151
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Dang Y, Luo L, Shi Y, Li S, Wang S, Zhang K. KDM5-mediated redistribution of H3K4me3 is required for oocyte-to-embryonic transition in cattle. Biol Reprod 2022; 106:1059-1071. [PMID: 35243485 DOI: 10.1093/biolre/ioac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/12/2022] Open
Abstract
Reprogramming of histone modifications is critical to safeguard correct gene expression profile during preimplantation development. Of interest, trimethylation of lysine 4 on histone 3 (H3K4me3) exhibits a unique and dynamic landscape with a potential species-specific feature. Here, we address how it is reprogrammed and its functional significance during oocyte maturation and early embryonic development in cows. Notably, the overall signal of H3K4me3 decreased sharply during embryonic genome activation (EGA). By using low input ChIP-seq, we find widespread broad H3K4me3 domains in oocytes and early cleaved embryos. The broad domains are gradually removed after fertilization, which is obviously seen during EGA. Meanwhile, H3K4me3 become enriched at promoter regions after the removal of broad H3K4me3. Interestingly, the gene expression level displays a positive correlation with the relative H3K4me3 signal of their promoters when embryos reach 16-cell stage. Importantly, disruption of H3K4me3 demethylases KDM5 increases H3K4me3 level, decreases the embryonic developmental rate and results in dysregulation of over a thousand genes. Meanwhile, KDM5 deficiency causes a redistribution of H3K4me3 across genome. In particular, H3K4me3 in gene body or intergenic regions can't be removed and H3K4me3 in promoter regions is aberrantly reduced. Besides, the positive correlation between promoter H3K4me3 enrichment and gene expression level disappear. Overall, we describe the genomic reprogramming of H3K4me3 with a greater resolution during bovine preimplantation development and propose that KDM5-mediated redistribution of H3K4me3 plays an important role in modulating oocyte-to-embryonic transition.
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Affiliation(s)
- Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Luo
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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152
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Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
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Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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153
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Al-Mousawi J, Boskovic A. Transcriptional and epigenetic control of early life cell fate decisions. Curr Opin Oncol 2022; 34:148-154. [PMID: 35025815 DOI: 10.1097/cco.0000000000000814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Global epigenetic reprogramming of the parental genomes after fertilization ensures the establishment of genome organization permissive for cell specialization and differentiation during development. In this review, we highlight selected, well-characterized relationships between epigenetic factors and transcriptional cell fate regulators during the initial stages of mouse development. RECENT FINDINGS Blastomeres of the mouse embryo are characterized by atypical and dynamic histone modification arrangements, noncoding RNAs and DNA methylation profiles. Moreover, asymmetries in epigenomic patterning between embryonic cells arise as early as the first cleavage, with potentially instructive roles during the first lineage allocations in the mouse embryo. Although it is widely appreciated that transcription factors and developmental signaling pathways play a crucial role in cell fate specification at the onset of development, it is increasingly clear that their function is tightly connected to the underlying epigenetic status of the embryonic cells in which they act. SUMMARY Findings on the interplay between genetic, epigenetic and environmental factors during reprogramming and differentiation in the embryo are crucial for understanding the molecular underpinnings of disease processes, particularly tumorigenesis, which is characterized by global epigenetic rewiring and progressive loss of cellular identity.
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Affiliation(s)
- Jasmina Al-Mousawi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
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154
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Smith R, Susor A, Ming H, Tait J, Conti M, Jiang Z, Lin CJ. The H3.3 chaperone Hira complex orchestrates oocyte developmental competence. Development 2022; 149:274223. [PMID: 35112132 PMCID: PMC8959146 DOI: 10.1242/dev.200044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/16/2022] [Indexed: 11/20/2022]
Abstract
Successful reproduction requires an oocyte competent to sustain early embryo development. By the end of oogenesis, the oocyte has entered a transcriptionally silenced state, the mechanisms and significance of which remain poorly understood. Histone H3.3, a histone H3 variant, has unique cell cycle-independent functions in chromatin structure and gene expression. Here, we have characterised the H3.3 chaperone Hira/Cabin1/Ubn1 complex, showing that loss of function of any of these subunits causes early embryogenesis failure in mouse. Transcriptome and nascent RNA analyses revealed that transcription is aberrantly silenced in mutant oocytes. Histone marks, including H3K4me3 and H3K9me3, are reduced and chromatin accessibility is impaired in Hira/Cabin1 mutants. Misregulated genes in mutant oocytes include Zscan4d, a two-cell specific gene involved in zygote genome activation. Overexpression of Zscan4 in the oocyte partially recapitulates the phenotypes of Hira mutants and Zscan4 knockdown in Cabin1 mutant oocytes partially restored their developmental potential, illustrating that temporal and spatial expression of Zscan4 is fine-tuned at the oocyte-to-embryo transition. Thus, the H3.3 chaperone Hira complex has a maternal effect function in oocyte developmental competence and embryogenesis, through modulating chromatin condensation and transcriptional quiescence. Summary: The H3.3 chaperone Hira complex has a maternal effect function in oocyte developmental competence and embryogenesis by modulating chromatin condensation and transcriptional quiescence.
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Affiliation(s)
- Rowena Smith
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, Rumburska 89, 277 21 Libechov, Czech Republic
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Janet Tait
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Chih-Jen Lin
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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155
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The Novel Protease Activities of JMJD5–JMJD6–JMJD7 and Arginine Methylation Activities of Arginine Methyltransferases Are Likely Coupled. Biomolecules 2022; 12:biom12030347. [PMID: 35327545 PMCID: PMC8945206 DOI: 10.3390/biom12030347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/03/2022] [Accepted: 02/18/2022] [Indexed: 12/23/2022] Open
Abstract
The surreptitious discoveries of the protease activities on arginine-methylated targets of a subfamily of Jumonji domain-containing family including JMJD5, JMJD6, and JMJD7 pose several questions regarding their authenticity, function, purpose, and relations with others. At the same time, despite several decades of efforts and massive accumulating data regarding the roles of the arginine methyltransferase family (PRMTs), the exact function of this protein family still remains a mystery, though it seems to play critical roles in transcription regulation, including activation and inactivation of a large group of genes, as well as other biological activities. In this review, we aim to elucidate that the function of JMJD5/6/7 and PRMTs are likely coupled. Besides roles in the regulation of the biogenesis of membrane-less organelles in cells, they are major players in regulating stimulating transcription factors to control the activities of RNA Polymerase II in higher eukaryotes, especially in the animal kingdom. Furthermore, we propose that arginine methylation by PRMTs could be a ubiquitous action marked for destruction after missions by a subfamily of the Jumonji protein family.
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156
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Cao W, Zhao J, Qu P, Liu E. Current Progress and Prospects in Rabbit Cloning. Cell Reprogram 2022; 24:63-70. [PMID: 35167365 DOI: 10.1089/cell.2021.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) shows great value in the generation of transgenic animals, protection of endangered animals, and stem cell therapy. The combination of SCNT and gene editing has produced a variety of genetically modified animals for life science and medical research. Rabbits have unique advantages as transgenic bioreactors and human disease models; however, the low SCNT efficiency severely impedes the application of this technology. The difficulty in SCNT may be attributable to the abnormal reprogramming of somatic cells in rabbits. This review focuses on the abnormal reprogramming of cloned mammalian embryos and evaluates the progress and prospects of rabbit somatic cell cloning.
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Affiliation(s)
- Wenbin Cao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jinpeng Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Pengxiang Qu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
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157
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Innocenti F, Fiorentino G, Cimadomo D, Soscia D, Garagna S, Rienzi L, Ubaldi FM, Zuccotti M. Maternal effect factors that contribute to oocytes developmental competence: an update. J Assist Reprod Genet 2022; 39:861-871. [PMID: 35165782 PMCID: PMC9051001 DOI: 10.1007/s10815-022-02434-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
Oocyte developmental competence is defined as the capacity of the female gamete to be fertilized and sustain development to the blastocyst stage. Epigenetic reprogramming, a correct cell division pattern, and an efficient DNA damage response are all critical events that, before embryonic genome activation, are governed by maternally inherited factors such as maternal-effect gene (MEG) products. Although these molecules are stored inside the oocyte until ovulation and exert their main role during fertilization and preimplantation development, some of them are already functioning during folliculogenesis and oocyte meiosis resumption. This mini review summarizes the crucial roles played by MEGs during oocyte maturation, fertilization, and preimplantation development with a direct/indirect effect on the acquisition or maintenance of oocyte competence. Our aim is to inspire future research on a topic with potential clinical perspectives for the prediction and treatment of female infertility.
