1
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Wang Y, Tsukioka D, Oda S, Suzuki MG, Suzuki Y, Mitani H, Aoki F. Involvement of H2A variants in DNA damage response of zygotes. Cell Death Discov 2024; 10:231. [PMID: 38744857 PMCID: PMC11094039 DOI: 10.1038/s41420-024-01999-0] [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: 02/15/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Phosphorylated H2AX, known as γH2AX, forms in response to genotoxic insults in somatic cells. Despite the high abundance of H2AX in zygotes, the level of irradiation-induced γH2AX is low at this stage. Another H2A variant, TH2A, is present at a high level in zygotes and can also be phosphorylated at its carboxyl end. We constructed H2AX- or TH2A-deleted mice using CRISPR Cas9 and investigated the role of these H2A variants in the DNA damage response (DDR) of zygotes exposed to γ-ray irradiation at the G2 phase. Our results showed that compared to irradiated wild-type zygotes, irradiation significantly reduced the developmental rates to the blastocyst stage in H2AX-deleted zygotes but not in TH2A-deleted ones. Furthermore, live cell imaging revealed that the G2 checkpoint was activated in H2AX-deleted zygotes, but the duration of arrest was significantly shorter than in wild-type and TH2A-deleted zygotes. The number of micronuclei was significantly higher in H2AX-deleted embryos after the first cleavage, possibly due to the shortened cell cycle arrest of damaged embryos and, consequently, the insufficient time for DNA repair. Notably, FRAP analysis suggested the involvement of H2AX in chromatin relaxation. Moreover, phosphorylated CHK2 foci were found in irradiated wild-type zygotes but not in H2AX-deleted ones, suggesting a critical role of these foci in maintaining cell cycle arrest for DNA repair. In conclusion, H2AX, but not TH2A, is involved in the DDR of zygotes, likely by creating a relaxed chromatin structure with enhanced accessibility for DNA repair proteins and by facilitating the formation of pCHK2 foci to prevent premature cleavage.
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Affiliation(s)
- Yuan Wang
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
| | - Dai Tsukioka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Shoji Oda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Fugaku Aoki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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2
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Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [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: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
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Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
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3
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Hao H, Ren C, Lian Y, Zhao M, Bo T, Xu J, Wang W. Independent and Complementary Functions of Caf1b and Hir1 for Chromatin Assembly in Tetrahymena thermophila. Cells 2023; 12:2828. [PMID: 38132148 PMCID: PMC10741905 DOI: 10.3390/cells12242828] [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: 11/17/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Histones and DNA associate to form the nucleosomes of eukaryotic chromatin. Chromatin assembly factor 1 (CAF-1) complex and histone regulatory protein A (HIRA) complex mediate replication-couple (RC) and replication-independent (RI) nucleosome assembly, respectively. CHAF1B and HIRA share a similar domain but play different roles in nucleosome assembly by binding to the different interactors. At present, there is limited understanding for the similarities and differences in their respective functions. Tetrahymena thermophila contains transcriptionally active polyploid macronuclei (MAC) and transcriptionally silent diploid micronuclei (MIC). Here, the distribution patterns of Caf1b and Hir1 exhibited both similarities and distinctions. Both proteins localized to the MAC and MIC during growth, and to the MIC during conjugation. However, Hir1 exhibited additional signaling on parental MAC and new MAC during sexual reproduction and displayed a punctate signal on developing anlagen. Caf1b and Hir1 only co-localized in the MIC with Pcna1 during conjugation. Knockdown of CAF1B impeded cellular growth and arrested sexual reproductive development. Loss of HIR1 led to MIC chromosome defects and aborted sexual development. Co-interference of CAF1B and HIR1 led to a more severe phenotype. Moreover, CAF1B knockdown led to the up-regulation of HIR1 expression, while knockdown of HIR1 also led to an increase in CAF1B expression. Furthermore, Caf1b and Hir1 interacted with different interactors. These results showed that CAF-1 and Hir1 have independent and complementary functions for chromatin assembly in T. thermophila.
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Affiliation(s)
- Huijuan Hao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Chenhui Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Yinjie Lian
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Min Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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4
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Karam G, Molaro A. Casting histone variants during mammalian reproduction. Chromosoma 2023:10.1007/s00412-023-00803-9. [PMID: 37347315 PMCID: PMC10356639 DOI: 10.1007/s00412-023-00803-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
During mammalian reproduction, germ cell chromatin packaging is key to prepare parental genomes for fertilization and to initiate embryonic development. While chromatin modifications such as DNA methylation and histone post-translational modifications are well known to carry regulatory information, histone variants have received less attention in this context. Histone variants alter the stability, structure and function of nucleosomes and, as such, contribute to chromatin organization in germ cells. Here, we review histone variants expression dynamics during the production of male and female germ cells, and what is currently known about their parent-of-origin effects during reproduction. Finally, we discuss the apparent conundrum behind these important functions and their recent evolutionary diversification.
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Affiliation(s)
- Germaine Karam
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Antoine Molaro
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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5
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Zhu J, Chen K, Sun YH, Ye W, Liu J, Zhang D, Su N, Wu L, Kou X, Zhao Y, Wang H, Gao S, Kang L. LSM1-mediated Major Satellite RNA decay is required for nonequilibrium histone H3.3 incorporation into parental pronuclei. Nat Commun 2023; 14:957. [PMID: 36810573 PMCID: PMC9944933 DOI: 10.1038/s41467-023-36584-z] [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: 11/05/2021] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Epigenetic reprogramming of the parental genome is essential for zygotic genome activation and subsequent embryo development in mammals. Asymmetric incorporation of histone H3 variants into the parental genome has been observed previously, but the underlying mechanism remains elusive. In this study, we discover that RNA-binding protein LSM1-mediated major satellite RNA decay plays a central role in the preferential incorporation of histone variant H3.3 into the male pronucleus. Knockdown of Lsm1 disrupts nonequilibrium pronucleus histone incorporation and asymmetric H3K9me3 modification. Subsequently, we find that LSM1 mainly targets major satellite repeat RNA (MajSat RNA) for decay and that accumulated MajSat RNA in Lsm1-depleted oocytes leads to abnormal incorporation of H3.1 into the male pronucleus. Knockdown of MajSat RNA reverses the anomalous histone incorporation and modifications in Lsm1-knockdown zygotes. Our study therefore reveals that accurate histone variant incorporation and incidental modifications in parental pronuclei are specified by LSM1-dependent pericentromeric RNA decay.
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Affiliation(s)
- Jiang Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Kang Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu H Sun
- Departments of Biology, University of Rochester, 14642, Rochester, NY, USA
| | - Wen Ye
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Juntao Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Dandan Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Nan Su
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Li Wu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China. .,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Lan Kang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
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6
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Vetrivel S, Truong DJJ, Wurst W, Graw J, Giesert F. Identification of ocular regulatory functions of core histone variant H3.2. Exp Eye Res 2023; 226:109346. [PMID: 36529279 DOI: 10.1016/j.exer.2022.109346] [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: 06/23/2022] [Revised: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The posttranscriptional modifications (PTM) of the Histone H3 family play an important role in ocular system differentiation. However, there has been no study on the nature of specific Histone H3 subtype carrying these modifications. Fortuitously, we had previously identified a dominant small-eye mutant Aey69 mouse with a mutation in the H3.2 encoding Hist2h3c1 gene (Vetrivel et al., 2019). In continuation, in the present study, the role of Histone H3.2 with relation to the microphtalmic Aey69 has been elaborated. Foremost, a transgenic mouse line expressing the fusion protein H3.2-GFP was generated using Crispr/Cas9. The approach was intended to confer a unique tag to the Hist2h3c1 gene which is similar in sequence and encoded protein structure to other histones. The GFP tag was then used for ChIP Seq analysis of the genes regulated by H3.2. The approach revealed ocular specific H3.2 targets including Ephrin family genes. Altered enrichment of H3.2 was found in the mutant Aey69 mouse, specifically around the ligand Efna5 and the receptor Ephb2. The effect of this altered enrichment on Ephrin signaling was further analysed by QPCR and immunohistochemistry. This study identifies Hist2h3c1 encoded H3.2 as an important epigenetic player in ocular development. By binding to specific regions of ocular developmental factors Histone H3.2 facilitates the function of these genes for successful early ocular development.
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Affiliation(s)
- Sharmilee Vetrivel
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany.
| | - Dong-Jiunn Jeffery Truong
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Jochen Graw
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany.
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7
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Parental competition for the regulators of chromatin dynamics in mouse zygotes. Commun Biol 2022; 5:699. [PMID: 35835981 PMCID: PMC9283401 DOI: 10.1038/s42003-022-03623-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
The underlying mechanism for parental asymmetric chromatin dynamics is still unclear. To reveal this, we investigate chromatin dynamics in parthenogenetic, androgenic, and several types of male germ cells-fertilized zygotes. Here we illustrate that parental conflicting role mediates the regulation of chromatin dynamics. Sperm reduces chromatin dynamics in both parental pronuclei (PNs). During spermiogenesis, male germ cells acquire this reducing ability and its resistance. On the other hand, oocytes can increase chromatin dynamics. Notably, the oocytes-derived chromatin dynamics enhancing ability is dominant for the sperm-derived opposing one. This maternal enhancing ability is competed between parental pronuclei. Delayed fertilization timing is critical for this competition and compromises parental asymmetric chromatin dynamics and zygotic transcription. Together, parental competition for the maternal factor enhancing chromatin dynamics is a determinant to establish parental asymmetry, and paternal repressive effects have supporting roles to enhance asymmetry.
