedented genetic basis for understanding human sterility. Details of the role of a protein in the development of sperm cells in mice could lead to new understanding of sterility in men. An international research team led by Youngsok Choi and Kwonho Hong at Konkuk University, Seoul, South Korea, investigated the role of protein Cfp1, which they found to be required for sperm formation in mice. The protein is a component of an enzyme complex that transfers methyl groups (CH3) onto other proteins involved in controlling gene activity. The researchers identified key aspects of the mechanism by which Cfp1 controls the activity of genes essential for sperm formation to proceed normally. Absence of Cfp1 specifically interferes with the process of meiosis, which generates sperm cells containing only one copy of each chromosome instead of the two copies found in other cells.
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Affiliation(s)
- Byeong Seong Ki
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ok-Hee Lee
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - David G Skalnik
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, 113-0032, Japan
| | - Ho-Geun Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea.
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33
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Ma L, Xie D, Luo M, Lin X, Nie H, Chen J, Gao C, Duo S, Han C. Identification and characterization of BEND2 as a key regulator of meiosis during mouse spermatogenesis. SCIENCE ADVANCES 2022; 8:eabn1606. [PMID: 35613276 PMCID: PMC9132480 DOI: 10.1126/sciadv.abn1606] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/08/2022] [Indexed: 05/07/2023]
Abstract
The chromatin state, which undergoes global changes during spermatogenesis, is critical to meiotic initiation and progression. However, the key regulators involved and the underlying molecular mechanisms remain to be uncovered. Here, we report that mouse BEND2 is specifically expressed in spermatogenic cells around meiotic initiation and that it plays an essential role in meiotic progression. Bend2 gene knockout in male mice arrested meiosis at the transition from zygonema to pachynema, disrupted synapsis and DNA double-strand break repair, and induced nonhomologous chromosomal pairing. BEND2 interacted with chromatin-associated proteins that are components of certain transcription-repressor complexes. BEND2-binding sites were identified in diverse chromatin states and enriched in simple sequence repeats. BEND2 inhibited the expression of genes involved in meiotic initiation and regulated chromatin accessibility and the modification of H3K4me3. Therefore, our study identified BEND2 as a previously unknown key regulator of meiosis, gene expression, and chromatin state during mouse spermatogenesis.
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Affiliation(s)
- Longfei Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengcheng Luo
- Department of Tissue and Embryology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei Province, China
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Hengyu Nie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxu Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuguang Duo
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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34
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Wu X, Zhou L, Shi J, Cheng CY, Sun F. Multiomics analysis of male infertility. Biol Reprod 2022; 107:118-134. [PMID: 35639635 DOI: 10.1093/biolre/ioac109] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Infertility affects 8-12% of couples globally, and the male factor is a primary cause in approximately 50% of couples. Male infertility is a multifactorial reproductive disorder, which can be caused by paracrine and autocrine factors, hormones, genes, and epigenetic changes. Recent studies in rodents and most notably in humans using multiomics approach have yielded important insights into understanding the biology of spermatogenesis. Nonetheless, the etiology and pathogenesis of male infertility are still largely unknown. In this review, we summarized and critically evaluated findings based on the use of advanced technologies to compare normal and obstructive azoospermia (OA) versus non-obstructive azoospermia (NOA) men, including whole-genome bisulfite sequencing (WGBS), single cell RNA-seq (scRNA-seq), whole exome sequencing (WES), and ATAC-seq. It is obvious that the multiomics approach is the method of choice for basic research and clinical studies including clinical diagnosis of male infertility.
