351
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Wang H, Paulson EE, Ma L, Ross PJ, Schultz RM. Paternal genome rescues mouse preimplantation embryo development in the absence of maternally-recruited EZH2 activity. Epigenetics 2019; 14:94-108. [PMID: 30661456 DOI: 10.1080/15592294.2019.1570771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Enhancer of zeste homolog 2 (EZH2), a component of the PRC2 complex, trimethylates H3K27, a transcriptionally repressive histone mark. EZH2 is encoded by a dormant maternal mRNA and inhibiting the maturation-associated increase in EZH2 activity using either a combined siRNA/morpholino approach or a small molecule inhibitor (GSK343) inhibits development of diploidized parthenotes to the blastocyst stage but not inseminated eggs, with longer GSK343 treatments leading to progressively greater inhibition of development. GSK343 treatment also results in a decrease in H3K27me3 and a decrease in global transcription in 2-cell parthenotes but not 2-cell embryos derived from inseminated eggs. RNA-sequencing revealed the relative abundance of ~100 zygotically-expressed transcripts is decreased by GSK treatment in parthenotes, but not in embryos, with many of the affected transcripts encoding proteins involved in transcription. A previous study found that parthenotes deficient in maternal Ezh2 readily develop to the blastocyst stage. To reconcile these differences we propose that the H3K27me3 state present in the zygote needs to be faithfully propagated following DNA replication in at least one pronucleus, otherwise development is compromised.
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Affiliation(s)
- Huili Wang
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , China.,b Department of Anatomy, Physiology, and Cell Biology , University of California Davis , Davis , CA , USA.,c Department of Animal Science , University of California Davis , Davis , CA , USA
| | - Erika E Paulson
- c Department of Animal Science , University of California Davis , Davis , CA , USA
| | - Libing Ma
- d School of Life Science and Technology , Inner Mongolia University of Science & Technology , Baotou , China
| | - Pablo J Ross
- c Department of Animal Science , University of California Davis , Davis , CA , USA
| | - Richard M Schultz
- b Department of Anatomy, Physiology, and Cell Biology , University of California Davis , Davis , CA , USA.,e Department of Biology , University of Pennsylvania , Philadelphia , PA , USA
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352
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Chen G, Wang J. A regulatory circuitry locking pluripotent stemness to embryonic stem cell: Interaction between threonine catabolism and histone methylation. Semin Cancer Biol 2019; 57:72-78. [PMID: 30710616 DOI: 10.1016/j.semcancer.2019.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/15/2019] [Accepted: 01/23/2019] [Indexed: 12/20/2022]
Abstract
Mouse embryonic stem cell (ESC) is a prototype of pluripotent stem cell that undergoes endless self-renewal in culture without losing the pluripotency, the ability to differentiate to all somatic lineages. The self-renewal of ESC relies on a gene expression program, epigenetic state, and cellular metabolism specific to ESC. In this review, we will present the evidence to exemplify how gene regulation, chromatin methylation, and threonine catabolism are specialized to boost ESC self-renewal. It is evident that a feedforward regulatory circuitry forms at the interfaces between the transcriptional, epigenetic and metabolic control to consolidate the pluripotency of ESC.
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Affiliation(s)
- Guohua Chen
- Department of Pathology, Wayne State of University School of Medicine, United States
| | - Jian Wang
- Department of Pathology, Wayne State of University School of Medicine, United States; Cardiovascular Research Institute, Wayne State of University School of Medicine, United States.
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353
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An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos. Nat Commun 2019; 10:364. [PMID: 30664750 PMCID: PMC6341076 DOI: 10.1038/s41467-018-08244-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022] Open
Abstract
Human pre-implantation embryonic development involves extensive changes in chromatin structure and transcriptional activity. Here, we report on LiCAT-seq, a technique that enables simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells, and map the chromatin accessibility and transcriptome landscapes for human pre-implantation embryos. We observed global difference in chromatin accessibility between sperm and all stages of embryos, finding that the accessible regions in sperm tend to occur in gene-poor genomic regions. Integrative analyses between the two datasets reveals strong association between the establishment of accessible chromatin and embryonic genome activation (EGA), and uncovers transcription factors and endogenous retrovirus (ERVs) specific to EGA. In particular, a large proportion of the early activated genes and ERVs are bound by DUX4 and become accessible as early as the 2- to 4-cell stages. Our results thus offer mechanistic insights into the molecular events inherent to human pre-implantation development.
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354
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Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun 2019; 10:94. [PMID: 30626866 PMCID: PMC6327041 DOI: 10.1038/s41467-018-07829-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. However, the molecular basis of this allosteric enhancement is unclear. Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation. However, they vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. Furthermore, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) experiments reveal conformational changes in the allosterically enhanced state. Our findings may enable future development of anti-cancer therapies targeting regions involved in allosteric regulation. The demethylase activity of KDM5A is allosterically enhanced by binding of histone H3 to its PHD1 reader domain, through an unknown mechanism. Here the authors show that the PHD1 domain drives ligand-induced allosteric stimulation by stabilizing the binding of substrate to the catalytic domain.
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Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Cynthia M Chio
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | | | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Karen Ruiz
- TETRAD Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA. .,Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA.
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355
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Larose H, Shami AN, Abbott H, Manske G, Lei L, Hammoud SS. Gametogenesis: A journey from inception to conception. Curr Top Dev Biol 2019; 132:257-310. [PMID: 30797511 PMCID: PMC7133493 DOI: 10.1016/bs.ctdb.2018.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gametogenesis, the process of forming mature germ cells, is an integral part of both an individual's and a species' health and well-being. This chapter focuses on critical male and female genetic and epigenetic processes underlying normal gamete formation through their differentiation to fertilization. Finally, we explore how knowledge gained from this field has contributed to progress in areas with great clinical promise, such as in vitro gametogenesis.
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Affiliation(s)
- Hailey Larose
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | | | - Haley Abbott
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Gabriel Manske
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Lei Lei
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, United States.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, United States.
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356
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Pang YW, Jiang XL, Wang YC, Wang YY, Hao HS, Zhao SJ, Du WH, Zhao XM, Wang L, Zhu HB. Melatonin protects against paraquat-induced damage during in vitro maturation of bovine oocytes. J Pineal Res 2019; 66:e12532. [PMID: 30320949 DOI: 10.1111/jpi.12532] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
Abstract
Paraquat (PQ), a broad-spectrum agricultural pesticide, causes cellular toxicity by increasing oxidative stress levels in various biological systems, including the reproductive system. PQ exposure causes embryotoxicity and reduces the developmental abilities of embryos. However, there is little information regarding the toxic effects of PQ on oocyte maturation. In this study, we studied the toxic effects of PQ exposure and the effects of melatonin on PQ-induced damage in bovine oocytes. PQ exposure disrupted nuclear and cytoplasmic maturation, which was manifested as decreased cumulus cell expansion, reduced first polar body extrusion, and abnormal distribution patterns of cortical granules and mitochondria. In addition, PQ treatment severely disrupted the ability of the resulted in vitro-produced embryos to develop to the blastocyst stage. Moreover, PQ exposure significantly increased the intracellular reactive oxygen species (ROS) level and early apoptotic rate, and decreased the glutathione (GSH) level, antioxidative CAT and GPx4 mRNA, and apoptotic-related Bcl-2/Bax mRNA ratio. These results indicated that PQ causes reproductive toxicity in bovine oocytes. Melatonin application resulted in significant protection against the toxic effects of PQ in PQ-exposed oocytes. The mechanisms underlying the role of melatonin included the inhibition of PQ-induced p38 mitogen-activated protein kinase (MAPK) activation, and restoration of abnormal trimethyl-histone H3 lysine 4 (H3K4me3) and trimethyl-histone H3 lysine 9 (H3K9me3) levels. These results reveal that melatonin serves as a powerful agent against experimental PQ-induced toxicity during bovine oocyte maturation and could form a basis for further studies to develop therapeutic strategies against PQ poisoning.
