1
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Wang J, Zhou X, Han T, Zhang H. Epigenetic signatures of trophoblast lineage and their biological functions. Cells Dev 2024:203934. [PMID: 38942294 DOI: 10.1016/j.cdev.2024.203934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 06/30/2024]
Abstract
Trophoblasts play a crucial role in embryo implantation and in interacting with the maternal uterus. The trophoblast lineage develops into a substantial part of the placenta, a temporary extra-embryonic organ, capable of undergoing distinctive epigenetic events during development. The critical role of trophoblast-specific epigenetic signatures in regulating placental development has become known, significantly advancing our understanding of trophoblast identity and lineage development. Scientific efforts are revealing how trophoblast-specific epigenetic signatures mediate stage-specific gene regulatory programming during the development of the trophoblast lineage. These epigenetic signatures have a significant impact on blastocyst formation, placental development, as well as the growth and survival of embryos and fetuses. In evolution, DNA hypomethylation in the trophoblast lineage is conserved, and there is a significant disparity in the control of epigenetic dynamics and the landscape of genomic imprinting. Scientists have used murine and human multipotent trophoblast cells as in vitro models to recapitulate the essential epigenetic processes of placental development. Here, we review the epigenetic signatures of the trophoblast lineage and their biological functions to enhance our understanding of placental evolution, development, and function.
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Affiliation(s)
- Jianqi Wang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaobo Zhou
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Reproductive Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Tingli Han
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China; The Center for Reproductive Medicine, Obstetrics and Gynecology Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
| | - Hua Zhang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China.
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2
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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
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Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
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3
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Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons. Nat Commun 2024; 15:1781. [PMID: 38453932 PMCID: PMC10920760 DOI: 10.1038/s41467-024-45773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
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Affiliation(s)
- Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| | - Sergio Niñerola
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Ana M Martín-González
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Minji Kim
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Bioinformatics Unit, Hospital universitario Puerta de Hierro Majadahonda, 28220, Majadahonda, Spain
| | - Carina Racovac
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Jose V Sanchez-Mut
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Yijun Ruan
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
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4
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Nat Struct Mol Biol 2024; 31:125-140. [PMID: 38053013 PMCID: PMC10897904 DOI: 10.1038/s41594-023-01130-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/18/2023] [Indexed: 12/07/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the epiblast and the primitive endoderm. Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements through which transcriptional regulators enact these fates remain understudied. Here, we characterize, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observe extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although distinct groups of genes are irresponsive to topological changes. In each lineage, a high degree of connectivity, or 'hubness', positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a predictive model for transcriptional regulation (3D-HiChAT) that outperforms models using only 1D promoter or proximal variables to predict levels and cell-type specificity of gene expression. Using 3D-HiChAT, we identify, in silico, candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments, we validate several enhancers that control gene expression in their respective lineages. Our study identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to comprehensively understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- 3D Chromatin Conformation and RNA Genomics Laboratory, Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher M Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ly-Sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY, USA.
- Department of Medicine, New York University Langone Health, New York, NY, USA.
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA.
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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5
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Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E. Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape. Nat Commun 2023; 14:4826. [PMID: 37563143 PMCID: PMC10415281 DOI: 10.1038/s41467-023-40424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
The extravillous trophoblast cell lineage is a key feature of placentation and successful pregnancy. Knowledge of transcriptional regulation driving extravillous trophoblast cell development is limited. Here, we map the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem cells and their transition into extravillous trophoblast cells. We show that integrating chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enables identification of transcription factors and regulatory mechanisms critical for extravillous trophoblast cell development. We elucidate functional roles for TFAP2C, SNAI1, and EPAS1 in the regulation of extravillous trophoblast cell development. EPAS1 is identified as an upstream regulator of key extravillous trophoblast cell transcription factors, including ASCL2 and SNAI1 and together with its target genes, is linked to pregnancy loss and birth weight. Collectively, we reveal activation of a dynamic regulatory network and provide a framework for understanding extravillous trophoblast cell specification in trophoblast cell lineage development and human placentation.