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Affiliation(s)
- Xiaolong Wu
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - Liwei Zhou
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - Jie Shi
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - C Yan Cheng
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
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35
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Sun S, Jiang Y, Zhang Q, Pan H, Li X, Yang L, Huang M, Wei W, Wang X, Qiu M, Cao L, He H, Yu M, Liu H, Zhao B, Jiang N, Li R, Lin X. Znhit1 controls meiotic initiation in male germ cells by coordinating with Stra8 to activate meiotic gene expression. Dev Cell 2022; 57:901-913.e4. [PMID: 35413238 DOI: 10.1016/j.devcel.2022.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 01/25/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
Abstract
The switch from mitosis to meiosis ensures the successive formation of gametes. However, it remains unclear how meiotic initiation occurs within the context of chromatin. Recent studies have shown that zinc finger HIT-type containing 1 (Znhit1), a subunit of the SRCAP chromatin remodeling complex, plays essential roles in modulating the chromatin structure. Herein, we report that the germline-conditional deletion of Znhit1 in male mice specifically blocks meiotic initiation. We show that Znhit1 is required for meiotic prophase events, including synapsis, DNA double-strand break formation, and meiotic DNA replication. Mechanistically, Znhit1 controls the histone variant H2A.Z deposition, which facilitates the expression of meiotic genes, such as Meiosin, but not the expression of Stra8. Interestingly, Znhit1 deficiency disrupts the transcription bubbles of meiotic genes. Thus, our findings identify the essential role of Znhit1-dependent H2A.Z deposition in allowing activation of meiotic gene expression, thereby controlling the initiation of meiosis.
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Affiliation(s)
- Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yamei Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Qiaoli Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hongjie Pan
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Xinyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Li Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Meina Huang
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Wei Wei
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Xiaoye Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Mengdi Qiu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Lihuan Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hua He
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Miao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hanmin Liu
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China.
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China.
| | - Runsheng Li
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China.
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China.
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36
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Sperm Histone H3 Lysine 4 tri-methylation serves as a metabolic sensor of paternal obesity and is associated with the inheritance of metabolic dysfunction. Mol Metab 2022; 59:101463. [PMID: 35183795 PMCID: PMC8931445 DOI: 10.1016/j.molmet.2022.101463] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
Objective Parental environmental exposures can strongly influence descendant risks for adult disease. How paternal obesity changes the sperm chromatin leading to the acquisition of metabolic disease in offspring remains controversial and ill-defined. The objective of this study was to assess (1) whether obesity induced by a high-fat diet alters sperm histone methylation; (2) whether paternal obesity can induce metabolic disturbances across generations; (3) whether there could be cumulative damage to the sperm epigenome leading to enhanced metabolic dysfunction in descendants; and (4) whether obesity-sensitive regions associate with embryonic epigenetic and transcriptomic profiles. Using a genetic mouse model of epigenetic inheritance, we investigated the role of histone H3 lysine 4 methylation (H3K4me3) in the paternal transmission of metabolic dysfunction. This transgenic mouse overexpresses the histone demethylase enzyme KDM1A in the developing germline and has an altered sperm epigenome at the level of histone H3K4 methylation. We hypothesized that challenging transgenic sires with a high-fat diet would further erode the sperm epigenome and lead to enhanced metabolic disturbances in the next generations. Methods To assess whether paternal obesity can have inter- or transgenerational impacts, and if so to identify potential mechanisms of this non-genetic inheritance, we used wild-type C57BL/6NCrl and transgenic males with a pre-existing altered sperm epigenome. To induce obesity, sires were fed either a control or high-fat diet (10% or 60% kcal fat, respectively) for 10–12 weeks, then bred to wild-type C57BL/6NCrl females fed a regular diet. F1 and F2 descendants were characterized for metabolic phenotypes by examining the effects of paternal obesity by sex, on body weight, fat mass distribution, the liver transcriptome, intraperitoneal glucose, and insulin tolerance tests. To determine whether obesity altered the F0 sperm chromatin, native chromatin immunoprecipitation-sequencing targeting H3K4me3 was performed. To gain insight into mechanisms of paternal transmission, we compared our sperm H3K4me3 profiles with embryonic and placental chromatin states, histone modification, and gene expression profiles. Results Obesity-induced alterations in H3K4me3 occurred in genes implicated in metabolic, inflammatory, and developmental processes. These processes were associated with offspring metabolic dysfunction and corresponded to genes enriched for H3K4me3 in embryos and overlapped embryonic and placenta gene expression profiles. Transgenerational susceptibility to metabolic disease was only observed when obese F0 had a pre-existing modified sperm epigenome. This coincided with increased H3K4me3 alterations in sperm and more severe phenotypes affecting their offspring. Conclusions Our data suggest sperm H3K4me3 might serve as a metabolic sensor that connects paternal diet with offspring phenotypes via the placenta. This non-DNA-based knowledge of inheritance has the potential to improve our understanding of how environment shapes heritability and may lead to novel routes for the prevention of disease. This study highlights the need to further study the connection between the sperm epigenome, placental development, and children's health. Summary sentence Paternal obesity impacts sperm H3K4me3 and is associated with placenta, embryonic and metabolic outcomes in descendants. Sperm H3K4me3 serves as a metabolic sensor of HFD-induced obesity. Obesity-altered sperm H3K4me3 corresponds to embryonic transcription and chromatin profiles. HFD- and KDM1A-induced cumulative sperm epimutations enhanced F1 metabolic dysfunction. Sperm epimutations may influence placenta function inducing F1 metabolic phenotypes.