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Affiliation(s)
- Yun-Wei Pang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Long Jiang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agricultural Animal and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Chun Wang
- Key Laboratory of Agricultural Animal and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yang-Yang Wang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-Sheng Hao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Jiang Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei-Hua Du
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue-Ming Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Wang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua-Bin Zhu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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357
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Gu C, Liu S, Wu Q, Zhang L, Guo F. Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes. Cell Res 2018; 29:110-123. [PMID: 30560925 PMCID: PMC6355938 DOI: 10.1038/s41422-018-0125-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/22/2018] [Indexed: 11/09/2022] Open
Abstract
Oocyte growth is a key step in forming mature eggs that are ready to be fertilized. The states and modifications of chromatin represent critical sources of information for this process. However, the dynamics and interrelations of these chromatin characteristics remain elusive. In this study, we developed an improved scCOOL-seq technique (iscCOOL-seq), which is a multi-omics, single-cell and single-base resolution method with high mapping rates, and explored the chromatin accessibility landscape and its relationship to DNA methylation in growing mouse oocytes. The most dramatic change in chromatin accessibility occurs during oocyte growth initiation, accompanied with prominent transcriptome alterations and an elevated variation in DNA methylation levels among individual oocytes. Unlike CpG islands (CGIs), partially methylated domains (PMDs) are associated with a low density of nucleosome-depleted regions (NDRs) during the whole maturation period. Surprisingly, highly expressed genes are usually associated with NDRs at their transcriptional end sites (TESs). In addition, genes with de novo methylated gene bodies during oocyte maturation are already open at their promoters before oocyte growth initiation. Furthermore, epigenetic and transcription factors that might be involved in oocyte maturation are identified. Our work paves the way for dissecting the complex, yet highly coordinated, epigenetic alterations during mouse oocyte growth and the establishment of totipotency.
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Affiliation(s)
- Chan Gu
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shanling Liu
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qihong Wu
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lin Zhang
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Fan Guo
- Center for Translational Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. .,Ministry of Education Key Laboratory of Bio-resource and Eco-environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610041, China.
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358
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Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y. A chromatin integration labelling method enables epigenomic profiling with lower input. Nat Cell Biol 2018; 21:287-296. [DOI: 10.1038/s41556-018-0248-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022]
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359
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Liu T, Yue F. Dynamic chromatin accessibility unveils a regulatory landscape in early embryogenesis in human. Biol Reprod 2018; 99:1116-1118. [PMID: 30010722 DOI: 10.1093/biolre/ioy154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tingting Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, the Pennsylvania State University, Hershey, Pennsylvania, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, College of Medicine, the Pennsylvania State University, Hershey, Pennsylvania, USA
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360
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Tomizawa SI, Kobayashi Y, Shirakawa T, Watanabe K, Mizoguchi K, Hoshi I, Nakajima K, Nakabayashi J, Singh S, Dahl A, Alexopoulou D, Seki M, Suzuki Y, Royo H, Peters AHFM, Anastassiadis K, Stewart AF, Ohbo K. Kmt2b conveys monovalent and bivalent H3K4me3 in mouse spermatogonial stem cells at germline and embryonic promoters. Development 2018; 145:145/23/dev169102. [PMID: 30504434 DOI: 10.1242/dev.169102] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/01/2018] [Indexed: 12/20/2022]
Abstract
The mammalian male germline is sustained by a pool of spermatogonial stem cells (SSCs) that can transmit both genetic and epigenetic information to offspring. However, the mechanisms underlying epigenetic transmission remain unclear. The histone methyltransferase Kmt2b is highly expressed in SSCs and is required for the SSC-to-progenitor transition. At the stem-cell stage, Kmt2b catalyzes H3K4me3 at bivalent H3K27me3-marked promoters as well as at promoters of a new class of genes lacking H3K27me3, which we call monovalent. Monovalent genes are mainly activated in late spermatogenesis, whereas most bivalent genes are mainly not expressed until embryonic development. These data suggest that SSCs are epigenetically primed by Kmt2b in two distinguishable ways for the upregulation of gene expression both during the spermatogenic program and through the male germline into the embryo. Because Kmt2b is also the major H3K4 methyltransferase for bivalent promoters in embryonic stem cells, we also propose that Kmt2b has the capacity to prime stem cells epigenetically.
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Affiliation(s)
- Shin-Ichi Tomizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Yuki Kobayashi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Takayuki Shirakawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kumiko Watanabe
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Keita Mizoguchi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Ikue Hoshi
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kuniko Nakajima
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Jun Nakabayashi
- Bioinformatics Laboratory, Advanced Medical Research Center, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Sukhdeep Singh
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Andreas Dahl
- Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Dimitra Alexopoulou
- Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hélène Royo
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Faculty of Sciences, University of Basel, 4058 Basel, Switzerland
| | - Konstantinos Anastassiadis
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - A Francis Stewart
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
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361
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Xhabija B, Kidder BL. KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Semin Cancer Biol 2018; 57:79-85. [PMID: 30448242 DOI: 10.1016/j.semcancer.2018.11.001] [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: 07/27/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling stem cell function and tumorigenesis. The histone lysine demethylase, KDM5B, which catalyzes the demethylation of histone 3 lysine 4 (H3K4), is important for embryonic stem (ES) cell differentiation, and is a critical regulator of the H3K4-methylome during early mouse embryonic pre-implantation stage development. KDM5B is also overexpressed, amplified, or mutated in many cancer types. In cancer cells, KDM5B regulates expression of oncogenes and tumor suppressors by modulating H3K4 methylation levels. In this review, we examine how KDM5B regulates gene expression and cellular fates of stem cells and cancer cells by temporally and spatially controlling H3K4 methylation levels.
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Affiliation(s)
- Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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362
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Yadav T, Quivy JP, Almouzni G. Chromatin plasticity: A versatile landscape that underlies cell fate and identity. Science 2018; 361:1332-1336. [PMID: 30262494 DOI: 10.1126/science.aat8950] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During development and throughout life, a variety of specialized cells must be generated to ensure the proper function of each tissue and organ. Chromatin plays a key role in determining cellular state, whether totipotent, pluripotent, multipotent, or differentiated. We highlight chromatin dynamics involved in the generation of pluripotent stem cells as well as their influence on cell fate decision and reprogramming. We focus on the capacity of histone variants, chaperones, modifications, and heterochromatin factors to influence cell identity and its plasticity. Recent technological advances have provided tools to elucidate the underlying chromatin dynamics for a better understanding of normal development and pathological conditions, with avenues for potential therapeutic application.
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Affiliation(s)
- Tejas Yadav
- Institut Curie, 75248 Paris Cedex 05, France
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363
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Wu C, Jiao Y, Shen M, Pan C, Cheng G, Jia D, Zhu J, Zhang L, Zheng M, Jia J. Clustering-local-unique-enriched-signals (CLUES) promotes identification of novel regulators of ES cell self-renewal and pluripotency. PLoS One 2018; 13:e0206844. [PMID: 30399165 PMCID: PMC6219791 DOI: 10.1371/journal.pone.0206844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/19/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Key regulators of developmental processes can be prioritized through integrated analysis of ChIP-Seq data of master transcriptional factors (TFs) such as Nanog and Oct4, active histone modifications (HMs) such as H3K4me3 and H3K27ac, and repressive HMs such as H3K27me3. Recent studies show that broad enrichment signals such as super-enhancers and broad H3K4me3 enrichment signals play more dominant roles than short enrichment signals of the master TFs and H3K4me3 in epigenetic regulatory mechanism. Besides the broad enrichment signals, up to ten thousands of short enrichment signals of these TFs and HMs exist in genome. Prioritization of these broad enrichment signals from ChIP-Seq data is a prerequisite for such integrated analysis. RESULTS Here, we present a method named Clustering-Local-Unique-Enriched-Signals (CLUES), which uses an adaptive-size-windows strategy to identify enriched regions (ERs) and cluster them into broad enrichment signals. Tested on 62 ENCODE ChIP-Seq datasets of Ctcf and Nrsf, CLUES performs equally well as MACS2 regarding prioritization of ERs with the TF's motif. Tested on 165 ENCODE ChIP-Seq datasets of H3K4me3, H3K27me3, and H3K36me3, CLUES performs better than existing algorithms on prioritizing broad enrichment signals implicating cell functions influenced by epigenetic regulatory mechanism in cells. Most importantly, CLUES helps to confirm several novel regulators of mouse ES cell self-renewal and pluripotency through integrated analysis of prioritized broad enrichment signals of H3K4me3, H3K27me3, Nanog and Oct4 with the support of a CRISPR/Cas9 negative selection genetic screen. CONCLUSIONS CLUES holds promise for prioritizing broad enrichment signals from ChIP-Seq data. The download site for CLUES is https://github.com/Wuchao1984/CLUESv1.