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Affiliation(s)
- Kaela M Varberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Esteban M Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Ross P McNally
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Emily R Wesley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Michael Lydic
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Kristin Holoch
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Courtney Marsh
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Michael J Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Elin Grundberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
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6
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. Core conserved transcriptional regulatory networks define the invasive trophoblast cell lineage. Development 2023; 150:dev201826. [PMID: 37417811 PMCID: PMC10445752 DOI: 10.1242/dev.201826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
The invasive trophoblast cell lineages in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model for studying hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus ATAC-seq data from gestation day 15.5 and 19.5 rat uterine-placental interface tissues, and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial and smooth muscle cells, and compared invasive trophoblast chromatin accessibility with extravillous trophoblast cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy, Kansas City, MO 64108, USA
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
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7
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549714. [PMID: 37577543 PMCID: PMC10422694 DOI: 10.1101/2023.07.19.549714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the primitive endoderm (PrE). Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements via which transcriptional regulators enact these fates remain understudied. To address this gap, we have characterized, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observed extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although there are distinct groups of genes that are irresponsive to topological changes. In each lineage, a high degree of connectivity or "hubness" positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages, compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a novel predictive model for transcriptional regulation (3D-HiChAT), which outperformed models that use only 1D promoter or proximal variables in predicting levels and cell-type specificity of gene expression. Using 3D-HiChAT, we performed genome-wide in silico perturbations to nominate candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments we validated several novel enhancers that control expression of one or more genes in their respective lineages. Our study comprehensively identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
- 3D Chromatin Conformation and RNA genomics laboratory, Instituto Italiano di Tecnologia (IIT), Center for Human Technologies (CHT), Genova, Italy (current affiliation)
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, 10065, New York, USA
| | - Christopher M. Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Ly-sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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8
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Senner CE, Dong Z, Prater M, Branco MR, Watson ED. One-carbon metabolism is required for epigenetic stability in the mouse placenta. Front Cell Dev Biol 2023; 11:1209928. [PMID: 37440923 PMCID: PMC10333575 DOI: 10.3389/fcell.2023.1209928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023] Open
Abstract
One-carbon metabolism, including the folate cycle, has a crucial role in fetal development though its molecular function is complex and unclear. The hypomorphic Mtrr gt allele is known to disrupt one-carbon metabolism, and thus methyl group availability, leading to several developmental phenotypes (e.g., neural tube closure defects, fetal growth anomalies). Remarkably, previous studies showed that some of the phenotypes were transgenerationally inherited. Here, we explored the genome-wide epigenetic impact of one-carbon metabolism in placentas associated with fetal growth phenotypes and determined whether specific DNA methylation changes were inherited. Firstly, methylome analysis of Mtrr gt/gt homozygous placentas revealed genome-wide epigenetic instability. Several differentially methylated regions (DMRs) were identified including at the Cxcl1 gene promoter and at the En2 gene locus, which may have phenotypic implications. Importantly, we discovered hypomethylation and ectopic expression of a subset of ERV elements throughout the genome of Mtrr gt/gt placentas with broad implications for genomic stability. Next, we determined that known spermatozoan DMRs in Mtrr gt/gt males were reprogrammed in the placenta with little evidence of direct or transgenerational germline DMR inheritance. However, some spermatozoan DMRs were associated with placental gene misexpression despite normalisation of DNA methylation, suggesting the inheritance of an alternative epigenetic mechanism. Integration of published wildtype histone ChIP-seq datasets with Mtrr gt/gt spermatozoan methylome and placental transcriptome datasets point towards H3K4me3 deposition at key loci. These data suggest that histone modifications might play a role in epigenetic inheritance in this context. Overall, this study sheds light on the mechanistic complexities of one-carbon metabolism in development and epigenetic inheritance.
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Affiliation(s)
- Claire E. Senner
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Ziqi Dong
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Malwina Prater
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Miguel R. Branco
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Erica D. Watson
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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9
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Dejosez M, Dall'Agnese A, Ramamoorthy M, Platt J, Yin X, Hogan M, Brosh R, Weintraub AS, Hnisz D, Abraham BJ, Young RA, Zwaka TP. Regulatory architecture of housekeeping genes is driven by promoter assemblies. Cell Rep 2023; 42:112505. [PMID: 37182209 PMCID: PMC10329844 DOI: 10.1016/j.celrep.2023.112505] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/22/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
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Affiliation(s)
- Marion Dejosez
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Alessandra Dall'Agnese
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mahesh Ramamoorthy
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jesse Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Xing Yin
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Megan Hogan
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Ran Brosh
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- St. Jude Research Children's Hospital, Memphis, TN 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thomas P Zwaka
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA.
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10
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534962. [PMID: 37066272 PMCID: PMC10103937 DOI: 10.1101/2023.03.30.534962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The invasive trophoblast cell lineage in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model to study hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus (sn) ATAC-seq data from gestation day (gd) 15.5 and 19.5 rat uterine-placental interface tissues and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial, and smooth muscle cells, and compared invasive trophoblast chromatin accessibility to extravillous trophoblast (EVT) cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, MO, 64108
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
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11
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Weigert R, Hetzel S, Bailly N, Haggerty C, Ilik IA, Yung PYK, Navarro C, Bolondi A, Kumar AS, Anania C, Brändl B, Meierhofer D, Lupiáñez DG, Müller FJ, Aktas T, Elsässer SJ, Kretzmer H, Smith ZD, Meissner A. Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nat Cell Biol 2023; 25:579-591. [PMID: 37024684 PMCID: PMC10104784 DOI: 10.1038/s41556-023-01114-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb repressive complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extra-embryonic lineages display non-canonical, globally intermediate DNA methylation levels, including disruption of local Polycomb domains. Here, to better understand this unusual landscape's molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse trophoblast stem cells. We find that the extra-embryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extra-embryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.