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8
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Dynamic mRNA degradome analyses indicate a role of histone H3K4 trimethylation in association with meiosis-coupled mRNA decay in oocyte aging. Nat Commun 2022; 13:3191. [PMID: 35680896 PMCID: PMC9184541 DOI: 10.1038/s41467-022-30928-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 05/20/2022] [Indexed: 11/08/2022] Open
Abstract
A decrease in oocyte developmental potential is a major obstacle for successful pregnancy in women of advanced age. However, the age-related epigenetic modifications associated with dynamic transcriptome changes, particularly meiotic maturation-coupled mRNA clearance, have not been adequately characterized in human oocytes. This study demonstrates a decreased storage of transcripts encoding key factors regulating the maternal mRNA degradome in fully grown oocytes of women of advanced age. A similar defect in meiotic maturation-triggered mRNA clearance is also detected in aged mouse oocytes. Mechanistically, the epigenetic and cytoplasmic aspects of oocyte maturation are synchronized in both the normal development and aging processes. The level of histone H3K4 trimethylation (H3K4me3) is high in fully grown mouse and human oocytes derived from young females but decreased during aging due to the decreased expression of epigenetic factors responsible for H3K4me3 accumulation. Oocyte-specific knockout of the gene encoding CxxC-finger protein 1 (CXXC1), a DNA-binding subunit of SETD1 methyltransferase, causes ooplasm changes associated with accelerated aging and impaired maternal mRNA translation and degradation. These results suggest that a network of CXXC1-maintained H3K4me3, in association with mRNA decay competence, sets a timer for oocyte deterioration and plays a role in oocyte aging in both mouse and human oocytes.
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9
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Rong Y, Zhu YZ, Yu JL, Wu YW, Ji SY, Zhou Y, Jiang Y, Jin J, Fan HY, Shen L, Sha QQ. USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation. Nucleic Acids Res 2022; 50:5599-5616. [PMID: 35640597 PMCID: PMC9178006 DOI: 10.1093/nar/gkac468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 12/12/2022] Open
Abstract
Maternal-to-zygotic transition (MZT) is the first and key step in the control of animal development and intimately related to changes in chromatin structure and histone modifications. H2AK119ub1, an important epigenetic modification in regulating chromatin configuration and function, is primarily catalyzed by PRC1 and contributes to resistance to transcriptional reprogramming in mouse embryos. In this study, the genome-wide dynamic distribution of H2AK119ub1 during MZT in mice was investigated using chromosome immunoprecipitation and sequencing. The results indicated that H2AK119ub1 accumulated in fully grown oocytes and was enriched at the TSSs of maternal genes, but was promptly declined after meiotic resumption at genome-wide including the TSSs of early zygotic genes, by a previously unidentified mechanism. Genetic evidences indicated that ubiquitin-specific peptidase 16 (USP16) is the major deubiquitinase for H2AK119ub1 in mouse oocytes. Conditional knockout of Usp16 in oocytes did not impair their survival, growth, or meiotic maturation. However, oocytes lacking USP16 have defects when undergoing zygotic genome activation or gaining developmental competence after fertilization, potentially associated with high levels of maternal H2AK119ub1 deposition on the zygotic genomes. Taken together, H2AK119ub1 level is declined during oocyte maturation by an USP16-dependent mechanism, which ensures zygotic genome reprogramming and transcriptional activation of essential early zygotic genes.
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Affiliation(s)
- Yan Rong
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China.,MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jia-Li Yu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shu-Yan Ji
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yong Zhou
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Yu Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jin Jin
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qian-Qian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
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10
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Rajam SM, Varghese PC, Dutta D. Histone Chaperones as Cardinal Players in Development. Front Cell Dev Biol 2022; 10:767773. [PMID: 35445016 PMCID: PMC9014011 DOI: 10.3389/fcell.2022.767773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Dynamicity and flexibility of the chromatin landscape are critical for most of the DNA-dependent processes to occur. This higher-order packaging of the eukaryotic genome into the chromatin is mediated by histones and associated non-histone proteins that determine the states of chromatin. Histone chaperones- “the guardian of genome stability and epigenetic information” controls the chromatin accessibility by escorting the nucleosomal and non-nucleosomal histones as well as their variants. This distinct group of molecules is involved in all facets of histone metabolism. The selectivity and specificity of histone chaperones to the histones determine the maintenance of the chromatin in an open or closed state. This review highlights the functional implication of the network of histone chaperones in shaping the chromatin function in the development of an organism. Seminal studies have reported embryonic lethality at different stages of embryogenesis upon perturbation of some of the chaperones, suggesting their essentiality in development. We hereby epitomize facts and functions that emphasize the relevance of histone chaperones in orchestrating different embryonic developmental stages starting from gametogenesis to organogenesis in multicellular organisms.
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Affiliation(s)
- Sruthy Manuraj Rajam
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Pallavi Chinnu Varghese
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
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11
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Zhang Y, Yang Y, Qiao P, Wang X, Yu R, Sun H, Xing X, Zhang Y, Su J. CHAF1b, chromatin assembly factor-1 subunit b, is essential for mouse preimplantation embryos. Int J Biol Macromol 2022; 195:547-557. [PMID: 34906611 DOI: 10.1016/j.ijbiomac.2021.11.181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/15/2022]
Abstract
Chromatin assembly factor-1, subunit b (CHAF1b), the p60 subunit of the chromatin-assembly factor-1 (CAF-1) complex, is an evolutionarily conserved protein that has been implicated in various biological processes. Although a variety of functions have been attributed to CHAF1b, its function in preimplantation embryos remains obscure. In this study, we showed that CHAF1b knockdown did not affect the blastocyst rate, but resulted in a low blastocyst hatching rate, outgrowth failure in vitro, and embryonic lethality after implantation in vivo. Notably, CHAF1b depletion increased apoptosis and caused down-regulated expression of key regulators of cell fate specification, including Oct4, Cdx2, Sox2, and Nanog. Further analysis revealed that CHAF1b mediated the replacement of H3.3 with H3.1/3.2, which was associated with decreased repressive histone marks (H3K9me2/3 and H3K27me2/3) and increased active histone marks (H3K4me2/3). Moreover, RNA-sequencing analysis revealed that CHAF1b depletion resulted in the differential expression of 1508 genes, including epigenetic modifications genes, multiple lineage-specific genes, and several genes encoding apoptosis proteins. In addition, assay for transposase-accessible chromatin-sequencing analysis demonstrated that silencing CHAF1b altered the chromatin accessibility of lineage-specific genes and epigenetic modifications genes. Taken together, these data imply that CHAF1b plays significant roles in preimplantation embryos, probably by regulating epigenetic modifications and lineage specification.
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Affiliation(s)
- Yingbing Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Ying Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Peipei Qiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Xiyue Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Ruiluan Yu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Hongzheng Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Xupeng Xing
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
| | - Jianmin Su
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
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12
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Borsuk E, Michalkiewicz J, Kubiak JZ, Kloc M. Histone Modifications in Mouse Pronuclei and Consequences for Embryo Development. Results Probl Cell Differ 2022; 70:397-415. [PMID: 36348116 DOI: 10.1007/978-3-031-06573-6_14] [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] [Indexed: 06/16/2023]
Abstract
Epigenetic marks, such as DNA methylation and posttranslational modifications of core histones, are the key regulators of gene expression. In the mouse, many of these marks are erased during gamete formation and must be introduced de novo after fertilization. Some of them appear synchronously, but the others are deposited asynchronously and/or remain differently distributed on maternal and paternal chromatin. Although the mechanisms regulating these processes are not entirely understandable, it is commonly accepted that epigenetic reprogramming occurring during the first cell cycle of a mouse embryo is crucial for its further development. This chapter focuses on selected epigenetic modifications, such as DNA methylation, the introduction of histone variants, histones acetylation, phosphorylation, and methylation. Properly depositing these marks on maternal and paternal chromatin is crucial for normal embryonic development.
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Affiliation(s)
- Ewa Borsuk
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Julia Michalkiewicz
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jacek Z Kubiak
- Dynamics and Mechanics of Epithelia Group, Institute of Genetics and Development of Rennes, UMR 6290, CNRS, Faculty of Medicine, University of Rennes, Rennes, France
- Laboratory of Molecular Oncology and Innovative Therapies, Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, TX, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
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13
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Wang X, Wang L, Dou J, Yu T, Cao P, Fan N, Borjigin U, Nashun B. Distinct role of histone chaperone Asf1a and Asf1b during fertilization and pre-implantation embryonic development in mice. Epigenetics Chromatin 2021; 14:55. [PMID: 34906203 PMCID: PMC8670131 DOI: 10.1186/s13072-021-00430-7] [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] [Received: 09/02/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Background Asf1 is a well-conserved histone chaperone that regulates multiple cellular processes in different species. Two paralogous genes, Asf1a and Asf1b exist in mammals, but their role during fertilization and early embryogenesis remains to be investigated further. Methods We analyzed the dynamics of histone chaperone Asf1a and Asf1b in oocytes and pre-implantation embryos in mice by immunofluorescence and real-time quantitative PCR, and further investigated the role of Asf1a and Asf1b during fertilization and pre-implantation development by specific Morpholino oligos-mediated knock down approach. Results Immunofluorescence with specific antibodies revealed that both Asf1a and Asf1b were deposited in the nuclei of fully grown oocytes, accumulated abundantly in zygote and 2-cell embryonic nuclei, but turned low at 4-cell stage embryos. In contrast to the weak but definite nuclear deposition of Asf1a, Asf1b disappeared from embryonic nuclei at morula and blastocyst stages. The knockdown of Asf1a and Asf1b by specific Morpholino oligos revealed that Asf1a but not Asf1b was required for the histone H3.3 assembly in paternal pronucleus. However, knockdown of either Asf1a or Asf1b expression decreased developmental potential of pre-implantation embryos. Furthermore, while Asf1a KD severely reduced H3K56 acetylation level and the expression of Oct4 in blastocyst stage embryos, Asf1b KD almost eliminated nuclear accumulation of proliferating cell marker-PCNA in morula stage embryos. These results suggested that histone chaperone Asf1a and Asf1b play distinct roles during fertilization and pre-implantation development in mice. Conclusions Our data suggested that both Asf1a and Asf1b are required for pre-implantation embryonic development. Asf1a regulates H3K56ac levels and Oct4 expression, while Asf1b safeguards pre-implantation embryo development by regulating cell proliferation. We also showed that Asf1a, but not Asf1b, was necessary for the assembly of histone H3.3 in paternal pronuclei after fertilization. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00430-7.