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Affiliation(s)
- Chao Wu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
- * E-mail: (MZ); (CW); (JJ)
| | - Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
| | - Manli Shen
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
| | - Chen Pan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
| | - Guo Cheng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
| | - Danmei Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
| | - Jing Zhu
- Beijing Ming-tian Genetics Ltd., Beijing, PRC
| | - Long Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
| | - Min Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, PRC
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, PRC
- * E-mail: (MZ); (CW); (JJ)
| | - Junling Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, PRC
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, PRC
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, PRC
- * E-mail: (MZ); (CW); (JJ)
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364
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Hwang YS, Seo M, Kim SK, Bang S, Kim H, Han JY. Zygotic gene activation in the chicken occurs in two waves, the first involving only maternally derived genes. eLife 2018; 7:39381. [PMID: 30375976 PMCID: PMC6242549 DOI: 10.7554/elife.39381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/29/2018] [Indexed: 12/11/2022] Open
Abstract
The first wave of transcriptional activation occurs after fertilisation in a species-specific pattern. Despite its importance to initial embryonic development, the characteristics of transcription following fertilisation are poorly understood in Aves. Here, we report detailed insights into the onset of genome activation in chickens. We established that two waves of transcriptional activation occurred, one shortly after fertilisation and another at Eyal-Giladi and Kochav Stage V. We found 1544 single nucleotide polymorphisms across 424 transcripts derived from parents that were expressed in offspring during the early embryonic stages. Surprisingly, only the maternal genome was activated in the zygote, and the paternal genome remained silent until the second-wave, regardless of the presence of a paternal pronucleus or supernumerary sperm in the egg. The identified maternal genes involved in cleavage that were replaced by bi-allelic expression. The results demonstrate that only maternal alleles are activated in the chicken zygote upon fertilisation, which could be essential for early embryogenesis and evolutionary outcomes in birds. The early stages of animal development involve a handover of genetic control. Initially, the egg cell is maintained by genetic information inherited from the mother, but soon after fertilization it starts to depend on its own genes instead. Activating genes inside the fertilized egg cell (zygote) so that they can take control of development is known as zygotic genome activation. Despite the fact that birds are often used to study how embryos develop, zygotic genome activation in birds is not well understood. Fertilization in birds, including chickens, is different to mammals in that it requires multiple sperm to fertilize an egg cell. As such, zygotic genome activation in birds is likely to differ from that in mammals. By examining gene expression in embryos from mixed-breed chickens, Hwang, Seo et al. showed that there are two stages of zygotic genome activation in chickens. The genes derived from the mother become active in the first stage, while genes from the father become active in the second stage. Genome activation in birds is therefore very different to the same process in mammals, which involves genome activation of both parents from the first stage. This extra level of control may help to prevent genetic complications resulting from the presence of multiple sperm, each of which carries a different set of genes from the father.
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Affiliation(s)
- Young Sun Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minseok Seo
- C&K Genomics, Seoul, Republic of Korea.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Sang Kyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | | | - Heebal Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,C&K Genomics, Seoul, Republic of Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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365
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Liu Y, Wu F, Zhang L, Wu X, Li D, Xin J, Xie J, Kong F, Wang W, Wu Q, Zhang D, Wang R, Gao S, Li W. Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing. BMC Genomics 2018; 19:734. [PMID: 30305014 PMCID: PMC6180508 DOI: 10.1186/s12864-018-5091-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/19/2018] [Indexed: 11/25/2022] Open
Abstract
Background Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their gene transcription profile. This technology is widely used in medicine, animal husbandry and other industries. However, certain deficiencies severely restrict the applications of this technology. Results Using single-embryo RNA-seq, our study provides complete transcriptome blueprints of embryos generated by cumulus cell (CC) donor nuclear transfer (NT), embryos generated by mouse embryonic fibroblast (MEF) donor NT and in vivo embryos at each stage (zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst). According to the results from further analyses, NT embryos exhibit RNA processing and translation initiation defects during the zygotic genome activation (ZGA) period, and protein kinase activity and protein phosphorylation are defective during blastocyst formation. Two thousand three constant genes are not able to be reprogrammed in CCs and MEFs. Among these constant genes, 136 genes are continuously mis-transcribed throughout all developmental stages. These 136 differential genes may be reprogramming barrier genes (RBGs) and more studies are needed to identify. Conclusions These embryonic transcriptome blueprints provide new data for further mechanistic studies of somatic nuclear reprogramming. These findings may improve the efficiency of somatic cell nuclear transfer. Electronic supplementary material The online version of this article (10.1186/s12864-018-5091-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong Liu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Fengrui Wu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Ling Zhang
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Xiaoqing Wu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Dengkun Li
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Jing Xin
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Juan Xie
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Feng Kong
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Wenying Wang
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Qiaoqin Wu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Di Zhang
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Rong Wang
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China
| | - Shaorong Gao
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Wenyong Li
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui Province, China.
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366
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Hug CB, Vaquerizas JM. The Birth of the 3D Genome during Early Embryonic Development. Trends Genet 2018; 34:903-914. [PMID: 30292539 DOI: 10.1016/j.tig.2018.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/23/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Abstract
The 3D structure of chromatin in the nucleus is important for the regulation of gene expression and the correct deployment of developmental programs. The differentiation of germ cells and early embryonic development (when the zygotic genome is activated and transcription is taking place for the first time) are accompanied by dramatic changes in gene expression and the epigenetic landscape. Recent studies used Hi-C to investigate the 3D chromatin organization during these developmental transitions, uncovering remarkable remodeling of the 3D genome. Here, we highlight the changes described so far and discuss some of the implications that these findings have for our understanding of the mechanisms and functionality of 3D chromatin architecture.
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Affiliation(s)
- Clemens B Hug
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany. https://twitter.com/vaquerizasjm
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367
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Nimble and Ready to Mingle: Transposon Outbursts of Early Development. Trends Genet 2018; 34:806-820. [DOI: 10.1016/j.tig.2018.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/19/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
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368
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Ladstätter S, Tachibana K. Genomic insights into chromatin reprogramming to totipotency in embryos. J Cell Biol 2018; 218:70-82. [PMID: 30257850 PMCID: PMC6314560 DOI: 10.1083/jcb.201807044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
Ladstätter and Tachibana discuss changes in DNA methylation, chromatin accessibility, and topological architecture occurring during the reprogramming to totipotency in the early embryo. The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.
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Affiliation(s)
- Sabrina Ladstätter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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369
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Abstract
Epigenetic mechanisms allow the establishment and maintenance of multiple cellular phenotypes from a single genomic code. At the initiation of development, the oocyte and spermatozoa provide their fully differentiated chromatin that soon after fertilization undergo extensive remodeling, resulting in a totipotent state that can then drive cellular differentiation towards all cell types. These remodeling involves different epigenetic modifications, including DNA methylation, post-translational modifications of histones, non-coding RNAs, and large-scale chromatin conformation changes. Moreover, epigenetic remodeling is responsible for reprogramming somatic cells to totipotency upon somatic cell nuclear transfer/cloning, which is often incomplete and inefficient. Given that environmental factors, such as assisted reproductive techniques (ARTs), can affect epigenetic remodeling, there is interest in understanding the mechanisms driving these changes. We describe and discuss our current understanding of mechanisms responsible for the epigenetic remodeling that ensues during preimplantation development of mammals, presenting findings from studies of mouse embryos and when available comparing them to what is known for human and cattle embryos.