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Affiliation(s)
- Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Medical Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nina Bailly
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Chuck Haggerty
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ibrahim A Ilik
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Philip Yuk Kwong Yung
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carmen Navarro
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chiara Anania
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany
| | - David Meierhofer
- Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany
| | - Tugce Aktas
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, US.
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12
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Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia. Nat Commun 2023; 14:724. [PMID: 36759620 PMCID: PMC9911410 DOI: 10.1038/s41467-023-36262-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
The PML::RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML::RARA binding on gene expression and regulation in an inducible PML::RARA cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML::RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a computational machine learning implementation called Regulatory Element Behavior Extraction Learning to deconvolute the complex, local transcription factor binding site environment at PML::RARA bound positions to reveal distinct signatures that modulate how PML::RARA directs the transcriptional response.
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13
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Du C, Jiang J, Li Y, Yu M, Jin J, Chen S, Fan H, Macfarlan TS, Cao B, Sun MA. Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells. Genome Res 2023; 33:197-207. [PMID: 36806146 PMCID: PMC10069462 DOI: 10.1101/gr.277150.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023]
Abstract
The placenta is an organ with extraordinary phenotypic diversity in eutherian mammals. Recent evidence suggests that numerous human placental enhancers are evolved from lineage-specific insertions of endogenous retroviruses (ERVs), yet the transcription factors (TFs) underlying their regulation remain largely elusive. Here, by first focusing on MER41, a primate-specific ERV family previously linked to placenta and innate immunity, we uncover the binding motifs of multiple crucial trophoblast TFs (GATA2/3, MSX2, GRHL2) in addition to innate immunity TFs STAT1 and IRF1. Integration of ChIP-seq data confirms the binding of GATA2/3, MSX2, and their related factors on the majority of MER41-derived enhancers in human trophoblast stem cells (TSCs). MER41-derived enhancers that are constitutively active in human TSCs are distinct from those activated upon interferon stimulation, which is determined by the binding of relevant TFs and their subfamily compositions. We further demonstrate that GATA2/3 and MSX2 have prevalent binding to numerous other ERV families - indicating their broad impact on ERV-derived enhancers. Functionally, the derepression of many syncytiotrophoblast genes after MSX2 knockdown is likely to be mediated by regulatory elements derived from ERVs - suggesting ERVs are also important for mediating transcriptional repression. Overall, this study characterizes the regulation of ERV-derived regulatory elements by GATA2/3, MSX2, and their cofactors in human TSCs, and provides mechanistic insights into the importance of ERVs in human trophoblast regulatory network.
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Affiliation(s)
- Cui Du
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jing Jiang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuzhuo Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Miao Yu
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jian Jin
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shuai Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hairui Fan
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892, USA
| | - Bin Cao
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China;
| | - Ming-An Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; .,Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, Jiangsu 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
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14
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Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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15
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Bylino OV, Ibragimov AN, Digilio FA, Giordano E, Shidlovskii YV. Application of the 3C Method to Study the Developmental Genes in Drosophila Larvae. Front Genet 2022; 13:734208. [PMID: 35910225 PMCID: PMC9335292 DOI: 10.3389/fgene.2022.734208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
A transition from one developmental stage to another is accompanied by activation of developmental programs and corresponding gene ensembles. Changes in the spatial conformation of the corresponding loci are associated with this activation and can be investigated with the help of the Chromosome Conformation Capture (3C) methodology. Application of 3C to specific developmental stages is a sophisticated task. Here, we describe the use of the 3C method to study the spatial organization of developmental loci in Drosophila larvae. We critically analyzed the existing protocols and offered our own solutions and the optimized protocol to overcome limitations. To demonstrate the efficiency of our procedure, we studied the spatial organization of the developmental locus Dad in 3rd instar Drosophila larvae. Differences in locus conformation were found between embryonic cells and living wild-type larvae. We also observed the establishment of novel regulatory interactions in the presence of an adjacent transgene upon activation of its expression in larvae. Our work fills the gap in the application of the 3C method to Drosophila larvae and provides a useful guide for establishing 3C on an animal model.
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Affiliation(s)
- Oleg V. Bylino
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Airat N. Ibragimov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Ennio Giordano
- Department of Biology, Università di Napoli Federico II, Naples, Italy
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- *Correspondence: Yulii V. Shidlovskii,
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16
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Yan J, Huangfu D. Epigenome rewiring in human pluripotent stem cells. Trends Cell Biol 2022; 32:259-271. [PMID: 34955367 PMCID: PMC8840982 DOI: 10.1016/j.tcb.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/10/2023]
Abstract
The epigenome plays a crucial role in modulating the activity of regulatory elements, thereby orchestrating diverse transcriptional programs during embryonic development. Human (h)PSC stepwise differentiation provides an excellent platform for capturing dynamic epigenomic events during lineage transition in human development. Here we discuss how recent technological advances, from epigenomic mapping to targeted perturbation, are providing a more comprehensive appreciation of remodeling of the chromatin landscape during human development with implications for aberrant rewiring in disease. We predict that the continuous innovation of hPSC differentiation methods, epigenome mapping, and CRISPR (clustered regularly interspaced short palindromic repeats) perturbation technologies will allow researchers to build toward not only a comprehensive understanding of the epigenomic mechanisms governing development, but also a highly flexible way to model diseases with opportunities for translation.