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Affiliation(s)
- Xuemei Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Lu Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Jie Dou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Tianjiao Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Pengbo Cao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Na Fan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Uyunbilig Borjigin
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, 24 Zhaojun Road, Yuquan District, Hohhot, 010070, Inner Mongolia, China.
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14
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Kawamura M, Funaya S, Sugie K, Suzuki MG, Aoki F. Asymmetrical deposition and modification of histone H3 variants are essential for zygote development. Life Sci Alliance 2021; 4:4/8/e202101102. [PMID: 34168076 PMCID: PMC8321678 DOI: 10.26508/lsa.202101102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/02/2023] Open
Abstract
A low level of H3.1/2 deposition in the perinucleolar regions of male pronuclei in zygotes prevents accumulation of H3.1/2K27me3 modification which has detrimental effect on DNA replication. The pericentromeric heterochromatin of one-cell embryos forms a unique, ring-like structure around the nucleolar precursor body, which is absent in somatic cells. Here, we found that the histone H3 variants H3.1 and/or H3.2 (H3.1/H3.2) were localized asymmetrically between the male and female perinucleolar regions of the one-cell embryos; moreover, asymmetrical histone localization influenced DNA replication timing. The nuclear deposition of H3.1/3.2 in one-cell embryos was low relative to other preimplantation stages because of reduced H3.1/3.2 mRNA expression and incorporation efficiency. The forced incorporation of H3.1/3.2 into the pronuclei of one-cell embryos triggered a delay in DNA replication, leading to developmental failure. Methylation of lysine residue 27 (H3K27me3) of the deposited H3.1/3.2 in the paternal perinucleolar region caused this delay in DNA replication. These results suggest that reduced H3.1/3.2 in the paternal perinucleolar region is essential for controlled DNA replication and preimplantation development. The nuclear deposition of H3.1/3.2 is presumably maintained at a low level to avoid the detrimental effect of K27me3 methylation on DNA replication in the paternal perinucleolar region.
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Affiliation(s)
- Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kenta Sugie
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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15
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Guo SM, Liu XP, Zhou LQ. H3.3 kinetics predicts chromatin compaction status of parental genomes in early embryos. Reprod Biol Endocrinol 2021; 19:87. [PMID: 34116678 PMCID: PMC8194155 DOI: 10.1186/s12958-021-00776-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND After fertilization, the fusion of gametes results in the formation of totipotent zygote. During sperm-egg fusion, maternal factors participate in parental chromatin remodeling. H3.3 is a histone H3 variant that plays essential roles in mouse embryogenesis. METHODS Here, we used transgenic early embryos expressing H3.3-eGFP or H2B-mCherry to elucidate changes of histone mobility. RESULTS We used FRAP analysis to identify that maternally stored H3.3 has a more significant change than H2B during maternal-to-embryonic transition. We also found that H3.3 mobile fraction, which may be regulated by de novo H3.3 incorporation, reflects chromatin compaction of parental genomes in GV oocytes and early embryos. CONCLUSIONS Our results show that H3.3 kinetics in GV oocytes and early embryos is highly correlated with chromatin compaction status of parental genomes, indicating critical roles of H3.3 in higher-order chromatin organization.
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Affiliation(s)
- Shi-Meng Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xing-Ping Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
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16
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Fu B, Ma H, Liu D. Functions and Regulation of Endogenous Retrovirus Elements during Zygotic Genome Activation: Implications for Improving Somatic Cell Nuclear Transfer Efficiency. Biomolecules 2021; 11:829. [PMID: 34199637 PMCID: PMC8229993 DOI: 10.3390/biom11060829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
Endogenous retroviruses (ERVs), previously viewed as deleterious relics of ancestral retrovirus infections, are silenced in the vast majority of cells to minimize the risk of retrotransposition. Counterintuitively, bursts of ERV transcription usually occur during maternal-to-zygotic transition (MZT) in preimplantation embryos; this is regarded as a major landmark event in the zygotic genome activation (ZGA) process, indicating that ERVs play an active part in ZGA. Evolutionarily, the interaction between ERVs and hosts is mutually beneficial. The endogenization of retrovirus sequences rewires the gene regulatory network during ZGA, and ERV repression may lower germline fitness. Unfortunately, owing to various limitations of somatic cell nuclear transfer (SCNT) technology, both developmental arrest and ZGA abnormalities occur in a high percentage of cloned embryos, accompanied by ERV silencing, which may be caused by the activation failure of upstream ERV inducers. In this review, we discuss the functions and regulation of ERVs during the ZGA process and the feasibility of temporal control over ERVs in cloned embryos via exogenous double homeobox (DUX). We hypothesize that further accurate characterization of the ERV-rewired gene regulatory network during ZGA may provide a novel perspective on the development of preimplantation embryos.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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17
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Franklin R, Murn J, Cheloufi S. Cell Fate Decisions in the Wake of Histone H3 Deposition. Front Cell Dev Biol 2021; 9:654915. [PMID: 33959610 PMCID: PMC8093820 DOI: 10.3389/fcell.2021.654915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/18/2021] [Indexed: 12/19/2022] Open
Abstract
An expanding repertoire of histone variants and specialized histone chaperone partners showcases the versatility of nucleosome assembly during different cellular processes. Recent research has suggested an integral role of nucleosome assembly pathways in both maintaining cell identity and influencing cell fate decisions during development and normal homeostasis. Mutations and altered expression profiles of histones and corresponding histone chaperone partners are associated with developmental defects and cancer. Here, we discuss the spatiotemporal deposition mechanisms of the Histone H3 variants and their influence on mammalian cell fate during development. We focus on H3 given its profound effect on nucleosome stability and its recently characterized deposition pathways. We propose that differences in deposition of H3 variants are largely dependent on the phase of the cell cycle and cellular potency but are also affected by cellular stress and changes in cell fate. We also discuss the utility of modern technologies in dissecting the spatiotemporal control of H3 variant deposition, and how this could shed light on the mechanisms of cell identity maintenance and lineage commitment. The current knowledge and future studies will help us better understand how organisms employ nucleosome dynamics in health, disease, and aging. Ultimately, these pathways can be manipulated to induce cell fate change in a therapeutic setting depending on the cellular context.
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Affiliation(s)
- Reuben Franklin
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, United States
| | - Jernej Murn
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, United States
| | - Sihem Cheloufi
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, United States
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18
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Rashid M, Shah SG, Verma T, Chaudhary N, Rauniyar S, Patel VB, Gera PB, Smoot D, Ashaktorab H, Dalal SN, Gupta S. Tumor-specific overexpression of histone gene, H3C14 in gastric cancer is mediated through EGFR-FOXC1 axis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194703. [PMID: 33727172 DOI: 10.1016/j.bbagrm.2021.194703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/15/2021] [Accepted: 03/07/2021] [Indexed: 02/08/2023]
Abstract
Incorporation of different H3 histone isoforms/variants have been reported to differentially regulate gene expression via alteration in chromatin organization during diverse cellular processes. However, the differential expression of highly conserved histone H3.2 genes, H3C14 and H3C13 in human cancer has not been delineated. In this study, we investigated the expression of H3.2 genes in primary human gastric, brain, breast, colon, liver, and head and neck cancer tissues and tumor cell lines. The data showed overexpression of H3.2 transcripts in tumor samples and cell lines with respect to normal counterparts. Furthermore, TCGA data of individual and TCGA PANCAN cohort also showed significant up-regulation of H3.2 genes. Further, overexpressed H3C14 gene coding for H3.2 protein was regulated by FOXC1 transcription factor and G4-cassette in gastric cancer cell lines. Elevated expression of FOXC1 protein and transcripts were also observed in human gastric cancer samples and cell lines. Further, FOXC1 protein was predominantly localized in the nuclei of neoplastic gastric cells compared to normal counterpart. In continuation, studies with EGF induction, FOXC1 knockdown, and ChIP-qPCR for the first time identified a novel axis, EGFR-FOXC1-H3C14 for regulation of H3C14 gene overexpression in gastric cancer. Therefore, the changes the epigenomic landscape due to incorporation of differential expression H3 variant contributes to change in gene expression pattern and thereby contributing to pathogenesis of cancer.
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Affiliation(s)
- Mudasir Rashid
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanket Girish Shah
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Tripti Verma
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Nazia Chaudhary
- KS216, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sukanya Rauniyar
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Vidisha Bhavesh Patel
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India
| | - Poonam B Gera
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208, United States
| | - Hassan Ashaktorab
- Department of Medicine and Cancer Center, College of Medicine, Howard University, Washington DC, WA 20060, United States
| | - Sorab N Dalal
- KS216, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanjay Gupta
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India.