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Affiliation(s)
- Federica Innocenti
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy
| | - Giulia Fiorentino
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
| | - Danilo Cimadomo
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy.
| | - Daria Soscia
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy
| | - Silvia Garagna
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
| | - Laura Rienzi
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy
| | | | - Maurizio Zuccotti
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
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158
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CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency. Mol Cell 2022; 82:1169-1185.e7. [PMID: 35202573 DOI: 10.1016/j.molcel.2022.01.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/03/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022]
Abstract
Polycomb group (PcG) proteins are essential for post-implantation development by depositing repressive histone modifications at promoters, mainly CpG islands (CGIs), of developmental regulator genes. However, promoter PcG marks are erased after fertilization and de novo established in peri-implantation embryos, coinciding with the transition from naive to primed pluripotency. Nevertheless, the molecular basis for this establishment remains unknown. In this study, we show that the expression of the long KDM2B isoform (KDM2BLF), which contains the demethylase domain, is specifically induced at peri-implantation and that its H3K36me2 demethylase activity is required for PcG enrichment at CGIs. Moreover, KDM2BLF interacts with BRG1/BRM-associated factor (BAF) and stabilizes BAF occupancy at CGIs for subsequent gain of accessibility, which precedes PcG enrichment. Consistently, KDM2BLF inactivation results in significantly delayed post-implantation development. In summary, our data unveil dynamic chromatin configuration of CGIs during exit from naive pluripotency and provide a conceptual framework for the spatiotemporal establishment of PcG functions.
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159
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Yang M, Yu H, Yu X, Liang S, Hu Y, Luo Y, Izsvák Z, Sun C, Wang J. Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells. Cell Stem Cell 2022; 29:400-418.e13. [PMID: 35143761 DOI: 10.1016/j.stem.2022.01.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 10/18/2021] [Accepted: 01/18/2022] [Indexed: 11/03/2022]
Abstract
Totipotent cells have more robust developmental potency than any other cell types, giving rise to both embryonic and extraembryonic tissues. Stable totipotent cell cultures and deciphering the principles of totipotency regulation would be invaluable to understand cell plasticity and lineage segregation in early development. Our approach of remodeling the pericentromeric heterochromatin and re-establishing the totipotency-specific broad H3K4me3 domains promotes the pluri-to-totipotency transition. Our protocol establishes a closer match of mouse 2-cell (2C) embryos than any other 2C-like cells. These totipotent-like stem cells (TLSCs) are stable in culture and possess unique molecular features of the mouse 2C embryo. Functionally, TLSCs are competent for germline transmission and give rise to both embryonic and extraembryonic lineages at high frequency. Therefore, TLSCs represent a highly valuable cell type for studies of totipotency and embryology.
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Affiliation(s)
- Mingzhu Yang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Hanwen Yu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiu Yu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shiqi Liang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuanlang Hu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuxin Luo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13092, Germany
| | - Chuanbo Sun
- Guangzhou Institute of Pediatrics, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510623, China.
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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160
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Ma X, Fan Y, Xiao W, Ding X, Hu W, Xia Y. Glufosinate-Ammonium Induced Aberrant Histone Modifications in Mouse Sperm Are Concordant With Transcriptome in Preimplantation Embryos. Front Physiol 2022; 12:819856. [PMID: 35145430 PMCID: PMC8821811 DOI: 10.3389/fphys.2021.819856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/31/2021] [Indexed: 11/15/2022] Open
Abstract
Glufosinate-ammonium (GLA) is a widely used herbicide with emerging concern over its male reproductive toxicity. Abnormalities in sperm histone modification induced by GLA exposure observed in our previous study aroused our interest in whether such alterations could further affect embryonic gene expression. Here we administered adult male mice with 0.2 mg/kg⋅day of GLA for 5 weeks to collect their sperm or 4-cell embryos after copulation. Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing showed alterations of sperm H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), which are active histone modification marks involved in embryo development, while RNA sequencing identified differentially expressed genes in 4-cell embryos. Differentially H3K4me3 and H3K27ac occupied regions were mainly distributed at the gene promoters and putative enhancers, and were enriched in pathways related to the immune system and nervous system. Integrative analysis of these sequencing data showed that genes such as Mgl2 with increased H3K4me3 and H3K27ac in sperm were up-regulated in embryos, and vice versa for genes such as Dcn. Additionally, differentially occupied H3K4me3 and H3K27ac in sperm were linked to gene expression changes in both paternal and maternal alleles of 4-cell embryos. In conclusion, GLA-induced changes in sperm H3K4me3 and H3K27ac are concordant with gene expression in preimplantation embryos, which might further affect embryo development and offspring health.
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Affiliation(s)
- Xuan Ma
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yun Fan
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Microbes and Infection, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wenwen Xiao
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xingwang Ding
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weiyue Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Nutrition and Food Safety, School of Public Health, Nanjing Medical University, Nanjing, China
- Weiyue Hu,
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Yankai Xia,
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161
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Abstract
The zygotic genome is transcriptionally silent immediately after fertilization. In mice, initial activation of the zygotic genome occurs in the middle of the one-cell stage. At the mid-to-late two-cell stage, a burst of gene activation occurs after the second round of DNA replication, and the profile of transcribed genes changes dramatically. These two phases of gene activation are called minor and major zygotic gene activation (ZGA), respectively. As they mark the beginning of the gene expression program, it is important to elucidate gene expression regulation during these stages. This article reviews the outcomes of studies that have clarified the profiles and regulatory mechanisms of ZGA.
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Affiliation(s)
- Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan
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162
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Chromatin alterations during the epididymal maturation of mouse sperm refine the paternally inherited epigenome. Epigenetics Chromatin 2022; 15:2. [PMID: 34991687 PMCID: PMC8734183 DOI: 10.1186/s13072-021-00433-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Paternal lifestyle choices and male exposure history have a critical influence on the health and fitness of the next generation. Accordingly, defining the processes of germline programming is essential to resolving how the epigenetic memory of paternal experiences transmits to their offspring. Established dogma holds that all facets of chromatin organization and histone posttranslational modification are complete before sperm exits the testes. However, recent clinical and animal studies suggest that patterns of DNA methylation change during epididymal maturation. In this study, we used complementary proteomic and deep-sequencing approaches to test the hypothesis that sperm posttranslational histone modifications change during epididymal transit. RESULTS Using proteomic analysis to contrast immature spermatozoa and mature sperm isolated from the mouse epididymis, we find progressive changes in multiple histone posttranslational modifications, including H3K4me1, H3K27ac, H3K79me2, H3K64ac, H3K122ac, H4K16ac, H3K9me2, and H4K20me3. Interestingly, some of these changes only occurred on histone variant H3.3, and most involve chromatin modifications associated with gene enhancer activity. In contrast, the bivalent chromatin modifications, H3K4me3, and H3K27me3 remained constant. Using chromatin immunoprecipitation coupled with deep sequencing, we find that changes in histone h3, lysine 27 acetylation (H3K27ac) involve sharpening broad diffuse regions into narrow peaks centered on the promoter regions of genes driving embryonic development. Significantly, many of these regions overlap with broad domains of H3K4me3 in oocytes and ATAC-seq signatures of open chromatin identified in MII oocytes and sperm. In contrast, histone h3, lysine 9 dimethylation (H3K9me2) becomes enriched within the promoters of genes driving meiosis and in the distal enhancer regions of tissue-specific genes sequestered at the nuclear lamina. Maturing sperm contain the histone deacetylase enzymes HDAC1 and HDAC3, suggesting the NuRD complex may drive some of these changes. Finally, using Western blotting, we detected changes in chromatin modifications between caput and caudal sperm isolated from rams (Ovis aries), inferring changes in histone modifications are a shared feature of mammalian epididymal maturation. CONCLUSIONS These data extend our understanding of germline programming and reveal that, in addition to trafficking noncoding RNAs, changes in histone posttranslational modifications are a core feature of epididymal maturation.
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163
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Hickey GJM, Wike CL, Nie X, Guo Y, Tan M, Murphy PJ, Cairns BR. Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos. eLife 2022; 11:e67738. [PMID: 34982026 PMCID: PMC8769650 DOI: 10.7554/elife.67738] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal the order of chromatin states in establishing developmental gene poising in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with 'Placeholder' nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of polycomb repressive complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 - establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.
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Affiliation(s)
- Graham JM Hickey
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
| | - Candice L Wike
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
| | - Xichen Nie
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
| | - Yixuan Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
| | - Mengyao Tan
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
| | - Patrick J Murphy
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
- Department of Biomedical Genetics, Wilmot Cancer Center, University of Rochester School of MedicineRochesterUnited States
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUnited States
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164
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Jang S, Hwang J, Jeong HS. The Role of Histone Acetylation in Mesenchymal Stem Cell Differentiation. Chonnam Med J 2022; 58:6-12. [PMID: 35169553 PMCID: PMC8813658 DOI: 10.4068/cmj.2022.58.1.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/06/2022] Open
Abstract
The mechanism and action concerning epigenetic modifications, especially that of histone modifications, are not fully understood. However, it is clear that histone modifications play an essential role in several biological processes that are involved in cell proliferation and differentiation. In this article, we focused on how histone acetylation may result in differentiation into mesenchymal stem cells as well as histone acetylation function. Moreover, histone acetylation followed by the action of histone deacetylase inhibitors, which can result in the differentiation of stem cells into other types of cells such as adipocytes, chondrocytes, osteocytes, neurons, and other lineages, were also reviewed.