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Affiliation(s)
- Jielin Yan
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Danwei Huangfu
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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17
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Fang H, Luo Z, Lin C. Epigenetic reorganization during early embryonic lineage specification. Genes Genomics 2022; 44:379-387. [PMID: 35133623 DOI: 10.1007/s13258-021-01213-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dynamic chromatin reorganization occurs during two waves of cell lineage specification process, blastocyst formation and gastrulation, to generate distinct cell types. Epigenetic defects have been associated with severe developmental defects and diseases. How epigenetic remodeling coordinates the two lineage specification waves is becoming uncovered, benefiting from the development and application of new technologies including low-input or single-cell epigenome analysis approached in the past few years. OBJECTIVE In this review, we aim to highlight the most recent findings on epigenetic remodeling in cell lineage specification during blastocyst formation and gastrulation. METHODS First, we introduce how DNA methylation dynamically changes in blastocyst formation and gastrulation and its function in transcriptional regulation lineage-specific genes. Then, we discuss widespread remodeling of histone modification at promoters and enhancers in orchestrating the trajectory of cell lineage specification. Finally, we review dynamics of chromatin accessibility and 3D structure regulating developmental gene expression and associating with specific transcription factor binding events at stage specific manner. We also highlight the key questions that remain to be answered to fully understand chromatin regulation and reorganization in lineage specification. CONCLUSION Here, we summarize the recent advances and discoveries on epigenetic reorganization and its roles in blastocyst formation and gastrulation, and how it cooperates with the lineage specification, painting from global sequencing data from mouse in vivo tissues.
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Affiliation(s)
- Haitong Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
| | - Zhuojuan Luo
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Chengqi Lin
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China. .,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
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18
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Cornejo-Paramo P, Roper K, Degnan S, Degnan B, Wong ES. Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis. Genome Res 2022; 32:474-487. [PMID: 35045977 PMCID: PMC8896464 DOI: 10.1101/gr.275864.121] [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: 06/04/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
The chromatin environment plays a central role in regulating developmental gene expression in metazoans. Yet, the ancestral regulatory landscape of metazoan embryogenesis is unknown. Here, we generate chromatin accessibility profiles for six embryonic, plus larval and adult stages in the sponge Amphimedon queenslandica. These profiles are reproducible within stages, reflect histone modifications, and identify transcription factor (TF) binding sequence motifs predictive of cis-regulatory elements operating during embryogenesis in other metazoans, but not the unicellular relative Capsaspora. Motif analysis of chromatin accessibility profiles across Amphimedon embryogenesis identifies three major developmental periods. As in bilaterian embryogenesis, early development in Amphimedon involves activating and repressive chromatin in regions both proximal and distal to transcription start sites. Transcriptionally repressive elements (“silencers”) are prominent during late embryogenesis. They coincide with an increase in cis-regulatory regions harboring metazoan TF binding motifs, as well as an increase in the expression of metazoan-specific genes. Changes in chromatin state and gene expression in Amphimedon suggest the conservation of distal enhancers, dynamically silenced chromatin, and TF-DNA binding specificity in animal embryogenesis.
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19
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Orozco G, Schoenfelder S, Walker N, Eyre S, Fraser P. 3D genome organization links non-coding disease-associated variants to genes. Front Cell Dev Biol 2022; 10:995388. [PMID: 36340032 PMCID: PMC9631826 DOI: 10.3389/fcell.2022.995388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing has revealed over 300 million genetic variations in human populations. Over 90% of variants are single nucleotide polymorphisms (SNPs), the remainder include short deletions or insertions, and small numbers of structural variants. Hundreds of thousands of these variants have been associated with specific phenotypic traits and diseases through genome wide association studies which link significant differences in variant frequencies with specific phenotypes among large groups of individuals. Only 5% of disease-associated SNPs are located in gene coding sequences, with the potential to disrupt gene expression or alter of the function of encoded proteins. The remaining 95% of disease-associated SNPs are located in non-coding DNA sequences which make up 98% of the genome. The role of non-coding, disease-associated SNPs, many of which are located at considerable distances from any gene, was at first a mystery until the discovery that gene promoters regularly interact with distal regulatory elements to control gene expression. Disease-associated SNPs are enriched at the millions of gene regulatory elements that are dispersed throughout the non-coding sequences of the genome, suggesting they function as gene regulation variants. Assigning specific regulatory elements to the genes they control is not straightforward since they can be millions of base pairs apart. In this review we describe how understanding 3D genome organization can identify specific interactions between gene promoters and distal regulatory elements and how 3D genomics can link disease-associated SNPs to their target genes. Understanding which gene or genes contribute to a specific disease is the first step in designing rational therapeutic interventions.