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19
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Bogolyubova I, Bogolyubov D. DAXX Is a Crucial Factor for Proper Development of Mammalian Oocytes and Early Embryos. Int J Mol Sci 2021; 22:ijms22031313. [PMID: 33525665 PMCID: PMC7866053 DOI: 10.3390/ijms22031313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
The Death-domain associated protein 6 (DAXX) is an evolutionarily conserved and ubiquitously expressed multifunctional protein that is implicated in many cellular processes, including transcription, cellular proliferation, cell cycle regulation, Fas-induced apoptosis, and many other events. In the nucleus, DAXX interacts with transcription factors, epigenetic modifiers, and chromatin-remodeling proteins such as the transcription regulator ATRX-the α-thalassemia/mental retardation syndrome X-linked ATP-dependent helicase II. Accordingly, DAXX is considered one of the main players involved in chromatin silencing and one of the most important factors that maintain integrity of the genome. In this brief review, we summarize available data regarding the general and specific functions of DAXX in mammalian early development, with special emphasis on the function of DAXX as a chaperone of the histone variant H3.3. Since H3.3 plays a key role in the developmental processes, especially in the pronounced rearrangements of heterochromatin compartment during oogenesis and embryogenesis, DAXX can be considered as an important factor supporting proper development. Specifically, loss of DAXX affects the recruitment of ATRX, transcription of tandem repeats and telomere functions, which results in a decrease in the viability of early embryos.
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20
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Sugie K, Funaya S, Kawamura M, Nakamura T, Suzuki MG, Aoki F. Expression of Dux family genes in early preimplantation embryos. Sci Rep 2020; 10:19396. [PMID: 33173118 PMCID: PMC7655946 DOI: 10.1038/s41598-020-76538-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
After fertilization, the zygotic genome is activated through two phases, minor zygotic activation (ZGA) and major ZGA.
Recently, it was suggested that DUX is expressed during minor ZGA and activates some genes during major ZGA. However, it has not been proven that Dux is expressed during minor ZGA and functions to activate major ZGA genes, because there are several Dux paralogs that may be expressed in zygotes instead of Dux. In this study, we found that more than a dozen Dux paralogs, as well as Dux, are expressed during minor ZGA. Overexpression of some of these genes induced increased expression of major ZGA genes. These results suggest that multiple Dux paralogs are expressed to ensure a sufficient amount of functional Dux and its paralogs which are generated during a short period of minor ZGA with a low transcriptional activity. The mechanism by which multiple Dux paralogs are expressed is discussed.
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Affiliation(s)
- Kenta Sugie
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Toshinobu Nakamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan.
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21
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Ishiuchi T, Abe S, Inoue K, Yeung WKA, Miki Y, Ogura A, Sasaki H. Reprogramming of the histone H3.3 landscape in the early mouse embryo. Nat Struct Mol Biol 2020; 28:38-49. [PMID: 33169018 DOI: 10.1038/s41594-020-00521-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
Epigenetic reprogramming of the zygote involves dynamic incorporation of histone variant H3.3. However, the genome-wide distribution and dynamics of H3.3 during early development remain unknown. Here, we delineate the H3.3 landscapes in mouse oocytes and early embryos. We unexpectedly identify a non-canonical H3.3 pattern in mature oocytes and zygotes, in which local enrichment of H3.3 at active chromatin is suppressed and H3.3 is relatively evenly distributed across the genome. Interestingly, although the non-canonical H3.3 pattern forms gradually during oogenesis, it quickly switches to a canonical pattern at the two-cell stage in a transcription-independent and replication-dependent manner. We find that incorporation of H3.1/H3.2 mediated by chromatin assembly factor CAF-1 is a key process for the de novo establishment of the canonical pattern. Our data suggest that the presence of the non-canonical pattern and its timely transition toward a canonical pattern support the developmental program of early embryos.
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Affiliation(s)
- Takashi Ishiuchi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yuka Miki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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22
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Sha QQ, Zhang J, Fan HY. Function and Regulation of Histone H3 Lysine-4 Methylation During Oocyte Meiosis and Maternal-to-Zygotic Transition. Front Cell Dev Biol 2020; 8:597498. [PMID: 33163498 PMCID: PMC7581939 DOI: 10.3389/fcell.2020.597498] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
During oogenesis and fertilization, histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs) tightly regulate the methylation of histone H3 on lysine-4 (H3K4me) by adding and removing methyl groups, respectively. Female germline-specific conditional knockout approaches that abolish the maternal store of target mRNAs and proteins are used to examine the functions of H3K4 KMTs and KDMs during oogenesis and early embryogenesis. In this review, we discuss the recent advances in information regarding the deposition and removal of histone H3K4 methylations, as well as their functional roles in sculpting and poising the oocytic and zygotic genomes. We start by describing the role of KMTs in establishing H3K4 methylation patterns in oocytes and the impact of H3K4 methylation on oocyte maturation and competence to undergo MZT. We then introduce the latest information regarding H3K4 demethylases that account for the dynamic changes in H3K4 modification levels during development and finish the review by specifying important unanswered questions in this research field along with promising future directions for H3K4-related epigenetic studies.
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Affiliation(s)
- Qian-Qian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Jue Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, China
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23
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Martire S, Banaszynski LA. The roles of histone variants in fine-tuning chromatin organization and function. Nat Rev Mol Cell Biol 2020; 21:522-541. [PMID: 32665685 PMCID: PMC8245300 DOI: 10.1038/s41580-020-0262-8] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Histones serve to both package and organize DNA within the nucleus. In addition to histone post-translational modification and chromatin remodelling complexes, histone variants contribute to the complexity of epigenetic regulation of the genome. Histone variants are characterized by a distinct protein sequence and a selection of designated chaperone systems and chromatin remodelling complexes that regulate their localization in the genome. In addition, histone variants can be enriched with specific post-translational modifications, which in turn can provide a scaffold for recruitment of variant-specific interacting proteins to chromatin. Thus, through these properties, histone variants have the capacity to endow specific regions of chromatin with unique character and function in a regulated manner. In this Review, we provide an overview of recent advances in our understanding of the contribution of histone variants to chromatin function in mammalian systems. First, we discuss new molecular insights into chaperone-mediated histone variant deposition. Next, we discuss mechanisms by which histone variants influence chromatin properties such as nucleosome stability and the local chromatin environment both through histone variant sequence-specific effects and through their role in recruiting different chromatin-associated complexes. Finally, we focus on histone variant function in the context of both embryonic development and human disease, specifically developmental syndromes and cancer.
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Affiliation(s)
- Sara Martire
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura A Banaszynski
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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24
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Abstract
Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.
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Affiliation(s)
- Benjamin Loppin
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007 Lyon, France;
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria;
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25
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Burkhart KB, Sando SR, Corrionero A, Horvitz HR. H3.3 Nucleosome Assembly Mutants Display a Late-Onset Maternal Effect. Curr Biol 2020; 30:2343-2352.e3. [PMID: 32470364 DOI: 10.1016/j.cub.2020.04.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023]
Abstract
Maternally inherited RNA and proteins control much of embryonic development. The effect of such maternal information beyond embryonic development is largely unclear. Here, we report that maternal contribution of histone H3.3 assembly complexes can prevent the expression of late-onset anatomical, physiologic, and behavioral abnormalities of C. elegans. We show that mutants lacking hira-1, an evolutionarily conserved H3.3-deposition factor, have severe pleiotropic defects that manifest predominantly at adulthood. These late-onset defects can be maternally rescued, and maternally derived HIRA-1 protein can be detected in hira-1(-/-) progeny. Mitochondrial stress likely contributes to the late-onset defects, given that hira-1 mutants display mitochondrial stress, and the induction of mitochondrial stress results in at least some of the hira-1 late-onset abnormalities. A screen for mutants that mimic the hira-1 mutant phenotype identified PQN-80-a HIRA complex component, known as UBN1 in humans-and XNP-1-a second H3.3 chaperone, known as ATRX in humans. pqn-80 and xnp-1 abnormalities are also maternally rescued. Furthermore, mutants lacking histone H3.3 have a late-onset defect similar to a defect of hira-1, pqn-80, and xnp-1 mutants. These data demonstrate that H3.3 assembly complexes provide non-DNA-based heritable information that can markedly influence adult phenotype. We speculate that similar maternal effects might explain the missing heritability of late-onset human diseases, such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes.
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Affiliation(s)
- Kirk B Burkhart
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Steven R Sando
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna Corrionero
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - H Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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26
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Liu Z, Tardat M, Gill ME, Royo H, Thierry R, Ozonov EA, Peters AH. SUMOylated PRC1 controls histone H3.3 deposition and genome integrity of embryonic heterochromatin. EMBO J 2020; 39:e103697. [PMID: 32395866 PMCID: PMC7327501 DOI: 10.15252/embj.2019103697] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Chromatin integrity is essential for cellular homeostasis. Polycomb group proteins modulate chromatin states and transcriptionally repress developmental genes to maintain cell identity. They also repress repetitive sequences such as major satellites and constitute an alternative state of pericentromeric constitutive heterochromatin at paternal chromosomes (pat‐PCH) in mouse pre‐implantation embryos. Remarkably, pat‐PCH contains the histone H3.3 variant, which is absent from canonical PCH at maternal chromosomes, which is marked by histone H3 lysine 9 trimethylation (H3K9me3), HP1, and ATRX proteins. Here, we show that SUMO2‐modified CBX2‐containing Polycomb Repressive Complex 1 (PRC1) recruits the H3.3‐specific chaperone DAXX to pat‐PCH, enabling H3.3 incorporation at these loci. Deficiency of Daxx or PRC1 components Ring1 and Rnf2 abrogates H3.3 incorporation, induces chromatin decompaction and breakage at PCH of exclusively paternal chromosomes, and causes their mis‐segregation. Complementation assays show that DAXX‐mediated H3.3 deposition is required for chromosome stability in early embryos. DAXX also regulates repression of PRC1 target genes during oogenesis and early embryogenesis. The study identifies a novel critical role for Polycomb in ensuring heterochromatin integrity and chromosome stability in mouse early development.