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Affiliation(s)
- Sujeong Jang
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| | - Jinsu Hwang
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| | - Han-Seong Jeong
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
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165
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Hanna CW, Huang J, Belton C, Reinhardt S, Dahl A, Andrews S, Stewart A, Kranz A, Kelsey G. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1993-2004. [PMID: 35137160 PMCID: PMC8887468 DOI: 10.1093/nar/gkac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - Susanne Reinhardt
- Dresden Concept Genome Center, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Germany
| | - Andreas Dahl
- Dresden Concept Genome Center, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Germany
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Germany
- Max-Planck-Institute for Cell Biology and Genetics, Dresden 01307, Germany
| | - Andrea Kranz
- Correspondence may also be addressed to Andrea Kranz.
| | - Gavin Kelsey
- To whom correspondence should be addressed. Tel: +44 1223 496332;
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166
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Ma X, Wang B, Li Z, Ding X, Wen Y, Shan W, Hu W, Wang X, Xia Y. Effects of glufosinate-ammonium on male reproductive health: Focus on epigenome and transcriptome in mouse sperm. CHEMOSPHERE 2022; 287:132395. [PMID: 34597628 DOI: 10.1016/j.chemosphere.2021.132395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/18/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Glufosinate-ammonium (GLA) is a widely used herbicide with emerging concern over its neural and reproductive toxicity. To uncover potential effects of GLA on male reproductive health in mammals, adult male C57BL/6J mice were administered 0.2 mg/kg·d GLA for 5 weeks. After examination on fertility, testis histology and semen quality in the GLA group, we performed deep sequencing to identify repressive epigenetic marks including DNA methylation and histone modifications (H3K27me3 and H3K9me3), together with mRNA transcript levels in sperm. Then, we integrated multi-omics sequencing data to comprehensively explore GLA-induced epigenetic and transcriptomic alterations. We found no significant difference either on fertility, testis histology or semen quality-related indicators. As for epigenome, the protein level of H3K27me3 was significantly increased in GLA sperm. Next generation sequencing showed alterations of these epigenetic marks and extensive transcription inhibition in sperm. These differential repressive marks were mainly distributed at intergenic regions and introns. According to results by Gene Ontology enrichment analysis, both differentially methylated and expressed genes were mainly enriched in pathways related to synapse organization. Subtle differences in genomic imprinting were also observed between the two groups. These results suggested that GLA predominantly impaired sperm epigenome and transcriptome in mice, with little effect on fertility, testis histology or semen quality. Further studies on human sperm using similar strategies need to be conducted for a better understanding of the male reproductive toxicity of GLA.
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Affiliation(s)
- Xuan Ma
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Bingqian Wang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhe Li
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xingwang Ding
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Ya Wen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Wenqi Shan
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Weiyue Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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167
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Brind'Amour J, Lorincz MC. Profiling Histone Methylation in Low Numbers of Cells. Methods Mol Biol 2022; 2529:229-251. [PMID: 35733018 DOI: 10.1007/978-1-0716-2481-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chromatin immunoprecipitation (ChIP) enables the study of DNA-protein interactions. When coupled with high-throughput sequencing (ChIP-seq), this method allows the generation of genome-wide profiles of the distribution of specific proteins in a given cellular context. Typical ChIP-seq experiments require millions of cells as input material and thus are not ideal to study many in vivo cell populations. Here, we describe an ultra-low-input native ChIP-seq method, ULI-NChIP-seq, to profile histone modification patterns in as low as 150 cells.
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Affiliation(s)
- Julie Brind'Amour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Département de Biomédecine Vétérinaire, Université de Montréal, Montréal, QC, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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168
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Zhu Y, Yu J, Rong Y, Wu YW, Li Y, Zhang L, Pan Y, Fan HY, Shen L. Genomewide decoupling of H2AK119ub1 and H3K27me3 in early mouse development. Sci Bull (Beijing) 2021; 66:2489-2497. [PMID: 36654208 DOI: 10.1016/j.scib.2021.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023]
Abstract
Polycomb group (PcG) proteins are crucial chromatin regulators during development. H2AK119ub1 (H2Aub) and H3K27me3 are catalyzed by Polycomb-repressive complex 1 and 2 (PRC1/2) respectively, and they largely overlap in the genome due to mutual recruitment of the two complexes. However, it is unclear whether PRC1/H2Aub and PRC2/H3K27me3 can also function independently. By developing an ultra-sensitive carrier-DNA-assisted chromatin immunoprecipitation sequencing method termed CATCH-Seq, we generated allelic H2Aub profiles in mouse gametes and early embryos. Our results revealed an unexpected genomewide decoupling of H2Aub and H3K27me3 in mouse preimplantation embryos, where H2Aub but not H3K27me3 was enriched at PcG targets while only H3K27me3 was deposited in the broad distal domains associated with DNA methylation-independent non-canonical imprinting. These observations suggest that H2Aub represses future bivalent genes during early embryogenesis without H3K27me3, but it is not required for the maintenance of non-canonical imprinting, which is mediated by maternal H3K27me3. Thus, our study reveals the distinct depositions and independent functions of H2Aub and H3K27me3 during early mammalian development.
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Affiliation(s)
- Yezhang Zhu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jiali Yu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yan Rong
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yang Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Lejiao Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yinghao Pan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Department of Orthopedics Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China; Hangzhou Innovation Center, Zhejiang University, Hangzhou 311215, China.
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169
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Wu X, Zhang H, Zhang B, Zhang Y, Wang Q, Shen W, Wu X, Li L, Xia W, Nakamura R, Liu B, Liu F, Takeda H, Meng A, Xie W. Methylome inheritance and enhancer dememorization reset an epigenetic gate safeguarding embryonic programs. SCIENCE ADVANCES 2021; 7:eabl3858. [PMID: 34936444 PMCID: PMC8694617 DOI: 10.1126/sciadv.abl3858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/10/2021] [Indexed: 05/31/2023]
Abstract
Marked epigenetic reprogramming is essential to convert terminally differentiated gametes to totipotent embryos. It remains puzzling why postfertilization global DNA reprogramming occurs in mammals but not in nonmammalian vertebrates. In zebrafish, global methylome inheritance is however accompanied by extensive enhancer “dememorization” as they become fully methylated. By depleting maternal dnmt1 using oocyte microinjection, we eliminated DNA methylation in early embryos, which died around gastrulation with severe differentiation defects. Notably, methylation deficiency leads to derepression of adult tissue–specific genes and CG-rich enhancers, which acquire ectopic transcription factor binding and, unexpectedly, histone H3 lysine 4 trimethylation (H3K4me3). By contrast, embryonic enhancers are generally CG-poor and evade DNA methylation repression. Hence, global DNA hypermethylation inheritance coupled with enhancer dememorization installs an epigenetic gate that safeguards embryonic programs and ensures temporally ordered gene expression. We propose that “enhancer dememorization” underlies and unifies distinct epigenetic reprogramming modes in early development between mammals and nonmammals.
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Affiliation(s)
- Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongmei Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bingjie Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiuyan Wang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijia Li
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weikun Xia
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bofeng Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, University of Chinese Academy of Science, Beijing, China
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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170
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Yamazaki W, Badescu D, Tan SL, Ragoussis J, Taketo T. Effects of the Sex Chromosome Complement, XX, XO, or XY, on the Transcriptome and Development of Mouse Oocytes During Follicular Growth. Front Genet 2021; 12:792604. [PMID: 34987552 PMCID: PMC8721172 DOI: 10.3389/fgene.2021.792604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022] Open
Abstract
The sex chromosome complement, XX or XY, determines sexual differentiation of the gonadal primordium into a testis or an ovary, which in turn directs differentiation of the germ cells into sperm and oocytes, respectively, in eutherian mammals. When the X monosomy or XY sex reversal occurs, XO and XY females exhibit subfertility and infertility in the mouse on the C57BL/6J genetic background, suggesting that functional germ cell differentiation requires the proper sex chromosome complement. Using these mouse models, we asked how the sex chromosome complement affects gene transcription in the oocytes during follicular growth. An oocyte accumulates cytoplasmic components such as mRNAs and proteins during follicular growth to support subsequent meiotic progression, fertilization, and early embryonic development without de novo transcription. However, how gene transcription is regulated during oocyte growth is not well understood. Our results revealed that XY oocytes became abnormal in chromatin configuration, mitochondria distribution, and de novo transcription compared to XX or XO oocytes near the end of growth phase. Therefore, we compared transcriptomes by RNA-sequencing among the XX, XO, and XY oocytes of 50–60 µm in diameter, which were still morphologically comparable. The results showed that the X chromosome dosage limited the X-linked and autosomal gene transcript levels in XO oocytes whereas many genes were transcribed from the Y chromosome and made the transcriptome in XY oocytes closer to that in XX oocytes. We then compared the transcript levels of 3 X-linked, 3 Y-linked and 2 autosomal genes in the XX, XO, and XY oocytes during the entire growth phase as well as at the end of growth phase using quantitative RT-PCR. The results indicated that the transcript levels of most genes increased with oocyte growth while largely maintaining the X chromosome dosage dependence. Near the end of growth phase, however, transcript levels of some X-linked genes did not increase in XY oocytes as much as XX or XO oocytes, rendering their levels much lower than those in XX oocytes. Thus, XY oocytes established a distinct transcriptome at the end of growth phase, which may be associated with abnormal chromatin configuration and mitochondria distribution.