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Affiliation(s)
- Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, United Kingdom
| | - Stefan Schoenfelder
- Enhanc3D Genomics Ltd., Cambridge, United Kingdom.,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, CB22 3AT Cambridge, Cambridge, United Kingdom
| | | | - Stephan Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, United Kingdom
| | - Peter Fraser
- Enhanc3D Genomics Ltd., Cambridge, United Kingdom.,Department of Biological Science, Florida State University, Tallahassee, FL, United States
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20
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Laverre A, Tannier E, Necsulea A. Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. Genome Res 2021; 32:280-296. [PMID: 34930799 PMCID: PMC8805723 DOI: 10.1101/gr.275901.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022]
Abstract
Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements are rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny, or contacts with target genes, is significantly associated with gene expression evolution.
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Affiliation(s)
- Alexandre Laverre
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive
| | - Eric Tannier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Centre de recherche Inria de Lyon
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21
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Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
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22
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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23
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Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Front Cell Dev Biol 2021; 9:723859. [PMID: 34422840 PMCID: PMC8371409 DOI: 10.3389/fcell.2021.723859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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24
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Defective folate metabolism causes germline epigenetic instability and distinguishes Hira as a phenotype inheritance biomarker. Nat Commun 2021; 12:3714. [PMID: 34140513 PMCID: PMC8211854 DOI: 10.1038/s41467-021-24036-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/29/2021] [Indexed: 02/02/2023] Open
Abstract
The mechanism behind transgenerational epigenetic inheritance is unclear, particularly through the maternal grandparental line. We previously showed that disruption of folate metabolism in mice by the Mtrr hypomorphic mutation results in transgenerational epigenetic inheritance of congenital malformations. Either maternal grandparent can initiate this phenomenon, which persists for at least four wildtype generations. Here, we use genome-wide approaches to reveal genetic stability in the Mtrr model and genome-wide differential DNA methylation in the germline of Mtrr mutant maternal grandfathers. We observe that, while epigenetic reprogramming occurs, wildtype grandprogeny and great grandprogeny exhibit transcriptional changes that correlate with germline methylation defects. One region encompasses the Hira gene, which is misexpressed in embryos for at least three wildtype generations in a manner that distinguishes Hira transcript expression as a biomarker of maternal phenotypic inheritance.
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25
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Lee BK, Kim J. Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development. Front Cell Dev Biol 2021; 9:673065. [PMID: 34150768 PMCID: PMC8206641 DOI: 10.3389/fcell.2021.673065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
The placenta is a temporary but pivotal organ for human pregnancy. It consists of multiple specialized trophoblast cell types originating from the trophectoderm of the blastocyst stage of the embryo. While impaired trophoblast differentiation results in pregnancy disorders affecting both mother and fetus, the molecular mechanisms underlying early human placenta development have been poorly understood, partially due to the limited access to developing human placentas and the lack of suitable human in vitro trophoblast models. Recent success in establishing human trophoblast stem cells and other human in vitro trophoblast models with their differentiation protocols into more specialized cell types, such as syncytiotrophoblast and extravillous trophoblast, has provided a tremendous opportunity to understand early human placenta development. Unfortunately, while high-throughput research methods and omics tools have addressed numerous molecular-level questions in various research fields, these tools have not been widely applied to the above-mentioned human trophoblast models. This review aims to provide an overview of various omics approaches that can be utilized in the study of human in vitro placenta models by exemplifying some important lessons obtained from omics studies of mouse model systems and introducing recently available human in vitro trophoblast model systems. We also highlight some key unknown questions that might be addressed by such techniques. Integrating high-throughput omics approaches and human in vitro model systems will facilitate our understanding of molecular-level regulatory mechanisms underlying early human placenta development as well as placenta-associated complications.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-State University of New York, Rensselaer, NY, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, United States
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26
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Kishimoto K, Wilder CL, Buchanan J, Nguyen M, Okeke C, Hoffmann A, Cheng QJ. High Dose IFN- β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells. Front Immunol 2021; 12:651254. [PMID: 33897699 PMCID: PMC8062733 DOI: 10.3389/fimmu.2021.651254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Interferon β (IFN-β) signaling activates the transcription factor complex ISGF3 to induce gene expression programs critical for antiviral defense and host immune responses. It has also been observed that IFN-β activates a second transcription factor complex, γ-activated factor (GAF), but the significance of this coordinated activation is unclear. We report that in murine lung epithelial cells (MLE12) high doses of IFN-β indeed activate both ISGF3 and GAF, which bind to distinct genomic locations defined by their respective DNA sequence motifs. In contrast, low doses of IFN-β preferentially activate ISGF3 but not GAF. Surprisingly, in MLE12 cells GAF binding does not induce nearby gene expression even when strongly bound to the promoter. Yet expression of interferon stimulated genes is enhanced when GAF and ISGF3 are both active compared to ISGF3 alone. We propose that GAF may function as a dose-sensitive amplifier of ISG expression to enhance antiviral immunity and establish pro-inflammatory states.