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Affiliation(s)
- Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Rafael V Sampaio
- Department of Animal Science, University of California Davis, Davis, CA, United States.,Department of Animal Science, University of California Davis, Davis, CA, United States
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370
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Hanna CW, Demond H, Kelsey G. Epigenetic regulation in development: is the mouse a good model for the human? Hum Reprod Update 2018; 24:556-576. [PMID: 29992283 PMCID: PMC6093373 DOI: 10.1093/humupd/dmy021] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/20/2018] [Accepted: 06/05/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Over the past few years, advances in molecular technologies have allowed unprecedented mapping of epigenetic modifications in gametes and during early embryonic development. This work is allowing a detailed genomic analysis, which for the first time can answer long-standing questions about epigenetic regulation and reprogramming, and highlights differences between mouse and human, the implications of which are only beginning to be explored. OBJECTIVE AND RATIONALE In this review, we summarise new low-cell molecular methods enabling the interrogation of epigenetic information in gametes and early embryos, the mechanistic insights these have provided, and contrast the findings in mouse and human. SEARCH METHODS Relevant studies were identified by PubMed search. OUTCOMES We discuss the levels of epigenetic regulation, from DNA modifications to chromatin organisation, during mouse gametogenesis, fertilisation and pre- and post-implantation development. The recently characterised features of the oocyte epigenome highlight its exceptionally unique regulatory landscape. The chromatin organisation and epigenetic landscape of both gametic genomes are rapidly reprogrammed after fertilisation. This extensive epigenetic remodelling is necessary for zygotic genome activation, but the mechanistic link remains unclear. While the vast majority of epigenetic information from the gametes is erased in pre-implantation development, new insights suggest that repressive histone modifications from the oocyte may mediate a novel mechanism of imprinting. To date, the characterisation of epigenetics in human development has been almost exclusively limited to DNA methylation profiling; these data reinforce that the global dynamics are conserved between mouse and human. However, as we look closer, it is becoming apparent that the mechanisms regulating these dynamics are distinct. These early findings emphasise the importance of investigations of fundamental epigenetic mechanisms in both mouse and humans. WIDER IMPLICATIONS Failures in epigenetic regulation have been implicated in human disease and infertility. With increasing maternal age and use of reproductive technologies in countries all over the world, it is becoming ever more important to understand the necessary processes required to establish a developmentally competent embryo. Furthermore, it is essential to evaluate the extent to which these epigenetic patterns are sensitive to such technologies and other adverse environmental exposures.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Hannah Demond
- Epigenetics programme, Babraham Institute, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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371
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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: 48] [Impact Index Per Article: 8.0] [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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372
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Wu F, Liu Y, Wu Q, Li D, Zhang L, Wu X, Wang R, Zhang D, Gao S, Li W. Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos. BMC Genomics 2018; 19:631. [PMID: 30139326 PMCID: PMC6107955 DOI: 10.1186/s12864-018-5021-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/15/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modification disorders. The most dramatic epigenetic reprogramming event occurs during somatic cell nuclear transfer (SCNT) when the expression profile of a differentiated cell is abolished, and a newly embryo-specific expression profile is established. However, the molecular mechanism underlying somatic reprogramming remains unclear, and the dynamics and functions of lncRNAs in this process have not yet been illustrated, resulting in inefficient reprogramming. RESULTS In this study, 63 single-cell RNA-seq libraries were first generated and sequenced. A total of 7009 mouse polyadenylation lncRNAs (including 5204 novel lncRNAs) were obtained, and a comprehensive analysis of in vivo and SCNT mouse pre-implantation embryo lncRNAs was further performed based on our single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs were expressed in a developmental stage-specific manner during mouse early-stage embryonic development, whereas a more temporal and spatially specific expression pattern was identified in mouse SCNT embryos with changes in the state of chromatin during somatic cell reprogramming, leading to incomplete zygotic genome activation, oocyte to embryo transition and 2-cell to 4-cell transition. No obvious differences between other stages and mouse NTC or NTM embryos at the same stage were observed. Gene oncology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and weighted gene co-expression network analysis (WGCNA) of lncRNAs and their association with known protein-coding genes suggested that several lncRNAs and their associated with known protein-coding genes might be involved in mouse embryonic development and cell reprogramming. CONCLUSIONS This is a novel report on the expression landscapes of lncRNAs of mouse NT embryos by scRNA-seq analysis. This study will provide insight into the molecular mechanism underlying the involvement of lncRNAs in mouse pre-implantation embryonic development and epigenetic reprogramming in mammalian species after SCNT-based cloning.
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Affiliation(s)
- Fengrui Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Yong Liu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Qingqing Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Dengkun Li
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Ling Zhang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Xiaoqing Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Rong Wang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Di Zhang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenyong Li
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
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373
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Brind'Amour J, Kobayashi H, Richard Albert J, Shirane K, Sakashita A, Kamio A, Bogutz A, Koike T, Karimi MM, Lefebvre L, Kono T, Lorincz MC. LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat Commun 2018; 9:3331. [PMID: 30127397 PMCID: PMC6102241 DOI: 10.1038/s41467-018-05841-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/26/2018] [Indexed: 12/29/2022] Open
Abstract
De novo DNA methylation (DNAme) during mouse oogenesis occurs within transcribed regions enriched for H3K36me3. As many oocyte transcripts originate in long terminal repeats (LTRs), which are heterogeneous even between closely related mammals, we examined whether species-specific LTR-initiated transcription units (LITs) shape the oocyte methylome. Here we identify thousands of syntenic regions in mouse, rat, and human that show divergent DNAme associated with private LITs, many of which initiate in lineage-specific LTR retrotransposons. Furthermore, CpG island (CGI) promoters methylated in mouse and/or rat, but not human oocytes, are embedded within rodent-specific LITs and vice versa. Notably, at a subset of such CGI promoters, DNAme persists on the maternal genome in fertilized and parthenogenetic mouse blastocysts or in human placenta, indicative of species-specific epigenetic inheritance. Polymorphic LITs are also responsible for disparate DNAme at promoter CGIs in distantly related mouse strains, revealing that LITs also promote intra-species divergence in CGI DNAme.
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Affiliation(s)
- Julie Brind'Amour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.
| | - Julien Richard Albert
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kenjiro Shirane
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Akihiko Sakashita
- Department of BioScience, Tokyo University of Agriculture, Tokyo, 113-0033, Japan
- Division of Reproductive Sciences, Cincinnati's Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Asuka Kamio
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Aaron Bogutz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tasuku Koike
- Department of BioScience, Tokyo University of Agriculture, Tokyo, 113-0033, Japan
| | - Mohammad M Karimi
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- MRC London Institute of Medical Sciences, Imperial College, London, W12 0NN, UK
| | - Louis Lefebvre
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tomohiro Kono
- Department of BioScience, Tokyo University of Agriculture, Tokyo, 113-0033, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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374
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Zhang YL, Zhao LW, Zhang J, Le R, Ji SY, Chen C, Gao Y, Li D, Gao S, Fan HY. DCAF13 promotes pluripotency by negatively regulating SUV39H1 stability during early embryonic development. EMBO J 2018; 37:embj.201898981. [PMID: 30111536 DOI: 10.15252/embj.201898981] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/07/2018] [Accepted: 07/23/2018] [Indexed: 01/15/2023] Open
Abstract
Mammalian oocytes and zygotes have the unique ability to reprogram a somatic cell nucleus into a totipotent state. SUV39H1/2-mediated histone H3 lysine-9 trimethylation (H3K9me3) is a major barrier to efficient reprogramming. How SUV39H1/2 activities are regulated in early embryos and during generation of induced pluripotent stem cells (iPSCs) remains unclear. Since expression of the CRL4 E3 ubiquitin ligase in oocytes is crucial for female fertility, we analyzed putative CRL4 adaptors (DCAFs) and identified DCAF13 as a novel CRL4 adaptor that is essential for preimplantation embryonic development. Dcaf13 is expressed from eight-cell to morula stages in both murine and human embryos, and Dcaf13 knockout in mice causes preimplantation-stage mortality. Dcaf13 knockout embryos are arrested at the eight- to sixteen-cell stage before compaction, and this arrest is accompanied by high levels of H3K9me3. Mechanistically, CRL4-DCAF13 targets SUV39H1 for polyubiquitination and proteasomal degradation and therefore facilitates H3K9me3 removal and zygotic gene expression. Taken together, CRL4-DCAF13-mediated SUV39H1 degradation is an essential step for progressive genome reprogramming during preimplantation embryonic development.