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Liu R, Liu Z, Guo M, Zeng W, Zheng Y. SETDB1 Regulates Porcine Spermatogonial Adhesion and Proliferation through Modulating MMP3/10 Transcription. Cells 2022; 11:cells11030370. [PMID: 35159180 PMCID: PMC8834347 DOI: 10.3390/cells11030370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/30/2021] [Accepted: 01/20/2022] [Indexed: 12/16/2022] Open
Abstract
The transition from gonocytes into spermatogonia takes place during the homing process. A subpopulation of undifferentiated spermatogonia in niche then shifts to spermatogonial stem cells (SSCs), accompanied by the self-renewal ability to maintain life-long fertility in males. Enormous changes in cell morphology, gene expression, and epigenetic features have been reported during spermatogenesis. However, little is known about the difference of these features in SSCs during aging. Here, we examined the dynamics of SET domain bifurcated 1 (SETDB1) expression in porcine testes. SETDB1 was expressed in postnatal undifferentiated spermatogonia, while gradually disappeared after being packed within the basal compartment of seminiferous tubules. In addition, the cell-adhesion ability, proliferative activity, and trimethylation of the histone H3 lysine 9 (H3K9me3) level were significantly altered in SETDB1-deficient porcine SSCs. Moreover, the matrix metalloproteinases 3/10 (MMP3/10) was upregulated at both mRNA and protein levels. These results illustrate the significance of SETDB1 in modulating early male germ cell development.
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Alavattam KG, Maezawa S, Andreassen PR, Namekawa SH. Meiotic sex chromosome inactivation and the XY body: a phase separation hypothesis. Cell Mol Life Sci 2021; 79:18. [PMID: 34971404 DOI: 10.1007/s00018-021-04075-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 10/19/2022]
Abstract
In mammalian male meiosis, the heterologous X and Y chromosomes remain unsynapsed and, as a result, are subject to meiotic sex chromosome inactivation (MSCI). MSCI is required for the successful completion of spermatogenesis. Following the initiation of MSCI, the X and Y chromosomes undergo various epigenetic modifications and are transformed into a nuclear body termed the XY body. Here, we review the mechanisms underlying the initiation of two essential, sequential processes in meiotic prophase I: MSCI and XY-body formation. The initiation of MSCI is directed by the action of DNA damage response (DDR) pathways; downstream of the DDR, unique epigenetic states are established, leading to the formation of the XY body. Accumulating evidence suggests that MSCI and subsequent XY-body formation may be driven by phase separation, a physical process that governs the formation of membraneless organelles and other biomolecular condensates. Thus, here we gather literature-based evidence to explore a phase separation hypothesis for the initiation of MSCI and the formation of the XY body.
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Affiliation(s)
- Kris G Alavattam
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.,Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - So Maezawa
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA.