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Affiliation(s)
- Kensei Kishimoto
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, United States.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States
| | - Catera L Wilder
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Justin Buchanan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Minh Nguyen
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Chidera Okeke
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, United States.,Department of Life and Physical Sciences, Fisk University, Nashville, TN, United States
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Quen J Cheng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States.,Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
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27
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Abstract
Single-cell sequencing-based methods for profiling gene transcript levels have revealed substantial heterogeneity in expression levels among morphologically indistinguishable cells. This variability has important functional implications for tissue biology and disease states such as cancer. Mapping of epigenomic information such as chromatin accessibility, nucleosome positioning, histone tail modifications and enhancer-promoter interactions in both bulk-cell and single-cell samples has shown that these characteristics of chromatin state contribute to expression or repression of associated genes. Advances in single-cell epigenomic profiling methods are enabling high-resolution mapping of chromatin states in individual cells. Recent studies using these techniques provide evidence that variations in different aspects of chromatin organization collectively define gene expression heterogeneity among otherwise highly similar cells.
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Affiliation(s)
- Benjamin Carter
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
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28
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Chromatin Regulation in Development: Current Understanding and Approaches. Stem Cells Int 2021; 2021:8817581. [PMID: 33603792 PMCID: PMC7872760 DOI: 10.1155/2021/8817581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/29/2020] [Accepted: 01/21/2021] [Indexed: 11/24/2022] Open
Abstract
The regulation of mammalian stem cell fate during differentiation is complex and can be delineated across many levels. At the chromatin level, the replacement of histone variants by chromatin-modifying proteins, enrichment of specific active and repressive histone modifications, long-range gene interactions, and topological changes all play crucial roles in the determination of cell fate. These processes control regulatory elements of critical transcriptional factors, thereby establishing the networks unique to different cell fates and initiate waves of distinctive transcription events. Due to the technical challenges posed by previous methods, it was difficult to decipher the mechanism of cell fate determination at early embryogenesis through chromatin regulation. Recently, single-cell approaches have revolutionised the field of developmental biology, allowing unprecedented insights into chromatin structure and interactions in early lineage segregation events during differentiation. Here, we review the recent technological advancements and how they have furthered our understanding of chromatin regulation during early differentiation events.
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29
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Abstract
In the past several decades, the establishment of in vitro models of pluripotency has ushered in a golden era for developmental and stem cell biology. Research in this arena has led to profound insights into the regulatory features that shape early embryonic development. Nevertheless, an integrative theory of the epigenetic principles that govern the pluripotent nucleus remains elusive. Here, we summarize the epigenetic characteristics that define the pluripotent state. We cover what is currently known about the epigenome of pluripotent stem cells and reflect on the use of embryonic stem cells as an experimental system. In addition, we highlight insights from super-resolution microscopy, which have advanced our understanding of the form and function of chromatin, particularly its role in establishing the characteristically "open chromatin" of pluripotent nuclei. Further, we discuss the rapid improvements in 3C-based methods, which have given us a means to investigate the 3D spatial organization of the pluripotent genome. This has aided the adaptation of prior notions of a "pluripotent molecular circuitry" into a more holistic model, where hotspots of co-interacting domains correspond with the accumulation of pluripotency-associated factors. Finally, we relate these earlier hypotheses to an emerging model of phase separation, which posits that a biophysical mechanism may presuppose the formation of a pluripotent-state-defining transcriptional program.
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Affiliation(s)
| | - Eran Meshorer
- Department of Genetics, the Institute of Life Sciences
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel 9190400
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30
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Olan I, Parry AJ, Schoenfelder S, Narita M, Ito Y, Chan ASL, Slater GSC, Bihary D, Bando M, Shirahige K, Kimura H, Samarajiwa SA, Fraser P, Narita M. Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence. Nat Commun 2020; 11:6049. [PMID: 33247104 PMCID: PMC7695716 DOI: 10.1038/s41467-020-19878-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
Senescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue homeostasis. Enhancer-promoter interactions, facilitated by chromatin loops, play a key role in gene regulation but their relevance in senescence remains elusive. Here, we use Hi-C to show that oncogenic RAS-induced senescence in human diploid fibroblasts is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks often at the 3' end of a subset of active genes. RAS-induced de novo cohesin peaks are transcription-dependent and enriched for senescence-associated genes, exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Similar IL1B induction with de novo cohesin appearance and new loop formation are observed in terminally differentiated macrophages, but not TNFα-treated cells. These results suggest that RAS-induced senescence represents a cell fate determination-like process characterised by a unique gene expression profile and 3D genome folding signature, mediated in part through cohesin redistribution on chromatin.
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Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Aled J Parry
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Stefan Schoenfelder
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Masako Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Adelyne S L Chan
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Guy St C Slater
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Dóra Bihary
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Masashige Bando
- Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shamith A Samarajiwa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK.