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Affiliation(s)
- Wataru Yamazaki
- Department of Surgery, McGill University, Montreal, QC, Canada
- Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Dunarel Badescu
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Seang Lin Tan
- Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
- OriginElle Fertility Clinic and Women’s Health Centre, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Teruko Taketo
- Department of Surgery, McGill University, Montreal, QC, Canada
- Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
- Department of Biology, McGill University, Montreal, QC, Canada
- *Correspondence: Teruko Taketo,
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171
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Zhang A, Wei Y, Shi Y, Deng X, Gao J, Feng Y, Zheng D, Cheng X, Li Z, Wang T, Wang K, Liu F, Peng R, Zhang W. Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:761059. [PMID: 34975944 PMCID: PMC8714964 DOI: 10.3389/fpls.2021.761059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Cotton is an excellent model for studying crop polyploidization and domestication. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenomes in allotetraploid cotton. However, the detailed profiling and functional characterization of broad H3K4me3 and H3K27me3 are still understudied in cotton. In this study, we conducted H3K4me3- and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating the expression of genes between A and D subgenomes, respectively. More importantly, H3K4me3 exhibited enrichment level-, position-, and distance-related impacts on expression levels of related genes. Distinct GO term enrichment occurred between A/D-specific and homeologous genes with broad H3K4me3 enrichment in promoters and gene bodies, suggesting that broad H3K4me3-marked genes might have some unique biological functions between A and D subgenome. An anticorrelation between H3K27me3 enrichment and expression levels of homeologous genes was more pronounced in the A subgenome relative to the D subgenome, reflecting distinct enrichment of H3K27me3 in homeologous genes between A and D subgenome. In addition, H3K4me3 and H3K27me3 marks can indirectly influence gene expression through regulatory networks with TF mediation. Thus, our study provides detailed insights into functions of H3K4me3 and H3K27me3 in regulating differential gene expression and subfunctionalization of homeologous genes, therefore serving as a driving force for polyploidization and domestication in cotton.
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Affiliation(s)
- Aicen Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Yangyang Wei
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Xiaojuan Deng
- College of Agronomy, Xinjiang Agricultural University, Ürümqi, China
| | - Jingjing Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Dongyang Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Zhaoguo Li
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Tao Wang
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Kunbo Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renhai Peng
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
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172
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Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM. High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). J Cell Biol 2021; 220:e202103078. [PMID: 34783858 PMCID: PMC8600797 DOI: 10.1083/jcb.202103078] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 09/15/2021] [Accepted: 10/27/2021] [Indexed: 12/16/2022] Open
Abstract
Chromatin profiling in single cells has been extremely challenging and almost exclusively limited to histone proteins. In cases where single-cell methods have shown promise, many require highly specialized equipment or cell type-specific protocols and are relatively low throughput. Here, we combine the advantages of tagmentation, linear amplification, and combinatorial indexing to produce a high-throughput single-cell DNA binding site mapping method that is simple, inexpensive, and capable of multiplexing several independent samples per experiment. Targeted insertion of promoters sequencing (TIP-seq) uses Tn5 fused to proteinA to insert a T7 RNA polymerase promoter adjacent to a chromatin protein of interest. Linear amplification of flanking DNA with T7 polymerase before sequencing library preparation provides ∼10-fold higher unique reads per single cell compared with other methods. We applied TIP-seq to map histone modifications, RNA polymerase II (RNAPII), and transcription factor CTCF binding sites in single human and mouse cells.
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Affiliation(s)
- Daniel A. Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL
- San Diego Biomedical Research Institute, La Jolla, CA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Steven Henikoff
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL
- San Diego Biomedical Research Institute, La Jolla, CA
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173
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Ye Q, Zeng X, Cai S, Qiao S, Zeng X. Mechanisms of lipid metabolism in uterine receptivity and embryo development. Trends Endocrinol Metab 2021; 32:1015-1030. [PMID: 34625374 DOI: 10.1016/j.tem.2021.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/19/2021] [Accepted: 09/06/2021] [Indexed: 02/05/2023]
Abstract
Metabolic regulation plays important roles in embryo development and uterine receptivity during early pregnancy, ultimately influencing pregnancy efficiency in mammals. The important roles of lipid metabolism during early pregnancy have not been fully understood. Here, we described the regulatory roles of phospholipid, sphingolipid, and cholesterol metabolism on early embryo development, implantation, and uterine receptivity through production of cannabinoids, prostaglandins, lysophosphatidic acid, sphingosine-1-phosphate, and steroid hormones. Moreover, the impacts of lipids and fatty acids on embryo development potential and the related epigenetic modifications are also discussed. This review aims to elucidate the modulations of lipid metabolism on uterine receptivity and embryo development, contributing to novel strategies to establish dietary balanced lipids and fatty acids for reducing early embryo loss.
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Affiliation(s)
- Qianhong Ye
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing 100193, P. R. China; Beijing Key Laboratory of Biofeed Additives, Beijing 100193, P. R. China
| | - Xiangzhou Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing 100193, P. R. China; Beijing Key Laboratory of Biofeed Additives, Beijing 100193, P. R. China
| | - Shuang Cai
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing 100193, P. R. China; Beijing Key Laboratory of Biofeed Additives, Beijing 100193, P. R. China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing 100193, P. R. China; Beijing Key Laboratory of Biofeed Additives, Beijing 100193, P. R. China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Center, China Agricultural University, Beijing 100193, P. R. China; Beijing Key Laboratory of Biofeed Additives, Beijing 100193, P. R. China.
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174
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Lu X, Zhang Y, Wang L, Wang L, Wang H, Xu Q, Xiang Y, Chen C, Kong F, Xia W, Lin Z, Ma S, Liu L, Wang X, Ni H, Li W, Guo Y, Xie W. Evolutionary epigenomic analyses in mammalian early embryos reveal species-specific innovations and conserved principles of imprinting. SCIENCE ADVANCES 2021; 7:eabi6178. [PMID: 34818044 PMCID: PMC8612685 DOI: 10.1126/sciadv.abi6178] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/06/2021] [Indexed: 05/24/2023]
Abstract
While mouse remains the most popular model, the conservation of parental-to-embryonic epigenetic transition across mammals is poorly defined. Through analysis of oocytes and early embryos in human, bovine, porcine, rat, and mouse, we revealed remarkable species-specific innovations as no single animal model fully recapitulates the human epigenetic transition. In rodent oocytes, transcription-dependent DNA methylation allows methylation of maternal imprints but not intergenic paternal imprints. Unexpectedly, prevalent DNA hypermethylation, paralleled by H3K36me2/3, also occurs in nontranscribed regions in porcine and bovine oocytes, except for megabase-long “CpG continents (CGCs)” where imprinting control regions preferentially reside. Broad H3K4me3 and H3K27me3 domains exist in nonhuman oocytes, yet only rodent H3K27me3 survives beyond genome activation. Coincidently, regulatory elements preferentially evade H3K27me3 in rodent oocytes, and failure to do so causes aberrant embryonic gene repression. Hence, the diverse mammalian innovations of parental-to-embryonic transition center on a delicate “to-methylate-or-not” balance in establishing imprints while protecting other regulatory regions.
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Affiliation(s)
- Xukun Lu
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Zhang
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Huili Wang
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Qianhua Xu
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yunlong Xiang
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chaolei Chen
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weikun Xia
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zili Lin
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangguo Wang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Hemin Ni
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Guo
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
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175
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Pagni S, Mills JD, Frankish A, Mudge JM, Sisodiya SM. Non-coding regulatory elements: Potential roles in disease and the case of epilepsy. Neuropathol Appl Neurobiol 2021; 48:e12775. [PMID: 34820881 DOI: 10.1111/nan.12775] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/04/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022]
Abstract
Non-coding DNA (ncDNA) refers to the portion of the genome that does not code for proteins and accounts for the greatest physical proportion of the human genome. ncDNA includes sequences that are transcribed into RNA molecules, such as ribosomal RNAs (rRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and un-transcribed sequences that have regulatory functions, including gene promoters and enhancers. Variation in non-coding regions of the genome have an established role in human disease, with growing evidence from many areas, including several cancers, Parkinson's disease and autism. Here, we review the features and functions of the regulatory elements that are present in the non-coding genome and the role that these regions have in human disease. We then review the existing research in epilepsy and emphasise the potential value of further exploring non-coding regulatory elements in epilepsy. In addition, we outline the most widely used techniques for recognising regulatory elements throughout the genome, current methodologies for investigating variation and the main challenges associated with research in the field of non-coding DNA.
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Affiliation(s)
- Susanna Pagni
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - James D Mills
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK.,Amsterdam UMC, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, Netherlands
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
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176
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What defines the maternal transcriptome? Biochem Soc Trans 2021; 49:2051-2062. [PMID: 34415300 PMCID: PMC8589422 DOI: 10.1042/bst20201125] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/05/2021] [Accepted: 07/19/2021] [Indexed: 01/09/2023]
Abstract
In somatic cells, RNA polymerase II (Pol II) transcription initiation starts by the binding of the general transcription factor TFIID, containing the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs), to core promoters. However, in growing oocytes active Pol II transcription is TFIID/TBP-independent, as during oocyte growth TBP is replaced by its vertebrate-specific paralog TBPL2. TBPL2 does not interact with TAFs, but stably associates with TFIIA. The maternal transcriptome is the population of mRNAs produced and stored in the cytoplasm of growing oocytes. After fertilization, maternal mRNAs are inherited by the zygote from the oocyte. As transcription becomes silent after oocyte growth, these mRNAs are the sole source for active protein translation. They will participate to complete the protein pool required for oocyte terminal differentiation, fertilization and initiation of early development, until reactivation of transcription in the embryo, called zygotic genome activation (ZGA). All these events are controlled by an important reshaping of the maternal transcriptome. This procedure combines cytoplasmic readenylation of stored transcripts, allowing their translation, and different waves of mRNA degradation by deadenylation coupled to decapping, to eliminate transcripts coding for proteins that are no longer required. The reshaping ends after ZGA with an almost total clearance of the maternal transcripts. In the past, the murine maternal transcriptome has received little attention but recent progresses have brought new insights into the regulation of maternal mRNA dynamics in the mouse. This review will address past and recent data on the mechanisms associated with maternal transcriptome dynamic in the mouse.