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Affiliation(s)
- Zichuan Liu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Helene Royo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Raphael Thierry
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Antoine Hfm Peters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
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27
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Hu X, Mao J, Zhou B, Zhang H, Li B, Pang P, Shan H. Generation and phenotype analysis of CysLTR1 L118F mutant mice. J Cell Biochem 2019; 121:2372-2384. [PMID: 31742746 DOI: 10.1002/jcb.29460] [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: 12/03/2018] [Accepted: 10/04/2019] [Indexed: 11/06/2022]
Abstract
Cysteinyl leukotrienes (CysLTs) are a group of eicosanoids that regulate the pathogenesis of various human diseases, mainly by signaling through the cysteinyl leukotriene receptor 1 (CysLTR1). The aim of this study was to generate and examine the phenotype of CysLTR1 L118F mutant mice. CysLTR1 L118F mutant mice were generated by the simultaneous microinjection of single guide RNA, Cas9 messenger RNA, and donor plasmid into fertilized mouse eggs. The morphological and behavioral characteristics of the resultant CysLTR1 L118F mutant mice were analyzed using an animal phenotype analysis platform, which included the assessment of body length, tail length, grip strength, and locomotor activity. Immunoprecipitation coupled with mass spectrometry was performed to identify CysLTR1-interacting proteins, and the intracellular calcium levels were determined using fluorometric imaging plate reader assays. The body length and tail length of CysLTR1 L118F mutant mice were significantly increased compared with wild-type mice. In addition, the grip strength and locomotor activity were remarkably elevated in L118F mutant mice compared with wild-type mice. Only three proteins were found to interact with both wild-type and CysLTR1 L118F proteins, whereas 4 and 13 additional proteins interacted exclusively with wild-type and mutant CysLTR1, respectively. Lastly, the responsiveness of cardiac muscle cells to CysLTs were significantly impaired by the L118F substitution in CysLTR1 proteins. The CysLTR1 L118F point mutation induced significant changes in the mouse morphology and behavior, which might be mediated by alterations of its protein interaction profile.
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Affiliation(s)
- Xiaojun Hu
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Junjie Mao
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Bin Zhou
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Huitao Zhang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Bing Li
- Department of Ophthalmology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Hong Shan
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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28
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Paul S, Zhang X, He JQ. Homeobox gene Meis1 modulates cardiovascular regeneration. Semin Cell Dev Biol 2019; 100:52-61. [PMID: 31623926 DOI: 10.1016/j.semcdb.2019.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Regeneration of cardiomyocytes, endothelial cells and vascular smooth muscle cells (three major lineages of cardiac tissues) following myocardial infarction is the critical step to recover the function of the damaged heart. Myeloid ecotropic viral integration site 1 (Meis1) was first discovered in leukemic mice in 1995 and its biological function has been extensively studied in leukemia, hematopoiesis, the embryonic pattering of body axis, eye development and various genetic diseases, such as restless leg syndrome. It was found that Meis1 is highly associated with Hox genes and their cofactors to exert its regulatory effects on multiple intracellular signaling pathways. Recently with the advent of bioinformatics, biochemical methods and advanced genetic engineering tools, new function of Meis1 has been found to be involved in the cell cycle regulation of cardiomyocytes and endothelial cells. For example, inhibition of Meis1 expression increases the proliferative capacity of neonatal mouse cardiomyocytes, whereas overexpression of Meis1 results in the reduction in the length of cardiomyocyte proliferative window. Interestingly, downregulation of one of the circular RNAs, which acts downstream of Meis1 in the cardiomyocytes, promotes angiogenesis and restores the myocardial blood supply, thus reinforcing better regeneration of the damaged heart. It appears that Meis1 may play double roles in modulating proliferation and regeneration of cardiomyocytes and endothelial cells post-myocardial infarction. In this review, we propose to summarize the major findings of Meis1 in modulating fetal development and adult abnormalities, especially focusing on the recent discoveries of Meis1 in controlling the fate of cardiomyocytes and endothelial cells.
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Affiliation(s)
- Swagatika Paul
- Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiaonan Zhang
- Beijing Yulong Shengshi Biotechnology, Haidian District, Beijing, 100085, China
| | - Jia-Qiang He
- Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA.
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29
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Fulka H, Ogura A, Loi P, Fulka Jr J. Dissecting the role of the germinal vesicle nuclear envelope and soluble content in the process of somatic cell remodelling and reprogramming. J Reprod Dev 2019; 65:433-441. [PMID: 31423000 PMCID: PMC6815741 DOI: 10.1262/jrd.2019-017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Differentiated nuclei can be reprogrammed/remodelled to totipotency after their transfer to enucleated metaphase II (MII) oocytes. The process of reprogramming/remodelling is, however, only
partially characterized. It has been shown that the oocyte nucleus (germinal vesicle – GV) components are essential for a successful remodelling of the transferred nucleus by providing the
materials for pseudo-nucleus formation. However, the nucleus is a complex structure and exactly what nuclear components are required for a successful nucleus remodelling and reprogramming is
unknown. Till date, the only nuclear sub-structure experimentally demonstrated to be essential is the oocyte nucleolus (nucleolus-like body, NLB). In this study, we investigated what other
GV components might be necessary for the formation of normal-sized pseudo-pronuclei (PNs). Our results showed that the removal of the GV nuclear envelope with attached chromatin and
chromatin-bound factors does not substantially influence the size of the remodelled nuclei in reconstructed cells and that their nuclear envelopes seem to have normal parameters. Rather than
the insoluble nuclear lamina, the GV content, which is dissolved in the cytoplasm with the onset of oocyte maturation, influences the characteristics and size of transferred nuclei.
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Affiliation(s)
- Helena Fulka
- Institute of Molecular Genetics of the ASCR, 142 20 Prague, Czech Republic.,Institute of Experimental Medicine, 142 20 Prague, Czech Republic
| | - Atsuo Ogura
- RIKEN BioResource Center, Ibaraki 305-0074, Japan
| | - Pasqualino Loi
- Faculty of Veterinary Medicine, University of Teramo, Teramo 64100, Italy
| | - Josef Fulka Jr
- Institute of Animal Science, 140 00 Prague, Czech Republic
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30
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Fernandes CFDL, Iglesia RP, Melo-Escobar MI, Prado MB, Lopes MH. Chaperones and Beyond as Key Players in Pluripotency Maintenance. Front Cell Dev Biol 2019; 7:150. [PMID: 31428613 PMCID: PMC6688531 DOI: 10.3389/fcell.2019.00150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
Pluripotency is orchestrated by distinct players and chaperones and their partners have emerged as pivotal molecules in proteostasis control to maintain stemness. The proteostasis network consists of diverse interconnected pathways that function dynamically according to the needs of the cell to quality control and maintain protein homeostasis. The proteostasis machinery of pluripotent stem cells (PSCs) is finely adjusted in response to distinct stimuli during cell fate commitment to determine successful organism development. Growing evidence has shown different classes of chaperones regulating crucial cellular processes in PSCs. Histones chaperones promote proper nucleosome assembly and modulate the epigenetic regulation of factors involved in PSCs’ rapid turnover from pluripotency to differentiation. The life cycle of pluripotency proteins from synthesis and folding, transport and degradation is finely regulated by chaperones and co-factors either to maintain the stemness status or to cell fate commitment. Here, we summarize current knowledge of the chaperone network that govern stemness and present the versatile role of chaperones in stem cells resilience. Elucidation of the intricate regulation of pluripotency, dissecting in detail molecular determinants and drivers, is fundamental to understanding the properties of stem cells in order to provide a reliable foundation for biomedical research and regenerative medicine.
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Affiliation(s)
- Camila Felix de Lima Fernandes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rebeca Piatniczka Iglesia
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Isabel Melo-Escobar
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mariana Brandão Prado
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marilene Hohmuth Lopes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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31
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Non-neutral evolution of H3.3-encoding genes occurs without alterations in protein sequence. Sci Rep 2019; 9:8472. [PMID: 31186448 PMCID: PMC6560044 DOI: 10.1038/s41598-019-44800-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
Histone H3.3 is a developmentally essential variant encoded by two independent genes in human (H3F3A and H3F3B). While this two-gene arrangement is evolutionarily conserved, its origins and function remain unknown. Phylogenetics, synteny and gene structure analyses of H3.3 genes from 32 metazoan genomes indicate independent evolutionary paths for H3F3A and H3F3B. While H3F3B bears similarities with H3.3 genes in distant organisms and with canonical H3 genes, H3F3A is sarcopterygian-specific and evolves under strong purifying selection. Additionally, H3F3B codon-usage preferences resemble those of broadly expressed genes and 'cell differentiation-induced' genes, while codon-usage of H3F3A resembles that of 'cell proliferation-induced' genes. We infer that H3F3B is more similar to the ancestral H3.3 gene and likely evolutionarily adapted for a broad expression pattern in diverse cellular programs, while H3F3A adapted for a subset of gene expression programs. Thus, the arrangement of two independent H3.3 genes facilitates fine-tuning of H3.3 expression across cellular programs.