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK.
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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31
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Shendy NAM, Raghu D, Roy S, Perry CH, Safi A, Branco MR, Homayouni R, Abell AN. Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching. Commun Biol 2020; 3:475. [PMID: 32859943 PMCID: PMC7455715 DOI: 10.1038/s42003-020-01200-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Coordinated gene expression is required for phenotypic switching between epithelial and mesenchymal phenotypes during normal development and in disease states. Trophoblast stem (TS) cells undergo epithelial-mesenchymal transition (EMT) during implantation and placentation. Mechanisms coordinating gene expression during these processes are poorly understood. We have previously demonstrated that MAP3K4-regulated chromatin modifiers CBP and HDAC6 each regulate thousands of genes during EMT in TS cells. Here we show that CBP and HDAC6 coordinate expression of only 183 genes predicted to be critical regulators of phenotypic switching. The highest-ranking co-regulated gene is the NF-κB family member Rel. Although NF-κB is primarily regulated post-transcriptionally, CBP and HDAC6 control Rel transcript levels by binding Rel regulatory regions and controlling histone acetylation. REL re-expression in mesenchymal-like TS cells induces a mesenchymal-epithelial transition. Importantly, REL forms a feedback loop, blocking HDAC6 expression and nuclear localization. Together, our work defines a developmental program coordinating phenotypic switching. Noha Shendy et al. study the role of CBP and HDAC6 in phenotypic switching using trophoblast stem cells. They identify Rel, an NF-kB family member, to be transcriptionally coregulated by CBP and HDAC6. Surprisingly, Rel induces mesenchymal-epithelial transition and itself regulated Hdac6 expression and nuclear localization.
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Affiliation(s)
- Noha Ahmed Mohammed Shendy
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA.,Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Deepthi Raghu
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
| | - Sujoy Roy
- Department of Foundational Medical Studies, Oakland University William Beaumont School of Medicine, Rochester, MI, 48309-4482, USA
| | | | - Adiba Safi
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
| | - Miguel Ramos Branco
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Ramin Homayouni
- Department of Foundational Medical Studies, Oakland University William Beaumont School of Medicine, Rochester, MI, 48309-4482, USA
| | - Amy Noel Abell
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA.
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32
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Gentile C, Kmita M. Polycomb Repressive Complexes in Hox Gene Regulation: Silencing and Beyond: The Functional Dynamics of Polycomb Repressive Complexes in Hox Gene Regulation. Bioessays 2020; 42:e1900249. [PMID: 32743818 DOI: 10.1002/bies.201900249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/17/2020] [Indexed: 11/10/2022]
Abstract
The coordinated expression of the Hox gene family encoding transcription factors is critical for proper embryonic development and patterning. Major efforts have thus been dedicated to understanding mechanisms controlling Hox expression. In addition to the temporal and spatial sequential activation of Hox genes, proper embryonic development requires that Hox genes get differentially silenced in a cell-type specific manner as development proceeds. Factors contributing to Hox silencing include the polycomb repressive complexes (PRCs), which control gene expression through epigenetic modifications. This review focuses on PRC-dependent regulation of the Hox genes and is aimed at integrating the growing complexity of PRC functional properties in the context of Hox regulation. In particular, mechanisms underlying PRC binding dynamics as well as a series of studies that have revealed the impact of PRC on the 3D organization of the genome is discussed, which has a significant role on Hox regulation during development.
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Affiliation(s)
- Claudia Gentile
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Département de Médecine, Université de Montréal, Montréal, Quebec, H3C 3J7, Canada
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33
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Cissé YM, Chan JC, Nugent BM, Banducci C, Bale TL. Brain and placental transcriptional responses as a readout of maternal and paternal preconception stress are fetal sex specific. Placenta 2020; 100:164-170. [PMID: 32980048 DOI: 10.1016/j.placenta.2020.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Despite a wealth of epidemiological evidence that cumulative parental lifetime stress experiences prior to conception are determinant of offspring developmental trajectories, there is a lack of insight on how these previous stress experiences are stored and communicated intergenerationally. Preconception experiences may impact offspring development through alterations in transcriptional regulation of the placenta, a major determinant of offspring growth and sex-specific developmental outcomes. We evaluated the lasting influence of maternal and paternal preconception stress (PCS) on the mid-gestation placenta and fetal brain, utilizing their transcriptomes as proximate readouts of intergenerational impact. METHODS To assess the combined vs. dominant influence of maternal and paternal preconception environment on sex-specific fetal development, we compared transcriptional outcomes using a breeding scheme of one stressed parent, both stressed parents, or no stressed parents as controls. RESULTS Interestingly, offspring sex affected the directionality of transcriptional changes in response to PCS, where male tissues showed a predominant downregulation, and female tissues showed an upregulation. There was also an intriguing effect of parental sex on placental programming where paternal PCS drove more effects in female placentas, while maternal PCS produced more transcriptional changes in male placentas. However, in the fetal brain, maternal PCS produced overall more changes in gene expression than paternal PCS, supporting the idea that the intrauterine environment may have a larger overall influence on the developing brain than it does on shaping the placenta. DISCUSSION Preconception experiences drive changes in the placental and the fetal brain transcriptome at a critical developmental timepoint. While not determinant, these altered transcriptional states may underlie sex-biased risk or resilience to stressful experiences later in life.