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Zheng Y, Zhang L, Jin L, Zhang P, Li F, Guo M, Gao Q, Zeng Y, Li M, Zeng W. Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation. J Biol Chem 2021; 298:101559. [PMID: 34979097 PMCID: PMC8814405 DOI: 10.1016/j.jbc.2021.101559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/13/2022] Open
Abstract
Spermatogonial stem cells (SSCs) are able to undergo both self-renewal and differentiation. Unlike self-renewal, which replenishes the SSC and progenitor pool, differentiation is an irreversible process committing cells to meiosis. Although the preparations for meiotic events in differentiating spermatogonia (Di-SG) are likely to be accompanied by alterations in chromatin structure, the three-dimensional chromatin architectural differences between SSCs and Di-SG, and the higher-order chromatin dynamics during spermatogonial differentiation, have not been systematically investigated. Here, we performed in situ high-throughput chromosome conformation capture, RNA-seq, and chromatin immunoprecipitation-sequencing analyses on porcine undifferentiated spermatogonia (which consist of SSCs and progenitors) and Di-SG. We identified that Di-SG exhibited less compact chromatin structural organization, weakened compartmentalization, and diminished topologically associating domains in comparison with undifferentiated spermatogonia, suggesting that diminished higher-order chromatin architecture in meiotic cells, as shown by recent reports, might be preprogrammed in Di-SG. Our data also revealed that A/B compartments, representing open or closed chromatin regions respectively, and topologically associating domains were related to dynamic gene expression during spermatogonial differentiation. Furthermore, we unraveled the contribution of promoter-enhancer interactions to premeiotic transcriptional regulation, which has not been accomplished in previous studies due to limited cell input and resolution. Together, our study uncovered the three-dimensional chromatin structure of SSCs/progenitors and Di-SG, as well as the interplay between higher-order chromatin architecture and dynamic gene expression during spermatogonial differentiation. These findings provide novel insights into the mechanisms for SSC self-renewal and differentiation and have implications for diagnosis and treatment of male sub-/infertility.
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Affiliation(s)
- Yi Zheng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingkai Zhang
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Pengfei Zhang
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuyuan Li
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ming Guo
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiang Gao
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Zeng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Wenxian Zeng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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PRDM9-directed recombination hotspots depleted near meiotically transcribed genes. Gene 2021; 813:146123. [PMID: 34952174 DOI: 10.1016/j.gene.2021.146123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/22/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022]
Abstract
PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.
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Aldalaqan S, Dalgliesh C, Luzzi S, Siachisumo C, Reynard LN, Ehrmann I, Elliott DJ. Cryptic splicing: common pathological mechanisms involved in male infertility and neuronal diseases. Cell Cycle 2021; 21:219-227. [PMID: 34927545 PMCID: PMC8855859 DOI: 10.1080/15384101.2021.2015672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
High levels of transcription and alternative splicing are recognized hallmarks of gene expression in the testis and largely driven by cells in meiosis. Because of this, the male meiosis stage of the cell cycle is often viewed as having a relatively permissive environment for gene expression. In this review, we highlight recent findings that identify the RNA binding protein RBMXL2 as essential for male meiosis. RBMXL2 functions as a “guardian of the transcriptome” that protects against the use of aberrant (or “cryptic”) splice sites that would disrupt gene expression. This newly discovered protective role during meiosis links with a wider field investigating mechanisms of cryptic splicing control that protect neurons from amyotrophic lateral sclerosis and Alzheimer’s disease. We discuss how the mechanism repressing cryptic splicing patterns during meiosis evolved, and why it may be essential for sperm production and male fertility.
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Affiliation(s)
- Saad Aldalaqan
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
| | - Caroline Dalgliesh
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
| | - Sara Luzzi
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
| | - Chileleko Siachisumo
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
| | - Louise N Reynard
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
| | - Ingrid Ehrmann
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
| | - David J Elliott
- Newcastle University Bioscience Institute, Newcastle University, Central Parkway Newcastle, UK
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Cheuquemán C, Maldonado R. Non-coding RNAs and chromatin: key epigenetic factors from spermatogenesis to transgenerational inheritance. Biol Res 2021; 54:41. [PMID: 34930477 PMCID: PMC8686607 DOI: 10.1186/s40659-021-00364-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/07/2021] [Indexed: 02/07/2023] Open
Abstract
Cellular fate and gene expression patterns are modulated by different epigenetic factors including non-coding RNAs (ncRNAs) and chromatin organization. Both factors are dynamic throughout male germ cell differentiation on the seminiferous tubule, despite the transcriptional inactivation in the last stages of spermatogenesis. Sperm maturation during the caput-to-cauda transit on the epididymis involves changes in chromatin organization and the soma-to-germ line transference of ncRNAs that are essential to obtain a functional sperm for fertilization and embryo development. Here, the male environment (diseases, drugs, mental stress) is crucial to modulate these epigenetic factors throughout sperm maturation, affecting the corresponding offspring. Paternal transgenerational inheritance has been directly related to sperm epigenetic changes, most of them associated with variations in the ncRNA content and chromatin marks. Our aim is to give an overview about how epigenetics, focused on ncRNAs and chromatin, is pivotal to understand spermatogenesis and sperm maturation, and how the male environment impacts the sperm epigenome modulating the offspring gene expression pattern.