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32
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Vetrivel S, Tiso N, Kügler A, Irmler M, Horsch M, Beckers J, Hladik D, Giesert F, Gailus-Durner V, Fuchs H, Sabrautzki S, Hrabě de Angelis M, Graw J. Mutation in the mouse histone gene Hist2h3c1 leads to degeneration of the lens vesicle and severe microphthalmia. Exp Eye Res 2019; 188:107632. [PMID: 30991053 PMCID: PMC6876282 DOI: 10.1016/j.exer.2019.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/20/2019] [Accepted: 03/30/2019] [Indexed: 12/21/2022]
Abstract
During an ENU (N-ethyl-N-nitrosourea) mutagenesis screen, we observed a dominant small-eye mutant mouse with viable homozygotes. A corresponding mutant line was established and referred to as Aey69 (abnormality of the eye #69). Comprehensive phenotyping of the homozygous Aey69 mutants in the German Mouse Clinic revealed only a subset of statistically significant alterations between wild types and homozygous mutants. The mutation causes microphthalmia without a lens but with retinal hyperproliferation. Linkage was demonstrated to mouse chromosome 3 between the markers D3Mit188 and D3Mit11. Sequencing revealed a 358 A-> C mutation (Ile120Leu) in the Hist2h3c1 gene and a 71 T-> C (Val24Ala) mutation in the Gja8 gene. Detailed analysis of eye development in the homozygous mutant mice documented a perturbed lens development starting from the lens vesicle stage including decreasing expression of crystallins as well as of lens-specific transcription factors like PITX3 and FOXE3. In contrast, we observed an early expression of retinal progenitor cells characterized by several markers including BRN3 (retinal ganglion cells) and OTX2 (cone photoreceptors). The changes in the retina at the early embryonic stages of E11.5-E15.5 happen in parallel with apoptotic processes in the lens at the respective stages. The excessive retinal hyperproliferation is characterized by an increased level of Ki67. The hyperproliferation, however, does not disrupt the differentiation and appearance of the principal retinal cell types at postnatal stages, even if the overgrowing retina covers finally the entire bulbus of the eye. Morpholino-mediated knock-down of the hist2h3ca1 gene in zebrafish leads to a specific perturbation of lens development. When injected into zebrafish zygotes, only the mutant mouse mRNA leads to severe malformations, ranging from cyclopia to severe microphthalmia. The wild-type Hist2h3c1 mRNA can rescue the morpholino-induced defects corroborating its specific function in lens development. Based upon these data, it is concluded that the ocular function of the Hist2h3c1 gene (encoding a canonical H3.2 variant) is conserved throughout evolution. Moreover, the data highlight also the importance of Hist2h3c1 in the coordinated formation of lens and retina during eye development. A dominant small-eye mutant mouse is caused by a mutation in the histone gene Hist2H3c1. Morpholino-mediated knock-down of hist2h3ca1 in the zebrafish validated this finding. The mutation leads to degeneration of the lens vesicle and retina hyperproliferation.
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Affiliation(s)
- Sharmilee Vetrivel
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Natascia Tiso
- Department of Biology, University of Padova, I-35131 Padova, Italy.
| | - Andrea Kügler
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Martin Irmler
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Marion Horsch
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, D-85354 Freising, Germany; German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Daniela Hladik
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Florian Giesert
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Helmut Fuchs
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Sibylle Sabrautzki
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Comparative Medicine, D-85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, D-85354 Freising, Germany; German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Jochen Graw
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany.
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33
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Analysis of mRNA abundance for histone variants, histone- and DNA-modifiers in bovine in vivo and in vitro oocytes and embryos. Sci Rep 2019; 9:1217. [PMID: 30718778 PMCID: PMC6362035 DOI: 10.1038/s41598-018-38083-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 12/13/2018] [Indexed: 12/18/2022] Open
Abstract
Transcript abundance of histone variants, modifiers of histone and DNA in bovine in vivo oocytes and embryos were measured as mean transcripts per million (TPM). Six of 14 annotated histone variants, 8 of 52 histone methyl-transferases, 5 of 29 histone de-methylases, 5 of 20 acetyl-transferases, 5 of 19 de-acetylases, 1 of 4 DNA methyl-transferases and 0 of 3 DNA de-methylases were abundant (TPM >50) in at least one stage studied. Overall, oocytes and embryos contained more varieties of mRNAs for histone modification than for DNA. Three expression patterns were identified for histone modifiers: (1) transcription before embryonic genome activation (EGA) and down-regulated thereafter such as PRMT1; (2) low in oocytes but transiently increased for EGA such as EZH2; (3) high in oocytes but decreased by EGA such as SETD3. These expression patterns were altered by in vitro culture. Additionally, the presence of mRNAs for the TET enzymes throughout pre-implantation development suggests persistent de-methylation. Together, although DNA methylation changes are well-recognized, the first and second orders of significance in epigenetic changes by in vivo embryos may be histone variant replacements and modifications of histones.
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34
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Benoit M, Simon L, Desset S, Duc C, Cotterell S, Poulet A, Le Goff S, Tatout C, Probst AV. Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. THE NEW PHYTOLOGIST 2019; 221:385-398. [PMID: 29897636 DOI: 10.1111/nph.15248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/23/2023]
Abstract
Developmental phase transitions are often characterized by changes in the chromatin landscape and heterochromatin reorganization. In Arabidopsis, clustering of repetitive heterochromatic loci into so-called chromocenters is an important determinant of chromosome organization in nuclear space. Here, we investigated the molecular mechanisms involved in chromocenter formation during the switch from a heterotrophic to a photosynthetically competent state during early seedling development. We characterized the spatial organization and chromatin features at centromeric and pericentromeric repeats and identified mutant contexts with impaired chromocenter formation. We find that clustering of repetitive DNA loci into chromocenters takes place in a precise temporal window and results in reinforced transcriptional repression. Although repetitive sequences are enriched in H3K9me2 and linker histone H1 before repeat clustering, chromocenter formation involves increasing enrichment in H3.1 as well as H2A.W histone variants, hallmarks of heterochromatin. These processes are severely affected in mutants impaired in replication-coupled histone assembly mediated by CHROMATIN ASSEMBLY FACTOR 1 (CAF-1). We further reveal that histone deposition by CAF-1 is required for efficient H3K9me2 enrichment at repetitive sequences during chromocenter formation. Taken together, we show that chromocenter assembly during post-germination development requires dynamic changes in nucleosome composition and histone post-translational modifications orchestrated by the replication-coupled H3.1 deposition machinery.
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Affiliation(s)
- Matthias Benoit
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
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Sha QQ, Yu JL, Guo JX, Dai XX, Jiang JC, Zhang YL, Yu C, Ji SY, Jiang Y, Zhang SY, Shen L, Ou XH, Fan HY. CNOT6L couples the selective degradation of maternal transcripts to meiotic cell cycle progression in mouse oocyte. EMBO J 2018; 37:embj.201899333. [PMID: 30478191 DOI: 10.15252/embj.201899333] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/09/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Meiotic resumption-coupled degradation of maternal transcripts occurs during oocyte maturation in the absence of mRNA transcription. The CCR4-NOT complex has been identified as the main eukaryotic mRNA deadenylase. In vivo functional and mechanistic information regarding its multiple subunits remains insufficient. Cnot6l, one of four genes encoding CCR4-NOT catalytic subunits, is preferentially expressed in mouse oocytes. Genetic deletion of Cnot6l impaired deadenylation and degradation of a subset of maternal mRNAs during oocyte maturation. Overtranslation of these undegraded mRNAs caused microtubule-chromosome organization defects, which led to activation of spindle assembly checkpoint and meiotic cell cycle arrest at prometaphase. Consequently, Cnot6l -/- female mice were severely subfertile. The function of CNOT6L in maturing oocytes is mediated by RNA-binding protein ZFP36L2, not maternal-to-zygotic transition licensing factor BTG4, which interacts with catalytic subunits CNOT7 and CNOT8 of CCR4-NOT Thus, recruitment of different adaptors by different catalytic subunits ensures stage-specific degradation of maternal mRNAs by CCR4-NOT This study provides the first direct genetic evidence that CCR4-NOT-dependent and particularly CNOT6L-dependent decay of selective maternal mRNAs is a prerequisite for meiotic maturation of oocytes.
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Affiliation(s)
- Qian-Qian Sha
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jia-Li Yu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jing-Xin Guo
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xing-Xing Dai
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jun-Chao Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yin-Li Zhang
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chao Yu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shu-Yan Ji
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yu Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Song-Ying Zhang
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiang-Hong Ou
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China .,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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CFP1 coordinates histone H3 lysine-4 trimethylation and meiotic cell cycle progression in mouse oocytes. Nat Commun 2018; 9:3477. [PMID: 30154440 PMCID: PMC6113306 DOI: 10.1038/s41467-018-05930-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Trimethylation of histone H3 on lysine-4 (H3K4me3) is associated with gene-regulatory elements, but its transcription-independent function in cell division is unclear. CxxC-finger protein-1 (CFP1) is a major mediator of H3K4 trimethylation in mouse oocytes. Here we report that oocyte-specific knockout of Cxxc1, inhibition of CFP1 function, or abrogation of H3K4 methylation in oocytes each causes a delay of meiotic resumption as well as metaphase I arrest owing to defective spindle assembly and chromosome misalignment. These phenomena are partially attributed to insufficient phosphorylation of histone H3 at threonine-3. CDK1 triggers cell division–coupled degradation and inhibitory phosphorylation of CFP1. Preventing CFP1 degradation and phosphorylation causes CFP1 accumulation on chromosomes and impairs meiotic maturation and preimplantation embryo development. Therefore, CFP1-mediated H3K4 trimethylation provides 3a permission signal for the G2–M transition. Dual inhibition of CFP1 removes the SETD1–CFP1 complex from chromatin and ensures appropriate chromosome configuration changes during meiosis and mitosis. The transcription-independent function of trimethylation of histone H3 (H3K4me) in cell division is unclear. Here, Heng-Yu Fan and colleagues report that CFP1, a subunit of the H3K4 methyltransferase, is required for oocyte meiosis, being phosphorylated and degraded during cell cycle transition.