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Affiliation(s)
- Yin-Li Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, China.,Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Long-Wen Zhao
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jue Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shu-Yan Ji
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chuan Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, China
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375
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Abe KI, Funaya S, Tsukioka D, Kawamura M, Suzuki Y, Suzuki MG, Schultz RM, Aoki F. Minor zygotic gene activation is essential for mouse preimplantation development. Proc Natl Acad Sci U S A 2018; 115:E6780-E6788. [PMID: 29967139 PMCID: PMC6055165 DOI: 10.1073/pnas.1804309115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mice, transcription initiates at the mid-one-cell stage and transcriptional activity dramatically increases during the two-cell stage, a process called zygotic gene activation (ZGA). Associated with ZGA is a marked change in the pattern of gene expression that occurs after the second round of DNA replication. To distinguish ZGA before and after the second-round DNA replication, the former and latter are called minor and major ZGA, respectively. Although major ZGA are required for development beyond the two-cell stage, the function of minor ZGA is not well understood. Transiently inhibiting minor ZGA with 5, 6-dichloro-1-β-d-ribofuranosyl-benzimidazole (DRB) resulted in the majority of embryos arresting at the two-cell stage and retention of the H3K4me3 mark that normally decreases. After release from DRB, at which time major ZGA normally occurred, transcription initiated with characteristics of minor ZGA but not major ZGA, although degradation of maternal mRNA normally occurred. Thus, ZGA occurs sequentially starting with minor ZGA that is critical for the maternal-to-zygotic transition.
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Affiliation(s)
- Ken-Ichiro Abe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Dai Tsukioka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 277-0882 Kashiwa, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 277-8562 Kashiwa, Japan;
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376
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Gestational exposure to chlordecone promotes transgenerational changes in the murine reproductive system of males. Sci Rep 2018; 8:10274. [PMID: 29980752 PMCID: PMC6035262 DOI: 10.1038/s41598-018-28670-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/27/2018] [Indexed: 12/14/2022] Open
Abstract
Environmental factors can affect epigenetic events during germline reprogramming and impose distinctive transgenerational consequences onto the offspring. In this study, we examined the transgenerational effects of chlordecone (CD), an organochlorine insecticide with well-known estrogenic properties. We exposed pregnant mice to CD from embryonic day 6.5 to 15.5 and observed a reduction in spermatogonia (SG) numbers in F3, meiotic defects in spermatocytes and decrease in spermatozoa number in the first and third generation of male progeny. The RNA qRT-PCR expression analysis in F1 and transcriptomics analysis in F3 males using the whole testes revealed changes in the expression of genes associated with chromosome segregation, cell division and DNA repair. The expression of the master regulator of pluripotency, Pou5f1, decreased in foetal and increased in adult F1, but not in F3 adult testes. Analysis of histone H3K4me3 distribution revealed widespread changes in its occupancy in the genome of F1 and F3 generations. We established that 7.1% of altered epigenetic marks were conserved between F1 and F3 generations. The overlapping changes common to F1 and F3 include genes implicated in cell adhesion and transcription factor activities functions. Differential peaks observed in F1 males are significantly enriched in predicted ESR1 binding sites, some of which we confirmed to be functional. Our data demonstrate that CD-mediated impairment of reproductive functions could be transmitted to subsequent generations.
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377
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Zhao T, Fu Y, Zhu J, Liu Y, Zhang Q, Yi Z, Chen S, Jiao Z, Xu X, Xu J, Duo S, Bai Y, Tang C, Li C, Deng H. Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming. Cell Stem Cell 2018; 23:31-45.e7. [PMID: 29937202 DOI: 10.1016/j.stem.2018.05.025] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/20/2018] [Accepted: 05/23/2018] [Indexed: 12/31/2022]
Abstract
Chemical reprogramming provides a powerful platform for exploring the molecular dynamics that lead to pluripotency. Although previous studies have uncovered an intermediate extraembryonic endoderm (XEN)-like state during this process, the molecular underpinnings of pluripotency acquisition remain largely undefined. Here, we profile 36,199 single-cell transcriptomes at multiple time points throughout a highly efficient chemical reprogramming system using RNA-sequencing and reconstruct their progression trajectories. Through identifying sequential molecular events, we reveal that the dynamic early embryonic-like programs are key aspects of successful reprogramming from XEN-like state to pluripotency, including the concomitant transcriptomic signatures of two-cell (2C) embryonic-like and early pluripotency programs and the epigenetic signature of notable genome-wide DNA demethylation. Moreover, via enhancing the 2C-like program by fine-tuning chemical treatment, the reprogramming process is remarkably accelerated. Collectively, our findings offer a high-resolution dissection of cell fate dynamics during chemical reprogramming and shed light on mechanistic insights into the nature of induced pluripotency.
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Affiliation(s)
- Ting Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yao Fu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Jialiang Zhu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Yifang Liu
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qian Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies and School of Life Sciences, Center for Statistical Science and Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Zexuan Yi
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shi Chen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing 100083, China
| | - Zhonggang Jiao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaochan Xu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junquan Xu
- CapitalBio Technology Corporation, Beijing 102206, China
| | - Shuguang Duo
- Institute of Zoology, Chinese Academy Sciences, Beijing 100101, China
| | - Yun Bai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing 100083, China
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies and School of Life Sciences, Center for Statistical Science and Center for Bioinformatics, Peking University, Beijing 100871, China.
| | - Hongkui Deng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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378
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Li L, Guo F, Gao Y, Ren Y, Yuan P, Yan L, Li R, Lian Y, Li J, Hu B, Gao J, Wen L, Tang F, Qiao J. Single-cell multi-omics sequencing of human early embryos. Nat Cell Biol 2018; 20:847-858. [DOI: 10.1038/s41556-018-0123-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 05/16/2018] [Indexed: 11/09/2022]
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379
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Richard Albert J, Koike T, Younesy H, Thompson R, Bogutz AB, Karimi MM, Lorincz MC. Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). BMC Genomics 2018; 19:463. [PMID: 29907088 PMCID: PMC6003194 DOI: 10.1186/s12864-018-4835-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling imprinted genes are associated with DNA methylation (DNAme) and specific histone modifications, the interplay between transcription and these epigenetic marks at allelic resolution is typically not investigated genome-wide due to a lack of bioinformatic packages that can process and integrate multiple epigenomic datasets with allelic resolution. In addition, existing ad-hoc software only consider SNVs for allele-specific read discovery. This limitation omits potentially informative INDELs, which constitute about one fifth of the number of SNVs in mice, and introduces a systematic reference bias in allele-specific analyses. RESULTS Here, we describe MEA, an INDEL-aware Methylomic and Epigenomic Allele-specific analysis pipeline which enables user-friendly data exploration, visualization and interpretation of allelic imbalance. Applying MEA to mouse embryonic datasets yields robust allele-specific DNAme maps and low reference bias. We validate allele-specific DNAme at known differentially methylated regions and show that automated integration of such methylation data with RNA- and ChIP-seq datasets yields an intuitive, multidimensional view of allelic gene regulation. MEA uncovers numerous novel dynamically methylated loci, highlighting the sensitivity of our pipeline. Furthermore, processing and visualization of epigenomic datasets from human brain reveals the expected allele-specific enrichment of H3K27ac and DNAme at imprinted as well as novel monoallelically expressed genes, highlighting MEA's utility for integrating human datasets of distinct provenance for genome-wide analysis of allelic phenomena. CONCLUSIONS Our novel pipeline for standardized allele-specific processing and visualization of disparate epigenomic and methylomic datasets enables rapid analysis and navigation with allelic resolution. MEA is freely available as a Docker container at https://github.com/julienrichardalbert/MEA .