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Affiliation(s)
- Carolina Cheuquemán
- Núcleo de Ciencias Biológicas, Dirección de Núcleos Transversales, Facultad de estudios Interdisciplinarios, Universidad Mayor, Temuco, Chile
| | - Rodrigo Maldonado
- Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.
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Nair VD, Vasoya M, Nair V, Smith GR, Pincas H, Ge Y, Douglas CM, Esser KA, Sealfon SC. Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle. Genomics 2021; 113:3827-3841. [PMID: 34547403 DOI: 10.1016/j.ygeno.2021.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs were mapped to differentially expressed (DE) genes enriched in distinct biological processes in each tissue. Randomly selected DE genes were validated by qPCR. Top enriched motifs in DARs predicted binding sites for transcription factors (TFs) showing tissue-specific up-regulation. The correlation between differential chromatin accessibility at a given TF binding motif and differential expression of target genes further supported the functional relevance of that motif. Our study identified cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.
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Affiliation(s)
- Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vishnu Nair
- Department of Computer Sciences, Columbia University, New York, NY 10027, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Collin M Douglas
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021; 184:4251-4267.e20. [PMID: 34260899 DOI: 10.1016/j.cell.2021.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
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Yin H, Kang Z, Zhang Y, Gong Y, Liu M, Xue Y, He W, Wang Y, Zhang S, Xu Q, Fu K, Zheng B, Xie J, Zhang J, Wang Y, Lin M, Zhang Y, Feng H, Xin C, Guan Y, Huang C, Guo X, Wang P, Baur JA, Zheng K, Sun Z, Ye L. HDAC3 controls male fertility through enzyme-independent transcriptional regulation at the meiotic exit of spermatogenesis. Nucleic Acids Res 2021; 49:5106-5123. [PMID: 33939832 PMCID: PMC8136829 DOI: 10.1093/nar/gkab313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The transition from meiotic spermatocytes to postmeiotic haploid germ cells constitutes an essential step in spermatogenesis. The epigenomic regulatory mechanisms underlying this transition remain unclear. Here, we find a prominent transcriptomic switch from the late spermatocytes to the early round spermatids during the meiotic-to-postmeiotic transition, which is associated with robust histone acetylation changes across the genome. Among histone deacetylases (HDACs) and acetyltransferases, we find that HDAC3 is selectively expressed in the late meiotic and early haploid stages. Three independent mouse lines with the testis-specific knockout of HDAC3 show infertility and defects in meiotic exit with an arrest at the late stage of meiosis or early stage of round spermatids. Stage-specific RNA-seq and histone acetylation ChIP-seq analyses reveal that HDAC3 represses meiotic/spermatogonial genes and activates postmeiotic haploid gene programs during meiotic exit, with associated histone acetylation alterations. Unexpectedly, abolishing HDAC3 catalytic activity by missense mutations in the nuclear receptor corepressor (NCOR or SMRT) does not cause infertility, despite causing histone hyperacetylation as HDAC3 knockout, demonstrating that HDAC3 enzyme activity is not required for spermatogenesis. Motif analysis of the HDAC3 cistrome in the testes identified SOX30, which has a similar spatiotemporal expression pattern as HDAC3 during spermatogenesis. Depletion of SOX30 in the testes abolishes the genomic recruitment of the HDAC3 to the binding sites. Collectively, these results establish the SOX30/HDAC3 signaling as a key regulator of the transcriptional program in a deacetylase-independent manner during the meiotic-to-postmeiotic transition in spermatogenesis.