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177
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Sun Z, Tang Y, Zhang Y, Fang Y, Jia J, Zeng W, Fang D. Joint single-cell multiomic analysis in Wnt3a induced asymmetric stem cell division. Nat Commun 2021; 12:5941. [PMID: 34642323 PMCID: PMC8511096 DOI: 10.1038/s41467-021-26203-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Wnt signaling usually functions through a spatial gradient. Localized Wnt3a signaling can induce the asymmetric division of mouse embryonic stem cells, where proximal daughter cells maintain self-renewal and distal daughter cells acquire hallmarks of differentiation. Here, we develop an approach, same cell epigenome and transcriptome sequencing, to jointly profile the epigenome and transcriptome in the same single cell. Utilizing this method, we profiled H3K27me3 and H3K4me3 levels along with gene expression in mouse embryonic stem cells with localized Wnt3a signaling, revealing the cell type-specific maps of the epigenome and transcriptome in divided daughter cells. H3K27me3, but not H3K4me3, is correlated with gene expression changes during asymmetric cell division. Furthermore, cell clusters identified by H3K27me3 recapitulate the corresponding clusters defined by gene expression. Our study provides a convenient method to jointly profile the epigenome and transcriptome in the same cell and reveals mechanistic insights into the gene regulatory programs that maintain and reset stem cell fate during differentiation. A localized Wnt3a signal has been shown to induce asymmetric division of mouse embryonic stem cells. Here the authors develop SET-seq, an approach to jointly profile epigenome and transcriptome in the same single cell and use it to provide mechanistic insights into the gene regulatory programs for maintaining and resetting stem cell fate during differentiation.
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Affiliation(s)
- Zhongxing Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yin Tang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yanjun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yuan Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junqi Jia
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Weiwu Zeng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dong Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China. .,Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.
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178
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Bilmez Y, Talibova G, Ozturk S. Dynamic changes of histone methylation in mammalian oocytes and early embryos. Histochem Cell Biol 2021; 157:7-25. [PMID: 34599660 DOI: 10.1007/s00418-021-02036-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2021] [Indexed: 12/18/2022]
Abstract
Histone methylation is a key epigenetic mechanism and plays a major role in regulating gene expression during oocyte maturation and early embryogenesis. This mechanism can be briefly defined as the process by which methyl groups are transferred to lysine and arginine residues of histone tails extending from nucleosomes. While methylation of the lysine residues is catalyzed by histone lysine methyltransferases (KMTs), protein arginine methyltransferases (PRMTs) add methyl groups to the arginine residues. When necessary, the added methyl groups can be reversibly removed by histone demethylases (HDMs) by a process called histone demethylation. The spatiotemporal regulation of methylation and demethylation in histones contributes to modulating the expression of genes required for proper oocyte maturation and early embryonic development. In this review, we comprehensively evaluate and discuss the functional importance of dynamic histone methylation in mammalian oocytes and early embryos, regulated by KMTs, PRMTs, and HDMs.
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Affiliation(s)
- Yesim Bilmez
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Gunel Talibova
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey.
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179
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Zhao J, Yao K, Yu H, Zhang L, Xu Y, Chen L, Sun Z, Zhu Y, Zhang C, Qian Y, Ji S, Pan H, Zhang M, Chen J, Correia C, Weiskittel T, Lin DW, Zhao Y, Chandrasekaran S, Fu X, Zhang D, Fan HY, Xie W, Li H, Hu Z, Zhang J. Metabolic remodelling during early mouse embryo development. Nat Metab 2021; 3:1372-1384. [PMID: 34650276 DOI: 10.1038/s42255-021-00464-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/31/2021] [Indexed: 01/09/2023]
Abstract
During early mammalian embryogenesis, changes in cell growth and proliferation depend on strict genetic and metabolic instructions. However, our understanding of metabolic reprogramming and its influence on epigenetic regulation in early embryo development remains elusive. Here we show a comprehensive metabolomics profiling of key stages in mouse early development and the two-cell and blastocyst embryos, and we reconstructed the metabolic landscape through the transition from totipotency to pluripotency. Our integrated metabolomics and transcriptomics analysis shows that while two-cell embryos favour methionine, polyamine and glutathione metabolism and stay in a more reductive state, blastocyst embryos have higher metabolites related to the mitochondrial tricarboxylic acid cycle, and present a more oxidative state. Moreover, we identify a reciprocal relationship between α-ketoglutarate (α-KG) and the competitive inhibitor of α-KG-dependent dioxygenases, L-2-hydroxyglutarate (L-2-HG), where two-cell embryos inherited from oocytes and one-cell zygotes display higher L-2-HG, whereas blastocysts show higher α-KG. Lastly, increasing 2-HG availability impedes erasure of global histone methylation markers after fertilization. Together, our data demonstrate dynamic and interconnected metabolic, transcriptional and epigenetic network remodelling during early mouse embryo development.
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Affiliation(s)
- Jing Zhao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ling Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Yuyan Xu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Zhen Sun
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Cheng Zhang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Yuli Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongru Pan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Min Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jie Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Cristina Correia
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, NY, USA
| | - Taylor Weiskittel
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, NY, USA
| | - Da-Wei Lin
- Center of Computational Medicine and Bioinformatics, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai, China
| | - Sriram Chandrasekaran
- Center of Computational Medicine and Bioinformatics, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xudong Fu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, NY, USA
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China.
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
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180
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Lee SK. Sure, Fathers Give Birth, Too! Postnatal paternal folate deficiency increases congenital disabilities through H3K4me3 histone methylation changes in sperm and embryos. Mol Cells 2021; 44:696-698. [PMID: 34588323 PMCID: PMC8490204 DOI: 10.14348/molcells.2021.0202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Sun-Kyung Lee
- Department of Life Sciences, Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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181
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Quan H, Tian H, Liu S, Xue Y, Zhang Y, Xie W, Gao YQ. Progressive Domain Segregation in Early Embryonic Development and Underlying Correlation to Genetic and Epigenetic Changes. Cells 2021; 10:2521. [PMID: 34685501 PMCID: PMC8534146 DOI: 10.3390/cells10102521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin undergoes drastic structural organization and epigenetic reprogramming during embryonic development. We present here a consistent view of the chromatin structural change, epigenetic reprogramming, and the corresponding sequence-dependence in both mouse and human embryo development. The two types of domains, identified earlier as forests (CGI-rich domains) and prairies (CGI-poor domains) based on the uneven distribution of CGI in the genome, become spatially segregated during embryonic development, with the exception of zygotic genome activation (ZGA) and implantation, at which point significant domain mixing occurs. Structural segregation largely coincides with DNA methylation and gene expression changes. Genes located in mixed prairie domains show proliferation and ectoderm differentiation-related function in ZGA and implantation, respectively. The chromatin of the ectoderm shows the weakest and the endoderm the strongest domain segregation in germ layers. This chromatin structure difference between different germ layers generally enlarges upon further differentiation. The systematic chromatin structure establishment and its sequence-based segregation strongly suggest the DNA sequence as a possible driving force for the establishment of chromatin 3D structures that profoundly affect the expression profile. Other possible factors correlated with or influencing chromatin structures, including transcription, the germ layers, and the cell cycle, are discussed for an understanding of concerted chromatin structure and epigenetic changes in development.
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Affiliation(s)
- Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (H.Q.); (H.T.); (S.L.); (Y.X.)
| | - Hao Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (H.Q.); (H.T.); (S.L.); (Y.X.)
| | - Sirui Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (H.Q.); (H.T.); (S.L.); (Y.X.)
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (H.Q.); (H.T.); (S.L.); (Y.X.)
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100871, China; (Y.Z.); (W.X.)
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100871, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100871, China; (Y.Z.); (W.X.)
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (H.Q.); (H.T.); (S.L.); (Y.X.)
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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182
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Du Q, Smith GC, Luu PL, Ferguson JM, Armstrong NJ, Caldon CE, Campbell EM, Nair SS, Zotenko E, Gould CM, Buckley M, Chia KM, Portman N, Lim E, Kaczorowski D, Chan CL, Barton K, Deveson IW, Smith MA, Powell JE, Skvortsova K, Stirzaker C, Achinger-Kawecka J, Clark SJ. DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity. Cell Rep 2021; 36:109722. [PMID: 34551299 DOI: 10.1016/j.celrep.2021.109722] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.
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Affiliation(s)
- Qian Du
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Grady C Smith
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Phuc Loi Luu
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - James M Ferguson
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, Murdoch, WA 6150, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | | | - Shalima S Nair
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Elena Zotenko
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Cathryn M Gould
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Michael Buckley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kee-Ming Chia
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Neil Portman
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Dominik Kaczorowski
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kirston Barton
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Ira W Deveson
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Martin A Smith
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, UNSW Sydney, NSW 2010, Australia
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia.