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Affiliation(s)
- Julien Richard Albert
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Tasuku Koike
- Department of BioScience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Hamid Younesy
- Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.,Biomedical Research Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Richard Thompson
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Aaron B Bogutz
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Mohammad M Karimi
- MRC London Institute of Medical Sciences, Imperial College, London, UK.
| | - Matthew C Lorincz
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
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380
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Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res 2018; 28:998-1007. [PMID: 29844026 PMCID: PMC6028135 DOI: 10.1101/gr.228833.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 05/23/2018] [Indexed: 12/22/2022]
Abstract
For animals, epigenetic modifications can be globally or partially inherited from gametes after fertilization, and such information is required for proper transcriptional regulation, especially during the process of zygotic genome activation (ZGA). However, the mechanism underlying how the inherited epigenetic signatures affect transcriptional regulation during ZGA remains poorly understood. Here, we performed genome-wide profiling of chromatin accessibility during zebrafish ZGA, which is closely related to zygotic transcriptional regulation. We observed a clear trend toward a gradual increase in accessible chromatin during ZGA. Furthermore, accessible chromatin at the promoters displayed a sequential priority of emergence, and the locations of the accessible chromatin were precisely primed by the enrichment of unmethylated CpGs that were fully inherited from gametes. On the other hand, distal regions with high methylation levels that were inherited from the sperm facilitated the binding of DNA methylation-preferred transcription factors, such as Pou5f3 and Nanog, which contributed to the establishment of accessible chromatin at these loci. Our results demonstrate a model whereby inherited DNA methylation signatures from gametes prime the establishment of accessible chromatin during zebrafish ZGA through two distinct mechanisms.
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381
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Dai Z, Mentch SJ, Gao X, Nichenametla SN, Locasale JW. Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width. Nat Commun 2018; 9:1955. [PMID: 29769529 PMCID: PMC5955993 DOI: 10.1038/s41467-018-04426-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/27/2018] [Indexed: 01/07/2023] Open
Abstract
Nutrition and metabolism are known to influence chromatin biology and epigenetics through post-translational modifications, yet how this interaction influences genomic architecture and connects to gene expression is unknown. Here we consider, as a model, the metabolically-driven dynamics of H3K4me3, a histone methylation mark that is known to encode information about active transcription, cell identity, and tumor suppression. We analyze the genome-wide changes in H3K4me3 and gene expression in response to alterations in methionine availability in both normal mouse physiology and human cancer cells. Surprisingly, we find that the location of H3K4me3 peaks is largely preserved under methionine restriction, while the response of H3K4me3 peak width encodes almost all aspects of H3K4me3 biology including changes in expression levels, and the presence of cell identity and cancer-associated genes. These findings may reveal general principles for how nutrient availability modulates specific aspects of chromatin dynamics to mediate biological function.
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Affiliation(s)
- Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Samantha J Mentch
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xia Gao
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | | | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
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382
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Sado T. What makes the maternal X chromosome resistant to undergoing imprinted X inactivation? Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0365. [PMID: 28947661 DOI: 10.1098/rstb.2016.0365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 11/12/2022] Open
Abstract
In the mouse, while either X chromosome is chosen for inactivation in a random fashion in the embryonic tissue, the paternally derived X chromosome is preferentially inactivated in the extraembryonic tissues. It has been shown that the maternal X chromosome is imprinted so as not to undergo inactivation in the extraembryonic tissues. X-linked noncoding Xist RNA becomes upregulated on the X chromosome that is to be inactivated. An antisense noncoding RNA, Tsix, which occurs at the Xist locus and has been shown to negatively regulate Xist expression in cis, is imprinted to be expressed from the maternal X in the extraembryonic tissues. Although Tsix appears to be responsible for the imprint laid on the maternal X, those who disagree with this idea would point out the fact that Tsix has not yet been expressed from the maternal X when Xist becomes upregulated on the paternal but not the maternal X at the onset of imprinted X-inactivation in preimplantation embryos. Recent studies have demonstrated, however, that there is a prominent difference in the chromatin structure at the Xist locus depending on the parental origin, which I suggest might account for the repression of maternal Xist in the absence of maternal Tsix at the preimplantation stages.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Takashi Sado
- Department of Bioscience, Graduate School of Agriculture, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan
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383
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Zylicz JJ, Borensztein M, Wong FC, Huang Y, Lee C, Dietmann S, Surani MA. G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst. eLife 2018; 7:33361. [PMID: 29745895 PMCID: PMC5959720 DOI: 10.7554/elife.33361] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/09/2018] [Indexed: 01/14/2023] Open
Abstract
Early mouse development is regulated and accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2). Previously, we provided insights into its role in post-implantation development (Zylicz et al., 2015). Here we explore the impact of depleting the maternally inherited G9a in oocytes on development shortly after fertilisation. We show that G9a accumulates typically at 4 to 8 cell stage to promote timely repression of a subset of 4 cell stage-specific genes. Loss of maternal inheritance of G9a disrupts the gene regulatory network resulting in developmental delay and destabilisation of inner cell mass lineages by the late blastocyst stage. Our results indicate a vital role of this maternally inherited epigenetic regulator in creating conducive conditions for developmental progression and on cell fate choices.
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Affiliation(s)
- Jan J Zylicz
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Maud Borensztein
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Frederick Ck Wong
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Yun Huang
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Lee
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Sabine Dietmann
- Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - M Azim Surani
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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384
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Wu J, Xu J, Liu B, Yao G, Wang P, Lin Z, Huang B, Wang X, Li T, Shi S, Zhang N, Duan F, Ming J, Zhang X, Niu W, Song W, Jin H, Guo Y, Dai S, Hu L, Fang L, Wang Q, Li Y, Li W, Na J, Xie W, Sun Y. Chromatin analysis in human early development reveals epigenetic transition during ZGA. Nature 2018; 557:256-260. [DOI: 10.1038/s41586-018-0080-8] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/26/2018] [Indexed: 12/29/2022]
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385
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Liu C, Ma Y, Shang Y, Huo R, Li W. Post-translational regulation of the maternal-to-zygotic transition. Cell Mol Life Sci 2018; 75:1707-1722. [PMID: 29427077 PMCID: PMC11105290 DOI: 10.1007/s00018-018-2750-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/24/2017] [Accepted: 01/08/2018] [Indexed: 02/07/2023]
Abstract
The maternal-to-zygotic transition (MZT) is essential for the developmental control handed from maternal products to newly synthesized zygotic genome in the earliest stages of embryogenesis, including maternal component (mRNAs and proteins) degradation and zygotic genome activation (ZGA). Various protein post-translational modifications have been identified during the MZT, such as phosphorylation, methylation and ubiquitination. Precise post-translational regulation mechanisms are essential for the timely transition of early embryonic development. In this review, we summarize recent progress regarding the molecular mechanisms underlying post-translational regulation of maternal component degradation and ZGA during the MZT and discuss some important issues in the field.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Department of Animal Science and Technology, Northeast Agricultural University, Haerbin, 150030, People's Republic of China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029, People's Republic of China.
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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386
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Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol 2018; 20:620-631. [DOI: 10.1038/s41556-018-0093-4] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 03/21/2018] [Indexed: 12/24/2022]
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387
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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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388
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Ebmeier CC, Erickson B, Allen BL, Allen MA, Kim H, Fong N, Jacobsen JR, Liang K, Shilatifard A, Dowell RD, Old WM, Bentley DL, Taatjes DJ. Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications. Cell Rep 2018; 20:1173-1186. [PMID: 28768201 DOI: 10.1016/j.celrep.2017.07.021] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 01/24/2023] Open
Abstract
CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3' ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5' ends and H3K36me3 was displaced toward gene 3' ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent "CTD code" that regulates chromatin marks in addition to RNA processing and pol II pausing.