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Affiliation(s)
- Huiqi Yin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Zhenlong Kang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yingwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yingyun Gong
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Mengrou Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yanfeng Xue
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wenxiu He
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Shuya Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Qiushi Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Kaiqiang Fu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Bangjin Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Jie Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yuanyuan Wang
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Mingyan Lin
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yihan Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences
| | - Hua Feng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences
| | - Changpeng Xin
- Center for Reproductive Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Peoples' Republic of China
| | - Yichun Guan
- Center for Reproductive Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Peoples' Republic of China
| | - Chaoyang Huang
- Department of Cardiology, the First Affiliated Hospital, Zhejiang University School of Medicine, People's Republic of China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joseph A Baur
- Institute for Diabetes, Obesity, and Metabolism and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Zheng Sun
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
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Geisinger A, Rodríguez-Casuriaga R, Benavente R. Transcriptomics of Meiosis in the Male Mouse. Front Cell Dev Biol 2021; 9:626020. [PMID: 33748111 PMCID: PMC7973102 DOI: 10.3389/fcell.2021.626020] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular studies of meiosis in mammals have been long relegated due to some intrinsic obstacles, namely the impossibility to reproduce the process in vitro, and the difficulty to obtain highly pure isolated cells of the different meiotic stages. In the recent years, some technical advances, from the improvement of flow cytometry sorting protocols to single-cell RNAseq, are enabling to profile the transcriptome and its fluctuations along the meiotic process. In this mini-review we will outline the diverse methodological approaches that have been employed, and some of the main findings that have started to arise from these studies. As for practical reasons most studies have been carried out in males, and mostly using mouse as a model, our focus will be on murine male meiosis, although also including specific comments about humans. Particularly, we will center on the controversy about gene expression during early meiotic prophase; the widespread existing gap between transcription and translation in meiotic cells; the expression patterns and potential roles of meiotic long non-coding RNAs; and the visualization of meiotic sex chromosome inactivation from the RNAseq perspective.
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Affiliation(s)
- Adriana Geisinger
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay.,Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
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Lismer A, Dumeaux V, Lafleur C, Lambrot R, Brind'Amour J, Lorincz MC, Kimmins S. Histone H3 lysine 4 trimethylation in sperm is transmitted to the embryo and associated with diet-induced phenotypes in the offspring. Dev Cell 2021; 56:671-686.e6. [PMID: 33596408 DOI: 10.1016/j.devcel.2021.01.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/01/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
A father's lifestyle impacts offspring health; yet, the underlying molecular mechanisms remain elusive. We hypothesized that a diet that changes methyl donor availability will alter the sperm and embryo epigenomes to impact embryonic gene expression and development. Here, we demonstrate that a folate-deficient (FD) diet alters histone H3 lysine 4 trimethylation (H3K4me3) in sperm at developmental genes and putative enhancers. A subset of H3K4me3 alterations in sperm are retained in the pre-implantation embryo and associated with deregulated embryonic gene expression. Using a genetic mouse model in which sires have pre-existing altered H3K4me2/3 in sperm, we show that a FD diet exacerbates alterations in sperm H3K4me3 and embryonic gene expression, leading to an increase in developmental defect severity. These findings imply that paternal H3K4me3 is transmitted to the embryo and influences gene expression and development. It further suggests that epigenetic errors can accumulate in sperm to worsen offspring developmental outcomes.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Vanessa Dumeaux
- PERFORM Center, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Romain Lambrot
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Julie Brind'Amour
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada.
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48
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Rodríguez-Casuriaga R, Geisinger A. Contributions of Flow Cytometry to the Molecular Study of Spermatogenesis in Mammals. Int J Mol Sci 2021; 22:1151. [PMID: 33503798 PMCID: PMC7865295 DOI: 10.3390/ijms22031151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 12/18/2022] Open
Abstract
Mammalian testes are very heterogeneous organs, with a high number of different cell types. Testicular heterogeneity, together with the lack of reliable in vitro culture systems of spermatogenic cells, have been an obstacle for the characterization of the molecular bases of the unique events that take place along the different spermatogenic stages. In this context, flow cytometry has become an invaluable tool for the analysis of testicular heterogeneity, and for the purification of stage-specific spermatogenic cell populations, both for basic research and for clinical applications. In this review, we highlight the importance of flow cytometry for the advances on the knowledge of the molecular groundwork of spermatogenesis in mammals. Moreover, we provide examples of different approaches to the study of spermatogenesis that have benefited from flow cytometry, including the characterization of mutant phenotypes, transcriptomics, epigenetic and genome-wide chromatin studies, and the attempts to establish cell culture systems for research and/or clinical aims such as infertility treatment.