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183
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Huang X, Lin X, Liu F, Wu G, Yang Z, Meng A. The rise of developmental biology in China. Dev Growth Differ 2021; 64:106-115. [PMID: 34510425 DOI: 10.1111/dgd.12751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/30/2022]
Abstract
Developmental biology research in China started from experimental embryology, in particular from studies on aquatic and reptile animals. The recent growth of the developmental biology community in China parallels the increased governmental funding support and the recruitment of overseas talents. This flourishing field in China embraces the activities of developmental biology-related societies, national meetings, key research initiatives and talented scientists. The first Development paper from China, published in 2000, marked the beginning of a new era. More recently, the second decade in the 21st century witnessed the blossoming of developmental biology research in China. Significant research spotlights, technical advances, and up-and-coming areas will be discussed in this overview.
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Affiliation(s)
- Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gen Wu
- High Technology Research and Development Center, Beijing, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
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184
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Yang M, Tao X, Titus S, Zhao T, Scott RT, Seli E. Analysis of accessible chromatin landscape in the inner cell mass and trophectoderm of human blastocysts. Mol Hum Reprod 2021; 26:702-711. [PMID: 32663300 DOI: 10.1093/molehr/gaaa048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Early embryonic development is characterized by drastic changes in chromatin structure that affects the accessibility of the chromatin. In human, the chromosome reorganization and its involvement in the first linage segregation are poorly characterized due to the difficulties in obtaining human embryonic material and limitation on low input technologies. In this study, we aimed to explore the chromatin remodeling pattern in human preimplantation embryos and gain insight into the epigenetic regulation of inner cell mass (ICM) and trophectoderm (TE) differentiation. We optimized ATAC-seq (an assay for transposase-accessible chromatin using sequencing) to analyze the chromatin accessibility landscape for low DNA input. Sixteen preimplantation human blastocysts frozen on Day 6 were used. Our data showed that ATAC peak distributions of the promoter regions (<1 kb) and distal regions versus other regions were significantly different between ICM versus TE samples (P < 0.01). We detected that a higher percentage of accessible binding loci were located within 1 kb of the transcription start site in ICM compared to TE (P < 0.01). However, a higher percentage of accessible regions was detected in the distal region of TE compared to ICM (P < 0.01). In addition, eight differential peaks with a false discovery rate <0.05 between ICM and TE were detected. This is the first study to compare the landscape of the accessible chromatin between ICM and TE of human preimplantation embryos, which unveiled chromatin-level epigenetic regulation of cell lineage specification in early embryo development.
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Affiliation(s)
- Min Yang
- The Foundation for Embryonic Competence, Basking Ridge, NJ, USA
| | - Xin Tao
- The Foundation for Embryonic Competence, Basking Ridge, NJ, USA
| | - Shiny Titus
- The Foundation for Embryonic Competence, Basking Ridge, NJ, USA
| | | | - Richard T Scott
- IVI-RMA, New Jersey, Basking Ridge, NJ, USA.,Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Emre Seli
- IVI-RMA, New Jersey, Basking Ridge, NJ, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
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185
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Zhao ZH, Schatten H, Sun QY. High-throughput sequencing reveals landscapes of female germ cell development. Mol Hum Reprod 2021; 26:738-747. [PMID: 32866227 DOI: 10.1093/molehr/gaaa059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/09/2020] [Indexed: 12/11/2022] Open
Abstract
Female germ cell development is a highly complex process that includes meiosis initiation, oocyte growth recruitment, oocyte meiosis retardation and resumption and final meiotic maturation. A series of coordinated molecular signaling factors ensure successful oogenesis. The recent rapid development of high-throughput sequencing technologies allows for the dynamic omics in female germ cells, which is essential for further understanding the regulatory mechanisms of molecular events comprehensively. In this review, we summarize the current literature of multi-omics sequenced by epigenome-, transcriptome- and proteome-associated technologies, which provide valuable information for understanding the regulation of key events during female germ cell development.
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Affiliation(s)
- Zheng-Hui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
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186
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Xiao Z, Locasale JW. Epigenomic links from metabolism-methionine and chromatin architecture. Curr Opin Chem Biol 2021; 63:11-18. [PMID: 33667809 PMCID: PMC9889272 DOI: 10.1016/j.cbpa.2021.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/12/2021] [Accepted: 01/31/2021] [Indexed: 02/03/2023]
Abstract
Chromatin and associated epigenetic marks provide important platforms for gene regulation in response to metabolic changes associated with environmental exposures, including physiological stress, nutritional deprivation, and starvation. Numerous studies have shown that fluctuations of key metabolites can influence chromatin modifications, but their effects on chromatin structure (e.g. chromatin compaction, nucleosome arrangement, and chromatin loops) and how they appropriately deposit specific chemical modification on chromatin are largely unknown. Here, focusing on methionine metabolism, we discuss recent developments of metabolic effects on chromatin modifications and structure, as well as consequences on gene regulation.
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Affiliation(s)
- Zhengtao Xiao
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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187
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Raas MWD, Zijlmans DW, Vermeulen M, Marks H. There is another: H3K27me3-mediated genomic imprinting. Trends Genet 2021; 38:82-96. [PMID: 34304914 DOI: 10.1016/j.tig.2021.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022]
Abstract
DNA methylation has long been considered the primary epigenetic mediator of genomic imprinting in mammals. Recent epigenetic profiling during early mouse development revealed the presence of domains of trimethylation of lysine 27 on histone H3 (H3K27me3) and chromatin compaction specifically at the maternally derived allele, independent of DNA methylation. Within these domains, genes are exclusively expressed from the paternally derived allele. This novel mechanism of noncanonical imprinting plays a key role in the development of mouse extraembryonic tissues and in the regulation of imprinted X-chromosome inactivation, highlighting the importance of parentally inherited epigenetic histone modifications. Here, we discuss the mechanisms underlying H3K27me3-mediated noncanonical imprinting in perspective of the dynamic chromatin landscape during early mouse development and explore evolutionary origins of noncanonical imprinting.
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Affiliation(s)
- Maximilian W D Raas
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands.
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188
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Harada A, Kimura H, Ohkawa Y. Recent advance in single-cell epigenomics. Curr Opin Struct Biol 2021; 71:116-122. [PMID: 34303078 DOI: 10.1016/j.sbi.2021.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/13/2021] [Accepted: 06/13/2021] [Indexed: 12/13/2022]
Abstract
The analysis of gene expression regulation, or the epigenome analysis, at the single-cell level is at the forefront of genomics research. To elucidate the mechanisms that regulate gene expression, chromatin immunoprecipitation has been conventionally used for determining the binding sites of DNA-binding proteins, such as histones and transcription factors. Now several new approaches have been emerged to reveal epigenome states at the single-cell level. Instead of using immunoprecipitation of fragmented chromatin, in situ reactions using cells or nuclei, combining with transposase tagging and other methods, have enabled single-cell analysis. Furthermore, single-cell multiomics techniques to simultaneously profiling transcriptome and open chromatin or histone modification have been developed. These single-cell analyses have the potential to identify different cell types in a cell population and reveal the dynamic changes of gene regulation, although those technologies have not yet reached a level for general application.
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Affiliation(s)
- Akihito Harada
- Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-0054, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-Ku, Yokohama, 226-8503, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-0054, Japan.
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189
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Bora P, Gahurova L, Hauserova A, Stiborova M, Collier R, Potěšil D, Zdráhal Z, Bruce AW. DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification. Open Biol 2021; 11:210092. [PMID: 34255976 PMCID: PMC8277471 DOI: 10.1098/rsob.210092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Successful navigation of the mouse preimplantation stages of development, during which three distinct blastocyst lineages are derived, represents a prerequisite for continued development. We previously identified a role for p38-mitogen-activated kinases (p38-MAPK) regulating blastocyst inner cell mass (ICM) cell fate, specifically primitive endoderm (PrE) differentiation, that is intimately linked to rRNA precursor processing, polysome formation and protein translation regulation. Here, we develop this work by assaying the role of DEAD-box RNA helicase 21 (DDX21), a known regulator of rRNA processing, in the context of p38-MAPK regulation of preimplantation mouse embryo development. We show nuclear DDX21 protein is robustly expressed from the 16-cell stage, becoming exclusively nucleolar during blastocyst maturation, a localization dependent on active p38-MAPK. siRNA-mediated clonal Ddx21 knockdown within developing embryos is associated with profound cell-autonomous and non-autonomous proliferation defects and reduced blastocyst volume, by the equivalent peri-implantation blastocyst stage. Moreover, ICM residing Ddx21 knockdown clones express the EPI marker NANOG but rarely express the PrE differentiation marker GATA4. These data contribute further significance to the emerging importance of lineage-specific translation regulation, as identified for p38-MAPK, during mouse preimplantation development.