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Affiliation(s)
- Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA; Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Benjamin Erickson
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Benjamin L Allen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hyunmin Kim
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Nova Fong
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jeremy R Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Kaiwei Liang
- Department of Biochemistry & Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry & Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Robin D Dowell
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - William M Old
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David L Bentley
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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389
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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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390
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Terranova C, Tang M, Orouji E, Maitituoheti M, Raman A, Amin S, Liu Z, Rai K. An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues. J Vis Exp 2018. [PMID: 29683440 DOI: 10.3791/56972] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Histone modifications constitute a major component of the epigenome and play important regulatory roles in determining the transcriptional status of associated loci. In addition, the presence of specific modifications has been used to determine the position and identity non-coding functional elements such as enhancers. In recent years, chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) has become a powerful tool in determining the genome-wide profiles of individual histone modifications. However, it has become increasingly clear that the combinatorial patterns of chromatin modifications, referred to as Chromatin States, determine the identity and nature of the associated genomic locus. Therefore, workflows consisting of robust high-throughput (HT) methodologies for profiling a number of histone modification marks, as well as computational analyses pipelines capable of handling myriads of ChIP-Seq profiling datasets, are needed for comprehensive determination of epigenomic states in large number of samples. The HT-ChIP-Seq workflow presented here consists of two modules: 1) an experimental protocol for profiling several histone modifications from small amounts of tumor samples and cell lines in a 96-well format; and 2) a computational data analysis pipeline that combines existing tools to compute both individual mark occupancy and combinatorial chromatin state patterns. Together, these two modules facilitate easy processing of hundreds of ChIP-Seq samples in a fast and efficient manner. The workflow presented here is used to derive chromatin state patterns from 6 histone mark profiles in melanoma tumors and cell lines. Overall, we present a comprehensive ChIP-seq workflow that can be applied to dozens of human tumor samples and cancer cell lines to determine epigenomic aberrations in various malignancies.
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Affiliation(s)
| | - Ming Tang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center
| | - Elias Orouji
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center
| | | | - Ayush Raman
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center
| | | | - Zhiyi Liu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center;
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391
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Ding B, Cao Z, Hong R, Li H, Zuo X, Luo L, Li Y, Huang W, Li W, Zhang K, Zhang Y. WDR5 in porcine preimplantation embryos: expression, regulation of epigenetic modifications and requirement for early development†. Biol Reprod 2018; 96:758-771. [PMID: 28379447 DOI: 10.1093/biolre/iox020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/29/2017] [Indexed: 11/12/2022] Open
Abstract
WD repeat-containing protein 5 (WDR5), a member of conserved WD40 protein family, is an essential component of the mixed lineage leukemia (MLL) complexes, which are crucial for numerous key biological processes including methylation of histone H3 lysine 4 (H3K4), self-renewal of embryonic stem cells, and formation of induced pluripotent stem cells. The expression pattern and functional role of WDR5 during porcine preimplantation embryonic development, however, remain unknown. Our results showed that the transcripts and protein of WDR5 exhibited stage-specific expression pattern in porcine early embryos. Moreover, blastocyst rate and total cell number per blastocyst were reduced by RNAi-mediated silencing of WDR5 or pharmacological inhibition of WDR5. Knockdown of WDR5 also disturbed the expression of several pluripotency genes. Interestingly, tri-methylation of H3K4 (H3K4me3) level was dramatically increased by WDR5 depletion. Further analysis revealed that loss of MLL3 phenocopied WDR5 knockdown, triggering increased H3K4me3 level. Simultaneously, WDR5 depletion significantly decreased the levels of histone H4 lysine 16 acetylation (H4K16ac) and its writer males absent on the first (MOF). Last but not least, WDR5 knockdown induced DNA damage and DNA repair defects during porcine preimplantation development. Taken together, results of described studies establish that WDR5 plays a significant role in porcine preimplantation embryos probably through regulating key epigenetic modifications and genome integrity.
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Affiliation(s)
- Biao Ding
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Key Laboratory of Embryo Development and Reproduction Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui, China
| | - Zubing Cao
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Renyun Hong
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Hui Li
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaoyuan Zuo
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Lei Luo
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Yunsheng Li
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Weiping Huang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Wenyong Li
- Key Laboratory of Embryo Development and Reproduction Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yunhai Zhang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
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392
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Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, Yi L, Yu G, Hou Z, Fan D, Tian Y, Liu J, Chen ZJ, Liu J. Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. Cell 2018. [PMID: 29526463 DOI: 10.1016/j.cell.2018.02.028] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamics of the chromatin regulatory landscape during human early embryogenesis remains unknown. Using DNase I hypersensitive site (DHS) sequencing, we report that the chromatin accessibility landscape is gradually established during human early embryogenesis. Interestingly, the DHSs with OCT4 binding motifs are enriched at the timing of zygotic genome activation (ZGA) in humans, but not in mice. Consistently, OCT4 contributes to ZGA in humans, but not in mice. We further find that lower CpG promoters usually establish DHSs at later stages. Similarly, younger genes tend to establish promoter DHSs and are expressed at later embryonic stages, while older genes exhibit these features at earlier stages. Moreover, our data show that human active transposons SVA and HERV-K harbor DHSs and are highly expressed in early embryos, but not in differentiated tissues. In summary, our data provide an evolutionary developmental view for understanding the regulation of gene and transposon expression.
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Affiliation(s)
- Lei Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenbo Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xuelong Yao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Lizhi Yi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Guanling Yu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Dongdong Fan
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yong Tian
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianqiao Liu
- Center for Reproductive Medicine, Third Affiliated Hospital, Guangzhou Medical University, 510150 Guangzhou, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China.
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, 100049 Beijing, China.
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393
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Zhang J, Zhao J, Dahan P, Lu V, Zhang C, Li H, Teitell MA. Metabolism in Pluripotent Stem Cells and Early Mammalian Development. Cell Metab 2018; 27:332-338. [PMID: 29414683 DOI: 10.1016/j.cmet.2018.01.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Emerging and seminal studies have shown that cell metabolism influences gene expression by modifying the epigenome, which can regulate stem cell pluripotency, differentiation, and somatic cell reprogramming. Core pluripotency factors and developmental regulators reciprocally control the expression of key metabolism genes and their encoded pathways. Recent technological advances enabling sensitive detection methods during early mammalian development revealed the state-specific and context-dependent coordination of signal transduction, histone modifications, and gene expression in developing, resting, and malnourished embryos. Here, we discuss metabolism as a potential driver of earliest cell fate through its influence on the epigenome and gene expression in embryos and their in vitro surrogate pluripotent stem cells.
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Affiliation(s)
- Jin Zhang
- The First Affiliated Hospital and Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Jing Zhao
- The First Affiliated Hospital and Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Perrine Dahan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Vivian Lu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cheng Zhang
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael A Teitell
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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394
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Dumdie JN, Cho K, Ramaiah M, Skarbrevik D, Mora-Castilla S, Stumpo DJ, Lykke-Andersen J, Laurent LC, Blackshear PJ, Wilkinson MF, Cook-Andersen H. Chromatin Modification and Global Transcriptional Silencing in the Oocyte Mediated by the mRNA Decay Activator ZFP36L2. Dev Cell 2018; 44:392-402.e7. [PMID: 29408237 DOI: 10.1016/j.devcel.2018.01.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 06/21/2017] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
Global transcriptional silencing is a highly conserved mechanism central to the oocyte-to-embryo transition. We report the unexpected discovery that global transcriptional silencing in oocytes depends on an mRNA decay activator. Oocyte-specific loss of ZFP36L2 an RNA-binding protein that promotes AU-rich element-dependent mRNA decay prevents global transcriptional silencing and causes oocyte maturation and fertilization defects, as well as complete female infertility in the mouse. Single-cell RNA sequencing revealed that ZFP36L2 downregulates mRNAs encoding transcription and chromatin modification regulators, including a large group of mRNAs for histone demethylases targeting H3K4 and H3K9, which we show are bound and degraded by ZFP36L2. Oocytes lacking Zfp36l2 fail to accumulate histone methylation at H3K4 and H3K9, marks associated with the transcriptionally silent, developmentally competent oocyte state. Our results uncover a ZFP36L2-dependent mRNA decay mechanism that acts as a developmental switch during oocyte growth, triggering wide-spread shifts in chromatin modification and global transcription.