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Affiliation(s)
- Rosana Rodríguez-Casuriaga
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11600 Montevideo, Uruguay
| | - Adriana Geisinger
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11600 Montevideo, Uruguay
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), 11400 Montevideo, Uruguay
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Yeh YH, Hu M, Nakagawa T, Sakashita A, Yoshida S, Maezawa S, Namekawa SH. Isolation of Murine Spermatogenic Cells using a Violet-Excited Cell-Permeable DNA Binding Dye. J Vis Exp 2021:10.3791/61666. [PMID: 33522502 PMCID: PMC8260464 DOI: 10.3791/61666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Isolation of meiotic spermatocytes is essential to investigate molecular mechanisms underlying meiosis and spermatogenesis. Although there are established cell isolation protocols using Hoechst 33342 staining in combination with fluorescence-activated cell sorting, it requires cell sorters equipped with an ultraviolet laser. Here we describe a cell isolation protocol using the DyeCycle Violet (DCV) stain, a low cytotoxicity DNA binding dye structurally similar to Hoechst 33342. DCV can be excited by both ultraviolet and violet lasers, which improves the flexibility of equipment choice, including a cell sorter not equipped with an ultraviolet laser. Using this protocol, one can isolate three live-cell subpopulations in meiotic prophase I, including leptotene/zygotene, pachytene, and diplotene spermatocytes, as well as post-meiotic round spermatids. We also describe a protocol to prepare single-cell suspension from mouse testes. Overall, the procedure requires a short time to complete (4-5 hours depending on the number of needed cells), which facilitates many downstream applications.
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Affiliation(s)
- Yu-Han Yeh
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine
| | - Mengwen Hu
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine
| | - Toshinori Nakagawa
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institutes of Natural Sciences; Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (Sokendai)
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine
| | - Shosei Yoshida
- Division of Germ Cell Biology, National Institute for Basic Biology, National Institutes of Natural Sciences; Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (Sokendai)
| | - So Maezawa
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University; Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine;
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Wu X, Lu M, Yun D, Gao S, Chen S, Hu L, Wu Y, Wang X, Duan E, Cheng CY, Sun F. Single cell ATAC-Seq reveals cell type-specific transcriptional regulation and unique chromatin accessibility in human spermatogenesis. Hum Mol Genet 2021; 31:321-333. [PMID: 33438010 DOI: 10.1093/hmg/ddab006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/25/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
During human spermatogenesis, germ cells undergo dynamic changes in chromatin organization/re-packaging and in transcriptomes. In order to better understand the underlying mechanism(s), scATAC-Seq of 5376 testicular cells from 3 normal men were performed. Data were analyzed in parallel with the scRNA-Seq data of human testicular cells. Ten germ cell types associated with spermatogenesis and 6 testicular somatic cell types were identified, along with 142 024 peaks located in promoter, genebody and CpG Island. We had examined chromatin accessibility of all chromosomes, with chromosomes 19 and 17 emerged as the leading chromosomes that displayed high chromatin accessibility. In accessible chromatin regions, transcription factor (TF)-binding sites were identified and specific motifs with high frequencies at different spermatogenesis stages were detected, including CTCF, BORIS, NFY, DMRT6, EN1, ISL1 and GLI3. Two most notable observations were noted. First, TLE3 was specifically expressed in differentiating spermatogonia. Second, PFN4 was found to be involved in actin cytoskeletal organization during meiosis. More important, unique regions upstream of PFN4 and TLE3 were shown to display high accessibility, illustrating their significance in supporting human spermatogenesis.
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Affiliation(s)
- Xiaolong Wu
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Mujun Lu
- International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory for Reproductive Medicine, School of Medicine, Shanghai Jiaotong University, Shanghai 200030, China
| | - Damin Yun
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Sheng Gao
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Shitao Chen
- Department of Urology and Andrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Longfei Hu
- Singleron Biotechnologies Ltd., 211 Pubin Road, Nanjing, Jiangsu, China
| | - Yunhao Wu
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Xiaorong Wang
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - C Yan Cheng
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, 1230 York Ave, New York, NY 10065
| | - Fei Sun
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
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