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Affiliation(s)
- Pablo Bora
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Lenka Gahurova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Andrea Hauserova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Martina Stiborova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Rebecca Collier
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Alexander W Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
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190
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Legoff L, D'Cruz SC, Lebosq M, Gely-Pernot A, Bouchekhchoukha K, Monfort C, Kernanec PY, Tevosian S, Multigner L, Smagulova F. Developmental exposure to chlordecone induces transgenerational effects in somatic prostate tissue which are associated with epigenetic histone trimethylation changes. ENVIRONMENT INTERNATIONAL 2021; 152:106472. [PMID: 33711761 DOI: 10.1016/j.envint.2021.106472] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/11/2021] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Chlordecone (CD), also known as Kepone, is an organochlorine insecticide that has been used in banana crops in the French West Indies. Due to long-term contamination of soils and water, the population is still exposed to CD. Exposure to CD in adulthood is associated with an increased risk of prostate cancer (PCa). OBJECTIVES We examined the transgenerational effects of CD on murine prostate tissue. METHODS We exposed pregnant Swiss mice to CD. The prostates from directly exposed (F1) and non-exposed (F3) male progeny were analyzed. We used immunofluorescence, RNA-seq and ChIP-seq techniques for the comprehensive analyses of chromatin states in prostate. RESULTS We observed an increased prostatic intraepithelial neoplasia phenotype (PIN) in both F1 and F3 generations. Transcriptomic analysis in CD-derived F1 and F3 prostate using RNA-seq revealed that 970 genes in F1 and 218 in F3 genes were differentially expressed. The differentially expressed genes in both datasets could be clustered accordingly to common biological processes, "cell differentiation", "developmental process", "regulating of signaling", suggesting that in both generations similar processes were perturbed. We detected that in both datasets several Hox genes were upregulated; in F1, the expression was detected mainly in Hoxb and Hoxd, and in F3, in Hoxa family genes. Using a larger number of biological replicates and RT-qPCR we showed that genes implicated in testosterone synthesis (Akr1b3, Cyp11a1, Cyp17a1, Srd5a1) were dramatically upregulated in PIN samples; Cyp19a1, converting testosterone to estradiol was elevated as well. We found a dramatic increase in Esr2 expression both in F1 and F3 prostates containing PIN. The PIN-containing samples have a strong increase in expression of self-renewal-related genes (Nanog, Tbx3, Sox2, Sox3, Rb1). We observed changes in liver, F1 CD-exposed males have an increased expression of genes related to DNA repair, matrix collagen and inflammation related pathways in F1 but not in F3 adult CD-derived liver. The changes in RNA transcription were associated with epigenetic changes. Specifically, we found a global increase in H3K4 trimethylation (H3K4me3) and a decrease in H3K27 trimethylation (H3K27me3) in prostate of F1 mice. ChIP-seq analysis showed that 129 regions in F1 and 240 in F3 acquired altered H3K4me3 occupancy in CD-derived prostate, including highest increase at several promoters of Hoxa family genes in both datasets. The alteration in H3K4me3 in both generations overlap 73 genes including genes involved in proliferation regulation, Tbx2, Stat3, Stat5a, Pou2f3 and homeobox genes Hoxa13, Hoxa9. CONCLUSIONS Our data suggest that developmental exposure to CD leads to epigenetic changes in prostate tissue. The PIN containing samples showed evidence of implication in hormonal pathway and self-renewal gene expression that have the capacity to promote neoplasia in CD-exposed mice.
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Affiliation(s)
- Louis Legoff
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Shereen Cynthia D'Cruz
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Morgane Lebosq
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Aurore Gely-Pernot
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Katia Bouchekhchoukha
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Christine Monfort
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Pierre-Yves Kernanec
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Sergei Tevosian
- University of Florida, Department of Physiological Sciences, Box 100144, 1333 Center Drive, 32610 Gainesville, FL, USA.
| | - Luc Multigner
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
| | - Fatima Smagulova
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.
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191
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p38-MAPK-mediated translation regulation during early blastocyst development is required for primitive endoderm differentiation in mice. Commun Biol 2021; 4:788. [PMID: 34172827 PMCID: PMC8233355 DOI: 10.1038/s42003-021-02290-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Successful specification of the two mouse blastocyst inner cell mass (ICM) lineages (the primitive endoderm (PrE) and epiblast) is a prerequisite for continued development and requires active fibroblast growth factor 4 (FGF4) signaling. Previously, we identified a role for p38 mitogen-activated protein kinases (p38-MAPKs) during PrE differentiation, but the underlying mechanisms have remained unresolved. Here, we report an early blastocyst window of p38-MAPK activity that is required to regulate ribosome-related gene expression, rRNA precursor processing, polysome formation and protein translation. We show that p38-MAPK inhibition-induced PrE phenotypes can be partially rescued by activating the translational regulator mTOR. However, similar PrE phenotypes associated with extracellular signal-regulated kinase (ERK) pathway inhibition targeting active FGF4 signaling are not affected by mTOR activation. These data indicate a specific role for p38-MAPKs in providing a permissive translational environment during mouse blastocyst PrE differentiation that is distinct from classically reported FGF4-based mechanisms.
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192
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Au Yeung WK, Maruyama O, Sasaki H. A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns. BMC Bioinformatics 2021; 22:341. [PMID: 34162326 PMCID: PMC8220828 DOI: 10.1186/s12859-021-04272-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/15/2021] [Indexed: 12/02/2022] Open
Abstract
Background Epigenetic modifications, including CG methylation (a major form of DNA methylation) and histone modifications, interact with each other to shape their genomic distribution patterns. However, the entire picture of the epigenetic crosstalk regulating the CG methylation pattern is unknown especially in cells that are available only in a limited number, such as mammalian oocytes. Most machine learning approaches developed so far aim at finding DNA sequences responsible for the CG methylation patterns and were not tailored for studying the epigenetic crosstalk.
Results We built a machine learning model named epiNet to predict CG methylation patterns based on other epigenetic features, such as histone modifications, but not DNA sequence. Using epiNet, we identified biologically relevant epigenetic crosstalk between histone H3K36me3, H3K4me3, and CG methylation in mouse oocytes. This model also predicted the altered CG methylation pattern of mutant oocytes having perturbed histone modification, was applicable to cross-species prediction of the CG methylation pattern of human oocytes, and identified the epigenetic crosstalk potentially important in other cell types. Conclusions Our findings provide insight into the epigenetic crosstalk regulating the CG methylation pattern in mammalian oocytes and other cells. The use of epiNet should help to design or complement biological experiments in epigenetics studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04272-8.
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Affiliation(s)
- Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Osamu Maruyama
- Faculty of Design, Kyushu University, Fukuoka, 815-0032, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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193
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Liehrmann A, Rigaill G, Hocking TD. Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models. BMC Bioinformatics 2021; 22:323. [PMID: 34126932 PMCID: PMC8201703 DOI: 10.1186/s12859-021-04221-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/19/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson distribution to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them. RESULTS Our comparisons on seven reference datasets of histone modifications (H3K36me3 & H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model with alternative noise assumptions and supervised learning of the penalty parameter reduces the over-dispersion exhibited by count data. These models, implemented in the R package CROCS ( https://github.com/aLiehrmann/CROCS ), detect the peaks more accurately than algorithms which rely on natural assumptions. CONCLUSION The segmentation models we propose can benefit researchers in the field of epigenetics by providing new high-quality peak prediction tracks for H3K36me3 and H3K4me3 histone modifications.