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HIRA directly targets the enhancers of selected cardiac transcription factors during in vitro differentiation of mouse embryonic stem cells. Mol Biol Rep 2018; 45:1001-1011. [PMID: 30030774 PMCID: PMC6156767 DOI: 10.1007/s11033-018-4247-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/08/2018] [Indexed: 01/06/2023]
Abstract
HIRA is a histone chaperone known to modulate gene expression through the deposition of H3.3. Conditional knockout of Hira in embryonic mouse hearts leads to cardiac septal defects. Loss of function mutation in HIRA, together with other chromatin modifiers, was found in patients with congenital heart diseases. However, the effects of HIRA on gene expression at earlier stages of cardiogenic mesoderm differentiation have not yet been studied. Differentiation of mouse embryonic stem cells (mESCs) towards cardiomyocytes mimics some of these early events and is an accepted model of these early stages. We performed RNA-Seq and H3.3-HA ChIP-seq on both WT and Hira-null mESCs and early cardiomyocyte progenitors of both genotypes. Analysis of RNA-seq data showed differential down regulation of cardiovascular development-related genes in Hira-null cardiomyocytes compared to WT cardiomyocytes. We found HIRA-dependent H3.3 deposition at these genes. In particular, we observed that HIRA influenced directly the expression of the transcription factors Gata6, Meis1 and Tbx2, essential for cardiac septation, through H3.3 deposition. We therefore identified new direct targets of HIRA during cardiac differentiation.
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Abstract
Successful cloning of monkeys, the first non-human primate species, by somatic cell nuclear transfer (SCNT) attracted worldwide attention earlier this year. Remarkably, it has taken more than 20 years since the cloning of Dolly the sheep in 1997 to achieve this feat. This success was largely due to recent understanding of epigenetic barriers that impede SCNT-mediated reprogramming and the establishment of key methods to overcome these barriers, which also allowed efficient derivation of human pluripotent stem cells for cell therapy. Here, we summarize recent advances in SCNT technology and its potential applications for both reproductive and therapeutic cloning.
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Affiliation(s)
- Shogo Matoba
- RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan; Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
| | - Yi Zhang
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA.
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39
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Western PS. Epigenomic drugs and the germline: Collateral damage in the home of heritability? Mol Cell Endocrinol 2018; 468:121-133. [PMID: 29471014 DOI: 10.1016/j.mce.2018.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 02/07/2023]
Abstract
The testis and ovary provide specialised environments that nurture germ cells and facilitate their maturation, culminating in the production of mature gametes that can found the following generation. The sperm and egg not only transmit genetic information, but also epigenetic modifications that affect the development and physiology of offspring. Importantly, the epigenetic information contained in mature sperm and oocytes can be influenced by a range of environmental factors, such as diet, chemicals and drugs. An increasing range of studies are revealing how gene-environment interactions are mediated through the germline. Outside the germline, altered epigenetic state is common in a range of diseases, including many cancers. As epigenetic modifications are reversible, pharmaceuticals that directly target epigenetic modifying proteins have been developed and are delivering substantial benefits to patients, particularly in oncology. While providing the most effective patient treatment is clearly the primary concern, some patients will want to conceive children after treatment. However, the impacts of epigenomic drugs on the male and female gametes are poorly understood and whether these drugs will have lasting effects on patients' germline epigenome and subsequent offspring remains largely undetermined. Currently, evidence based clinical guidelines for use of epigenomic drugs in patients of reproductive age are limited in this context. Developing a deeper understanding of the epigenetic mechanisms regulating the germline epigenome and its impact on inherited traits and disease susceptibility is required to determine how specific epigenomic drugs might affect the germline and inheritance. Understanding these potential effects will facilitate the development of informed clinical guidelines appropriate for the use of epigenomic drugs in patients of reproductive age, ultimately improving the safety of these therapies in the clinic.
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Affiliation(s)
- Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia.
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40
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Delaney K, Mailler J, Wenda JM, Gabus C, Steiner FA. Differential Expression of Histone H3.3 Genes and Their Role in Modulating Temperature Stress Response in Caenorhabditis elegans. Genetics 2018; 209:551-565. [PMID: 29636369 PMCID: PMC5972426 DOI: 10.1534/genetics.118.300909] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/08/2018] [Indexed: 01/12/2023] Open
Abstract
Replication-independent variant histones replace canonical histones in nucleosomes and act as important regulators of chromatin function. H3.3 is a major variant of histone H3 that is remarkably conserved across taxa and is distinguished from canonical H3 by just four key amino acids. Most genomes contain two or more genes expressing H3.3, and complete loss of the protein usually causes sterility or embryonic lethality. Here, we investigate the developmental expression patterns of the five Caenorhabditis elegans H3.3 homologs and identify two previously uncharacterized homologs to be restricted to the germ line. Despite these specific expression patterns, we find that neither loss of individual H3.3 homologs nor the knockout of all five H3.3-coding genes causes sterility or lethality. However, we demonstrate an essential role for the conserved histone chaperone HIRA in the nucleosomal loading of all H3.3 variants. This requirement can be bypassed by mutation of the H3.3-specific residues to those found in H3. While even removal of all H3.3 homologs does not result in lethality, it leads to reduced fertility and viability in response to high-temperature stress. Thus, our results show that H3.3 is nonessential in C. elegans but is critical for ensuring adequate response to stress.
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Affiliation(s)
- Kamila Delaney
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, University of Geneva, 1211, Switzerland
| | - Jonathan Mailler
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, University of Geneva, 1211, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, University of Geneva, 1211, Switzerland
| | - Caroline Gabus
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, University of Geneva, 1211, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, University of Geneva, 1211, Switzerland
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41
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Abstract
Environmental factors, particularly during early life, are important for the later metabolic health of the individual. In our obesogenic environment, it is of major socio-economic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Increasing evidence from a variety of model organisms suggests that non-genetically determined phenotypes, including metabolic effects such as glucose intolerance and obesity, can be passed between generations, which encourages us to revisit heredity. Inheritance of altered epigenetic information through the germ line has been proposed as one plausible mechanism. Whether the germline epigenome can be altered by environmental conditions such as diet and the extent to which this occurs in humans are the subject of intense current interest and debate, especially given that extensive germline epigenetic reprogramming is known to occur. As epigenetic mechanisms are often highly conserved between organisms, studying epigenetic inheritance in plants and lower metazoans has the potential to inform our investigation in mammals. This Review explores the extent to which epigenetic inheritance contributes to heredity in these different organisms, whether the environment can affect epigenetic inheritance and whether there is any evidence for the inheritance of acquired phenotypes.
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Affiliation(s)
- Elizabeth J Radford
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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42
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Champroux A, Cocquet J, Henry-Berger J, Drevet JR, Kocer A. A Decade of Exploring the Mammalian Sperm Epigenome: Paternal Epigenetic and Transgenerational Inheritance. Front Cell Dev Biol 2018; 6:50. [PMID: 29868581 PMCID: PMC5962689 DOI: 10.3389/fcell.2018.00050] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
The past decade has seen a tremendous increase in interest and progress in the field of sperm epigenetics. Studies have shown that chromatin regulation during male germline development is multiple and complex, and that the spermatozoon possesses a unique epigenome. Its DNA methylation profile, DNA-associated proteins, nucleo-protamine distribution pattern and non-coding RNA set up a unique epigenetic landscape which is delivered, along with its haploid genome, to the oocyte upon fertilization, and therefore can contribute to embryogenesis and to the offspring health. An emerging body of compelling data demonstrates that environmental exposures and paternal lifestyle can change the sperm epigenome and, consequently, may affect both the embryonic developmental program and the health of future generations. This short review will attempt to provide an overview of what is currently known about sperm epigenome and the existence of transgenerational epigenetic inheritance of paternally acquired traits that may contribute to the offspring phenotype.
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Affiliation(s)
- Alexandre Champroux
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julie Cocquet
- INSERM U1016, Institut Cochin, Centre National de la Recherche Scientifique UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Joëlle Henry-Berger
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Joël R. Drevet
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ayhan Kocer
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
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43
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Eckersley-Maslin MA, Alda-Catalinas C, Reik W. Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. Nat Rev Mol Cell Biol 2018; 19:436-450. [DOI: 10.1038/s41580-018-0008-z] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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44
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Ooga M, Funaya S, Hashioka Y, Fujii W, Naito K, Suzuki MG, Aoki F. Chd9 mediates highly loosened chromatin structure in growing mouse oocytes. Biochem Biophys Res Commun 2018; 500:583-588. [PMID: 29665362 DOI: 10.1016/j.bbrc.2018.04.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/13/2018] [Indexed: 11/25/2022]
Abstract
During oogenesis, oocytes prepare for embryonic development following fertilization. The mechanisms underlying this process are still unknown. Recently, it has been suggested that a loosened chromatin structure is involved in pluripotency and totipotency in embryonic stem (ES) cells and early preimplantation embryos, respectively. Here, we explored chromatin looseness in oocytes by fluorescence recovery after photobleaching (FRAP) using enhanced green fluorescent protein-tagged histone H2B. The results indicated that the chromatin in growing oocytes was already highly loosened to a level comparable to that in early preimplantation embryos. To elucidate the mechanism underlying the loosened chromatin structure in oocytes, we focused on chromodomain helicase DNA binding protein 9 (Chd9), which is highly expressed in growing oocytes. The oocytes from Chd9 knockout mice (Chd9-/-) generated using the CRISPR/Cas9 system exhibited a less loosened chromatin structure than that of wild-type mice, suggesting that Chd9 is involved in the loosened chromatin structure in growing oocytes. These results suggest that a loosened chromatin structure, which is mediated by Chd9, is a prerequisite for the acquisition of totipotency after fertilization.