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Affiliation(s)
- Jennifer N Dumdie
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyucheol Cho
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Skarbrevik
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Deborah J Stumpo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Louise C Laurent
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, NC 27703, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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395
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Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming. Cell 2018; 172:993-1006.e13. [DOI: 10.1016/j.cell.2018.01.022] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 11/28/2017] [Accepted: 01/10/2018] [Indexed: 11/16/2022]
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396
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Chokeshaiusaha K, Puthier D, Nguyen C, Sananmuang T. A demonstration of the H3 trimethylation ChIP-seq analysis of galline follicular mesenchymal cells and male germ cells. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:791-797. [PMID: 29381903 PMCID: PMC5933975 DOI: 10.5713/ajas.17.0744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/23/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Trimethylation of histone 3 (H3) at 4th lysine N-termini (H3K4me3) in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of trimethylation at 27th lysine (H3K27me3) in the same loci-the bivalent H3K4m3/H3K27me3 was known to suspend the gene transcription in germ cells, and could also be inherited to the developed stem cell. In galline species, throughout example of H3K4m3 and H3K27me3 ChIP-seq analysis was still not provided. We therefore designed and demonstrated such procedures using ChIP-seq and mRNA-seq data of chicken follicular mesenchymal cells and male germ cells. METHODS Analytical workflow was designed and provided in this study. ChIP-seq and RNA-seq datasets of follicular mesenchymal cells and male germ cells were acquired and properly preprocessed. Peak calling by Model-based analysis of ChIP-seq 2 was performed to identify H3K4m3 or H3K27me3 enriched regions (Fold-change≥2, FDR≤0.01) in gene promoter regions. Integrative genomics viewer was utilized for cellular retinoic acid binding protein 1 (CRABP1), growth differentiation factor 10 (GDF10), and gremlin 1 (GREM1) gene explorations. RESULTS The acquired results indicated that follicular mesenchymal cells and germ cells shared several unique gene promoter regions enriched with H3K4me3 (5,704 peaks) and also unique regions of bivalent H3K4m3/H3K27me3 shared between all cell types and germ cells (1,909 peaks). Subsequent observation of follicular mesenchyme-specific genes-CRABP1, GDF10, and GREM1 correctly revealed vigorous transcriptions of these genes in follicular mesenchymal cells. As expected, bivalent H3K4m3/H3K27me3 pattern was manifested in gene promoter regions of germ cells, and thus suspended their transcriptions. CONCLUSION According the results, an example of chicken H3K4m3/H3K27me3 ChIP-seq data analysis was successfully demonstrated in this study. Hopefully, the provided methodology should hereby be useful for galline ChIP-seq data analysis in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK 43 Moo 6 Bangpra, Sriracha Chonburi 20110, Thailand
| | - Denis Puthier
- Laboratoire TAGC/INSERM U1090, Parc Scientifique de Luminy case 928, 163, avenue de Luminy, Marseille cedex 09 13288, France
| | - Catherine Nguyen
- Laboratoire TAGC/INSERM U1090, Parc Scientifique de Luminy case 928, 163, avenue de Luminy, Marseille cedex 09 13288, France
| | - Thanida Sananmuang
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK 43 Moo 6 Bangpra, Sriracha Chonburi 20110, Thailand
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397
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Kong Q, Banaszynski LA, Geng F, Zhang X, Zhang J, Zhang H, O'Neill CL, Yan P, Liu Z, Shido K, Palermo GD, Allis CD, Rafii S, Rosenwaks Z, Wen D. Histone variant H3.3-mediated chromatin remodeling is essential for paternal genome activation in mouse preimplantation embryos. J Biol Chem 2018; 293:3829-3838. [PMID: 29358330 DOI: 10.1074/jbc.ra117.001150] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/02/2018] [Indexed: 12/22/2022] Open
Abstract
Derepression of chromatin-mediated transcriptional repression of paternal and maternal genomes is considered the first major step that initiates zygotic gene expression after fertilization. The histone variant H3.3 is present in both male and female gametes and is thought to be important for remodeling the paternal and maternal genomes for activation during both fertilization and embryogenesis. However, the underlying mechanisms remain poorly understood. Using our H3.3B-HA-tagged mouse model, engineered to report H3.3 expression in live animals and to distinguish different sources of H3.3 protein in embryos, we show here that sperm-derived H3.3 (sH3.3) protein is removed from the sperm genome shortly after fertilization and extruded from the zygotes via the second polar bodies (PBII) during embryogenesis. We also found that the maternal H3.3 (mH3.3) protein is incorporated into the paternal genome as early as 2 h postfertilization and is detectable in the paternal genome until the morula stage. Knockdown of maternal H3.3 resulted in compromised embryonic development both of fertilized embryos and of androgenetic haploid embryos. Furthermore, we report that mH3.3 depletion in oocytes impairs both activation of the Oct4 pluripotency marker gene and global de novo transcription from the paternal genome important for early embryonic development. Our results suggest that H3.3-mediated paternal chromatin remodeling is essential for the development of preimplantation embryos and the activation of the paternal genome during embryogenesis.
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Affiliation(s)
- Qingran Kong
- From the Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and.,Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China, and
| | - Laura A Banaszynski
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, New York, New York 10065
| | - Fuqiang Geng
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065
| | - Xiaolei Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China, and
| | - Jiaming Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China, and
| | - Heng Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China, and
| | - Claire L O'Neill
- From the Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and
| | - Peidong Yan
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China, and
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China, and
| | - Koji Shido
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065
| | - Gianpiero D Palermo
- From the Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, New York, New York 10065
| | - Shahin Rafii
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065
| | - Zev Rosenwaks
- From the Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and
| | - Duancheng Wen
- From the Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and
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398
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Theunissen TW, Jaenisch R. Mechanisms of gene regulation in human embryos and pluripotent stem cells. Development 2018; 144:4496-4509. [PMID: 29254992 DOI: 10.1242/dev.157404] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pluripotent stem cells have broad utility in biomedical research and their molecular regulation has thus garnered substantial interest. While the principles that establish and regulate pluripotency have been well defined in the mouse, it has been difficult to extrapolate these insights to the human system due to species-specific differences and the distinct developmental identities of mouse versus human embryonic stem cells. In this Review, we examine genome-wide approaches to elucidate the regulatory principles of pluripotency in human embryos and stem cells, and highlight where differences exist in the regulation of pluripotency in mice and humans. We review recent insights into the nature of human pluripotent cells in vivo, obtained by the deep sequencing of pre-implantation embryos. We also present an integrated overview of the principal layers of global gene regulation in human pluripotent stem cells. Finally, we discuss the transcriptional and epigenomic remodeling events associated with cell fate transitions into and out of human pluripotency.
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Affiliation(s)
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Hanna CW, Taudt A, Huang J, Gahurova L, Kranz A, Andrews S, Dean W, Stewart AF, Colomé-Tatché M, Kelsey G. MLL2 conveys transcription-independent H3K4 trimethylation in oocytes. Nat Struct Mol Biol 2018; 25:73-82. [DOI: 10.1038/s41594-017-0013-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 01/03/2023]
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400
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Suzuki S, Minami N. CHD1 Controls Cell Lineage Specification Through Zygotic Genome Activation. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2018; 229:15-30. [PMID: 29177762 DOI: 10.1007/978-3-319-63187-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In mammals, the processes spanning from fertilization to the generation of a new organism are very complex and are controlled by multiple genes. Life begins with the encounter of eggs and spermatozoa, in which gene expression is inactive prior to fertilization. After several cell divisions, cells arise that are specialized in implantation, a developmental process unique to mammals. Cells involved in the establishment and maintenance of implantation differentiate from totipotent embryos, and the remaining cells generate the embryo proper. Although this process of differentiation, termed cell lineage specification, is supported by various gene expression networks, many components have yet to be identified. Moreover, despite extensive research it remains unclear which genes are controlled by each of the factors involved. Although it has become clear that epigenetic factors regulate gene expression, elucidation of the underlying mechanisms remains challenging. In this chapter, we propose that the chromatin remodeling factor CHD1, together with epigenetic factors, is involved in a subset of gene expression networks involved in processes spanning from zygotic genome activation to cell lineage specification.
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Affiliation(s)
- Shinnosuke Suzuki
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8052, Japan.
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