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Affiliation(s)
- Arnaud Liehrmann
- Institut des Sciences des Plantes de Paris-Saclay (IPS2), Université Paris-Saclay, Université Evry, CNRS, INRAE, 91405 Orsay, France
- Laboratoire de Mathématiques et Modélisation d’Evry (LAMME), Université Paris-Saclay, Université Evry, CNRS, 91037 Evry, France
| | - Guillem Rigaill
- Institut des Sciences des Plantes de Paris-Saclay (IPS2), Université Paris-Saclay, Université Evry, CNRS, INRAE, 91405 Orsay, France
- Laboratoire de Mathématiques et Modélisation d’Evry (LAMME), Université Paris-Saclay, Université Evry, CNRS, 91037 Evry, France
| | - Toby Dylan Hocking
- School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University, 86011 Flagstaff, AZ USA
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194
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Lismer A, Lambrot R, Lafleur C, Dumeaux V, Kimmins S. ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance. STAR Protoc 2021; 2:100602. [PMID: 34159325 PMCID: PMC8202352 DOI: 10.1016/j.xpro.2021.100602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In the field of epigenetic inheritance, delineating molecular mechanisms implicated in the transfer of paternal environmental conditions to descendants has been elusive. This protocol details how to track sperm chromatin intergenerationally. We describe mouse model design to probe chromatin states in single mouse sperm and techniques to assess pre-implantation embryo chromatin and gene expression. We place emphasis on how to obtain high-quality and quantifiable data sets in sperm and embryos, as well as highlight the limitations of working with low input. For complete details on the use and execution of this protocol, please refer to Lismer et al. (2021). Assessment of paternal environmental exposure effects on sperm chromatin by ChIP-seq Tracking chromatin changes in sperm to embryos using ultra-low-input (ULI)-ChIP-seq Identification of gene expression changes in embryos using low-input mRNA-seq
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Romain Lambrot
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Vanessa Dumeaux
- PERFORM Center, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada.,Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
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195
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Hao N, Xin H, Shi X, Xin J, Zhang H, Guo S, Wang Z, Hao C. Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes. Bioinformatics 2021; 37:1039-1044. [PMID: 33119058 PMCID: PMC8150124 DOI: 10.1093/bioinformatics/btaa920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/26/2020] [Accepted: 10/15/2020] [Indexed: 01/17/2023] Open
Abstract
Motivation Exposure of mouse embryos to atrazine decreased histone tri-methylation at lysine 4 (H3K4me3) and increased expression of alternatively spliced RNA in the third generation. Specificity protein (SP) family motifs were enriched in the promoters of genes encoding differentially expressed alternative transcripts. Results H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) of mouse sperm, preimplantation embryo development and male gonad primordial germ cells (PGCs) were analysed to identify the paternal reprogramming-escape H3K4me3 regions (RERs). In total, 251 RERs selected harbour H3K4me3 marks in sperm, with signals occurring in the paternal genome during early development and in male gonad PGCs, and 179 genes had RERs within 1 kb of transcription start sites (TSSs). These genes were significantly enriched in the gene ontology term ‘RNA splicing’, and SP1/SP2/SP3 motifs were enriched in RER-associated H3K4me3 peaks. Overall, the H3K4me3 marks within TSSs of RNA splicing genes survived two rounds of the epigenetic reprogramming process. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nan Hao
- College of Pharmacy, Linyi University, Linyi 276000, China.,School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China
| | - Huawei Xin
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Xiaowei Shi
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Jie Xin
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Haijuan Zhang
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Shaofen Guo
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Zhen Wang
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Chunxiang Hao
- College of Pharmacy, Linyi University, Linyi 276000, China
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196
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Yan Z, An J, Peng Y, Kong S, Liu Q, Yang M, He Q, Song S, Chen Y, Chen W, Li R, Qiao J, Yan L. DevOmics: an integrated multi-omics database of human and mouse early embryo. Brief Bioinform 2021; 22:6294163. [PMID: 34097004 DOI: 10.1093/bib/bbab208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Transcriptomic and epigenetic alterations during early embryo development have been proven to play essential roles in regulating the cell fate. Nowadays, advances in single-cell transcriptomics and epigenomics profiling techniques provide large volumes of data for understanding the molecular regulatory mechanisms in early embryos and facilitate the investigation of assisted reproductive technology as well as preimplantation genetic testing. However, the lack of integrated data collection and unified analytic procedures greatly limits their usage in scientific research and clinical application. Hence, it is necessary to establish a database integrating the regulatory information of human and mouse early embryos with unified analytic procedures. Here, we introduce DevOmics (http://devomics.cn/), which contains normalized gene expression, DNA methylation, histone modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac), chromatin accessibility and 3D chromatin architecture profiles of human and mouse early embryos spanning six developmental stages (zygote, 2cell, 4cell, 8cell, morula and blastocyst (ICM, TE)). The current version of DevOmics provides Search and Advanced Search for retrieving genes a researcher is interested in, Analysis Tools including the differentially expressed genes (DEGs) analysis for acquiring DEGs between different types of samples, allelic explorer for displaying allele-specific gene expression as well as epigenetic modifications and correlation analysis for showing the dynamic changes in different layers of data across developmental stages, as well as Genome Browser and Ortholog for visualization. DevOmics offers a user-friendly website for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryos.
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Affiliation(s)
- Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Jianting An
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yong Peng
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Siming Kong
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Ming Yang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Qilong He
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Shi Song
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yidong Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Wei Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
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197
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Yang W, Ma Y, Jin J, Ren P, Zhou H, Xu S, Zhang Y, Hu Z, Rong Y, Dai Y, Zhang Y, Zhang S. Cyclophosphamide Exposure Causes Long-Term Detrimental Effect of Oocytes Developmental Competence Through Affecting the Epigenetic Modification and Maternal Factors' Transcription During Oocyte Growth. Front Cell Dev Biol 2021; 9:682060. [PMID: 34164401 PMCID: PMC8215553 DOI: 10.3389/fcell.2021.682060] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Cyclophosphamide (CTX) is widely used in various cancer therapies and in immunosuppression, and patients can still have babies after CTX chemotherapy. CTX directly causes primordial follicle loss with overactivation and DNA damage-induced apoptosis. Previous studies have shown that maternal exposure to CTX before conception increases the incidence of birth abnormalities and alters the methylation of genes in the oocytes of offspring. Mice were treated with a single dose of CTX (100 mg/kg) at post-natal day 21 and sacrificed 47 days later when primordial follicles surviving chemotherapy developed to the antral stage. Acute DNA damage and acceleration of the activation of primordial follicles after CTX treatment were repaired within several days, but the remaining follicle numbers remarkably decrease. Although partial surviving primordial follicle were developed to mature oocyte, oocyte quality hemostasis was impaired exhibiting aberrant meiosis progression, abnormal spindle and aneuploidy, mitochondrial dysfunction and increased endoplasmic reticulum stress. Thereafter, embryo development competency significantly decreased with fewer blastocyst formation after CTX exposure. CTX treatment resulted in alteration of DNA methylations and histone modifications in fully grown GV oocytes. Single-cell RNA-seq revealed CTX treatment suppressed multiple maternal genes’ transcription including many methyltransferases and maternal factor YAP1, which probably accounts for low quality of CTX-repaired oocyte. In vitro addition of lysophosphatidic acid (LPA) to embryo culture media to promote YAP1 nuclear localization improved CTX-repaired embryo developmental competence. This study provides evidence for the consistent toxic effect of CTX exposure during follicle development, and provide a new mechanism and new insights into future clinical interventions for fertility preservation.
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Affiliation(s)
- Weijie Yang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Yerong Ma
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Jiamin Jin
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Peipei Ren
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Hanjing Zhou
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Shiqian Xu
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Yingyi Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Zhanhong Hu
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Yan Rong
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Yongdong Dai
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Yinli Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
| | - Songying Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Department of Obstetrics and Gynecology, Hangzhou, China
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198
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Kibe K, Shirane K, Ohishi H, Uemura S, Toh H, Sasaki H. The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes. PLoS Genet 2021; 17:e1009570. [PMID: 34048432 PMCID: PMC8162659 DOI: 10.1371/journal.pgen.1009570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT3A. DNMT3A has a PWWP domain, which recognizes H3K36me2/3, and heterozygous mutations in this domain, including D329A substitution, cause aberrant CG hypermethylation of regions marked by H3K27me3 in somatic cells, leading to a dwarfism phenotype. We herein demonstrate that D329A homozygous mice show greater CG hypermethylation and severer dwarfism. In oocytes, D329A substitution did not affect CG methylation of H3K36me2/3-marked regions, including maternally methylated imprinting control regions; rather, it caused aberrant hypermethylation in regions lacking H3K36me2/3, including H3K27me3-marked regions. Thus, the role of the PWWP domain in CG methylation seems similar in somatic cells and oocytes; however, there were cell-type-specific differences in affected regions. The major satellite repeat was also hypermethylated in mutant oocytes. Contrary to the CA hypomethylation in somatic cells, the mutation caused hypermethylation at CH sites, including CA sites. Surprisingly, oocytes expressing only the mutated protein could support embryonic and postnatal development. Our study reveals that the DNMT3A PWWP domain is important for suppressing aberrant CG hypermethylation in both somatic cells and oocytes but that D329A mutation has little impact on the developmental potential of oocytes.
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Affiliation(s)
- Kanako Kibe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- * E-mail:
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199
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Yuan Y, Deng Q, Wei X, Liu Y, Lan Q, Jiang Y, Yu Y, Guo P, Xu J, Yu C, Han L, Cheng M, Wu P, Zhang X, Lai Y, Volpe G, Esteban MA, Yang H, Liu C, Liu L. The Chromatin Accessibility Landscape of Adult Rat. Front Genet 2021; 12:651604. [PMID: 34108989 PMCID: PMC8181391 DOI: 10.3389/fgene.2021.651604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yue Yuan
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Qiuting Deng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xiaoyu Wei
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Yang Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Yu Jiang
- First Hospital, Jilin University, Changchun, China
| | - Yeya Yu
- BGI-Shenzhen, Shenzhen, China.,BGI College, Zhengzhou University, Zhengzhou, China
| | - Pengcheng Guo
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiangshan Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Cong Yu
- BGI-Shenzhen, Shenzhen, China
| | - Lei Han
- BGI-Shenzhen, Shenzhen, China
| | - Mengnan Cheng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Xiao Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Miguel A Esteban
- BGI-Shenzhen, Shenzhen, China.,First Hospital, Jilin University, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China.,Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen, China
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200
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Wike CL, Guo Y, Tan M, Nakamura R, Shaw DK, Díaz N, Whittaker-Tademy AF, Durand NC, Aiden EL, Vaquerizas JM, Grunwald D, Takeda H, Cairns BR. Chromatin architecture transitions from zebrafish sperm through early embryogenesis. Genome Res 2021; 31:981-994. [PMID: 34006569 PMCID: PMC8168589 DOI: 10.1101/gr.269860.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/07/2021] [Indexed: 11/25/2022]
Abstract
Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated domains and instead displays “hinge-like” domains of ∼150 kb that repeat every 1–2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of ∼90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. Together, this study reveals hinge-like domains in histone-packaged zebrafish sperm chromatin and determines that the initial formation of high-order chromatin architecture in zebrafish embryos occurs after ZGA primarily at enhancers bearing high H3K27ac.
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Affiliation(s)
- Candice L Wike
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yixuan Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mengyao Tan
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Dana Klatt Shaw
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Aneasha F Whittaker-Tademy
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - David Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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