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Affiliation(s)
- Masatoshi Ooga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yuki Hashioka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Wataru Fujii
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Naito
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
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45
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Yu C, Fan X, Sha QQ, Wang HH, Li BT, Dai XX, Shen L, Liu J, Wang L, Liu K, Tang F, Fan HY. CFP1 Regulates Histone H3K4 Trimethylation and Developmental Potential in Mouse Oocytes. Cell Rep 2018; 20:1161-1172. [PMID: 28768200 DOI: 10.1016/j.celrep.2017.07.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/22/2017] [Accepted: 07/06/2017] [Indexed: 12/18/2022] Open
Abstract
Trimethylation of histone H3 at lysine-4 (H3K4me3) is associated with eukaryotic gene promoters and poises their transcriptional activation during development. To examine the in vivo function of H3K4me3 in the absence of DNA replication, we deleted CXXC finger protein 1 (CFP1), the DNA-binding subunit of the SETD1 histone H3K4 methyltransferase, in developing oocytes. We find that CFP1 is required for H3K4me3 accumulation and the deposition of histone variants onto chromatin during oocyte maturation. Decreased H3K4me3 in oocytes caused global downregulation of transcription activity. Oocytes lacking CFP1 failed to complete maturation and were unable to gain developmental competence after fertilization, due to defects in cytoplasmic lattice formation, meiotic division, and maternal-zygotic transition. Our study highlights the importance of H3K4me3 in continuous histone replacement for transcriptional regulation, chromatin remodeling, and normal developmental progression in a non-replicative system.
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Affiliation(s)
- Chao Yu
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Department of Chemistry and Molecular Biology, Goteborg University, Goteborg SE405 30, Sweden
| | - Xiaoying Fan
- Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Qian-Qian Sha
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hui-Han Wang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Bo-Tai Li
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xing-Xing Dai
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Junping Liu
- Institute of Aging Research, Hangzhou Normal University, Hangzhou 311121, China
| | - Lie Wang
- Institute of Immunology, Zhejiang University Medical School, Hangzhou 310058, China
| | - Kui Liu
- Department of Chemistry and Molecular Biology, Goteborg University, Goteborg SE405 30, Sweden
| | - Fuchou Tang
- Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Institute of Aging Research, Hangzhou Normal University, Hangzhou 311121, China.
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46
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Zhang K, Wang H, Rajput SK, Folger JK, Smith GW. Characterization of H3.3 and HIRA expression and function in bovine early embryos. Mol Reprod Dev 2018; 85:106-116. [PMID: 29232016 DOI: 10.1002/mrd.22939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023]
Abstract
Histone variant H3.3 is encoded by two distinct genes, H3F3A and H3F3B, that are closely associated with actively transcribed genes. H3.3 replacement is continuous and essential for maintaining correct chromatin structure during mouse oogenesis. Upon fertilization, H3.3 is incorporated to parental chromatin, and is required for blastocyst formation in mice. The H3.3 exchange process is facilitated by the chaperone HIRA, particularly during zygote development. We previously demonstrated that H3.3 is required for bovine early embryonic development; here, we explored the mechanisms of its functional requirement. H3F3A mRNA abundance is stable whereas H3F3B and HIRA mRNA are relatively dynamic during early embryonic development. H3F3B mRNA quantity is also considerably higher than H3F3A. Immunofluorescence analysis revealed an even distribution of H3.3 between paternal and maternal pronuclei in zygotes, and subsequent stage-specific localization of H3.3 in early bovine embryos. Knockdown of H3.3 by targeting both H3F3A and H3F3B dramatically decreased the expression of NANOG (a pluripotency marker) and CTGF (Connective tissue growth factor; a trophectoderm marker) in bovine blastocysts. Additionally, we noted that Histone H3 lysine 36 dimethylation and linker Histone H1 abundance is reduced in H3.3-deficient embryos, which was similar to effects following knockdown of CHD1 (Chromodomain helicase DNA-binding protein 1). By contrast, no difference was observed in the abundance of Histone H3 lysine 4 trimethylation, Histone H3 lysine 9 dimethylation, or Splicing factor 3 B1. Collectively, these results established that H3.3 is required for correct epigenetic modifications and H1 deposition, dysregulation of which likely mediate the poor development in H3.3-deficient embryos.
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Affiliation(s)
- Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Dairy Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - Han Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sandeep K Rajput
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - Joseph K Folger
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - George W Smith
- Laboratory of Mammalian Reproductive Biology and Genomics, Michigan State University, East Lansing, Michigan
- Department of Animal Science, Michigan State University, East Lansing, Michigan
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47
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Siwek W, Gómez-Rodríguez M, Sobral D, Corrêa IR, Jansen LET. time-ChIP: A Method to Determine Long-Term Locus-Specific Nucleosome Inheritance. Methods Mol Biol 2018; 1832:131-158. [PMID: 30073525 DOI: 10.1007/978-1-4939-8663-7_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding chromatin dynamics is essential to define the contribution of chromatin to heritable gene silencing and the long-term maintenance of gene expression. Here we present a detailed protocol for time-ChIP, a novel method to measure histone turnover at high resolution across long timescales. This method is based on the SNAP-tag, a self-labeling enzyme that can be pulse labeled with small molecules in cells. Upon pulse biotinylation of a cohort of SNAP-tagged histones we can determine their abundance and fate across a chase period using a biotin-specific chromatin pulldown followed by DNA sequencing or quantitative PCR. This method is unique in its ability to trace the long-term fate of a chromatin bound histone pool, genome wide. In addition to a step by step protocol, we outline advantages and limitations of the method in relation to other existing techniques. time-ChIP can define regions of high and low histone turnover and identify the location of pools of long lived histones.
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Affiliation(s)
| | - Mariluz Gómez-Rodríguez
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Departamento de Ciencias Naturales and Matemáticas, Pontificia Universidad Javeriana, Cali, Colombia
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48
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Xu Q, Xie W. Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment. Trends Cell Biol 2017; 28:237-253. [PMID: 29217127 DOI: 10.1016/j.tcb.2017.10.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023]
Abstract
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development. The latest studies, including many from genome-wide perspectives, have revealed unusual principles of reprogramming for histone modifications, chromatin accessibility, and 3D chromatin architecture. These advances have shed light on the regulatory network controlling the earliest development and maternal-zygotic transition.
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Affiliation(s)
- Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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49
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Cheloufi S, Hochedlinger K. Emerging roles of the histone chaperone CAF-1 in cellular plasticity. Curr Opin Genet Dev 2017; 46:83-94. [PMID: 28692904 PMCID: PMC5813839 DOI: 10.1016/j.gde.2017.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/07/2017] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
Abstract
During embryonic development, cells become progressively restricted in their differentiation potential. This is thought to be regulated by dynamic changes in chromatin structure and associated modifications, which act together to stabilize distinct specialized cell lineages. Remarkably, differentiated cells can be experimentally reprogrammed to a stem cell-like state or to alternative lineages. Thus, cellular reprogramming provides a valuable platform to study the mechanisms that normally safeguard cell identity and uncover factors whose manipulation facilitates cell fate transitions. Recent work has identified the chromatin assembly factor complex CAF-1 as a potent barrier to cellular reprogramming. In addition, CAF-1 has been implicated in the reversion of pluripotent cells to a totipotent-like state and in various lineage conversion paradigms, suggesting that modulation of CAF-1 levels may endow cells with a developmentally more plastic state. Here, we review these exciting results, discuss potential mechanisms and speculate on the possibility of exploiting chromatin assembly pathways to manipulate cell identity.
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Affiliation(s)
- Sihem Cheloufi
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA.
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50
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Tao J, Zhang Y, Zuo X, Hong R, Li H, Liu X, Huang W, Cao Z, Zhang Y. DOT1L inhibitor improves early development of porcine somatic cell nuclear transfer embryos. PLoS One 2017. [PMID: 28632762 PMCID: PMC5478106 DOI: 10.1371/journal.pone.0179436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Incomplete epigenetic reprogramming of the genome of donor cells causes poor early and full-term developmental efficiency of somatic cell nuclear transfer (SCNT) embryos. Previous research indicate that inhibition of the histone H3 K79 methyltransferase DOT1L, using a selective pharmacological inhibitor EPZ004777 (EPZ), significantly improved reprogramming efficiency during the generation of mouse induced pluripotent stem cells. However, the roles of DOT1L in porcine nuclear transfer-mediated cellular reprogramming are not yet known. Here we showed that DOT1L inhibition via 0.5 nM EPZ treatment for 12 or 24 h significantly enhanced the blastocyst rate of SCNT embryos and dramatically reduced the level of H3K79me2 during SCNT 1-cell embryonic development. Additionally, H3K79me2 level in the EPZ-treated SCNT embryos was similar to that in in vitro fertilized embryos, suggesting that DOT1L-mediated H3K79me2 is a reprogramming barrier to early development of porcine SCNT embryos. qRT-PCR analysis further demonstrated that DOT1L inactivation did not change the expression levels of DOT1L itself but increased the expression levels of POU5F1, LIN28, SOX2, CDX2 and GATA4 associated with pluripotency and early cell differentiation. In conclusion, DOT1L inhibitor improved early developmental efficiency of porcine SCNT embryos probably via inducing the increased expression of genes important for pluripotency and lineage specification.
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Affiliation(s)
- Jia Tao
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Yu Zhang
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaoyuan Zuo
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Renyun Hong
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Hui Li
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Xing Liu
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Weiping Huang
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Zubing Cao
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
- * E-mail:
| | - Yunhai Zhang
- Anhui Provincial Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
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