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Affiliation(s)
- Yasmine M Cissé
- Department of Pharmacology, School of Medicine, University of Maryland, Baltimore, MD, 21201, United States
| | - Jennifer C Chan
- Department of Pharmacology, School of Medicine, University of Maryland, Baltimore, MD, 21201, United States
| | - Bridget M Nugent
- Department of Pharmacology, School of Medicine, University of Maryland, Baltimore, MD, 21201, United States
| | - Caitlin Banducci
- Department of Pharmacology, School of Medicine, University of Maryland, Baltimore, MD, 21201, United States
| | - Tracy L Bale
- Department of Pharmacology, School of Medicine, University of Maryland, Baltimore, MD, 21201, United States.
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Ibragimov AN, Bylino OV, Shidlovskii YV. Molecular Basis of the Function of Transcriptional Enhancers. Cells 2020; 9:E1620. [PMID: 32635644 PMCID: PMC7407508 DOI: 10.3390/cells9071620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription.
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Affiliation(s)
- Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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Senner CE, Chrysanthou S, Burge S, Lin HY, Branco MR, Hemberger M. TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast. Stem Cell Reports 2020; 15:1301-1316. [PMID: 32442533 PMCID: PMC7724466 DOI: 10.1016/j.stemcr.2020.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
The ten-eleven translocation factor TET1 and its conferred epigenetic modification 5-hydroxymethylcytosine (5hmC) have important roles in maintaining the pluripotent state of embryonic stem cells (ESCs). We previously showed that TET1 is also essential to maintain the stem cell state of trophoblast stem cells (TSCs). Here, we establish an integrated panel of absolute 5hmC levels, genome-wide DNA methylation and hydroxymethylation patterns, transcriptomes, and TET1 chromatin occupancy in TSCs and differentiated trophoblast cells. We show that the combined presence of 5-methylcytosine (5mC) and 5hmC correlates with transcriptional activity of associated genes. Hypoxia can slow down the global loss of 5hmC that occurs upon differentiation of TSCs. Notably, unlike in ESCs and epiblast cells, most TET1-bound regions overlap with active chromatin marks and TFAP2C binding sites and demarcate putative trophoblast enhancer regions. These chromatin modification and occupancy patterns are highly informative to identify novel candidate regulators of the TSC state. 5hmC to 5mC ratios correlate with gene activity in TS cells TS cell differentiation-associated loss of 5hmC is slowed down in hypoxia TET1 binding in TS cells forms long-range interactions with key trophoblast genes Intergenic TET1 binding sites in TS cells demarcate putative trophoblast enhancers
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Affiliation(s)
- Claire E Senner
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK.
| | - Stephanie Chrysanthou
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Sarah Burge
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Hai-Yan Lin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Miguel R Branco
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Myriam Hemberger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK; Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, T2N 4N1, Canada.
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36
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Are Parallel Proliferation Pathways Redundant? Trends Biochem Sci 2020; 45:554-563. [PMID: 32345469 DOI: 10.1016/j.tibs.2020.03.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022]
Abstract
Are the receptor tyrosine kinase (RTK) and JAK-STAT-driven proliferation pathways 'parallel' or 'redundant'? And what about those of K-Ras4B versus N-Ras? 'Parallel' proliferation pathways accomplish a similar drug resistance outcome. Thus, are they 'redundant'? In this paper, it is argued that there is a fundamental distinction between 'parallel' and 'redundant'. Cellular proliferation pathways are influenced by the genome sequence, 3D organization and chromatin accessibility, and determined by protein availability prior to cancer emergence. In the opinion presented, if they operate the same downstream protein families, they are redundant; if evolutionary-independent, they are parallel. Thus, RTK and JAK-STAT-driven proliferation pathways are parallel; those of Ras isoforms are redundant. Our Precision Medicine Call to map cancer proliferation pathways is vastly important since it can expedite effective therapeutics.
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Blanco E, González-Ramírez M, Alcaine-Colet A, Aranda S, Di Croce L. The Bivalent Genome: Characterization, Structure, and Regulation. Trends Genet 2019; 36:118-131. [PMID: 31818514 DOI: 10.1016/j.tig.2019.11.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/28/2019] [Accepted: 11/08/2019] [Indexed: 02/05/2023]
Abstract
An intricate molecular machinery is at the core of gene expression regulation in every cell. During the initial stages of organismal development, the coordinated activation of diverse transcriptional programs is crucial and must be carefully executed to shape every organ and tissue. Bivalent promoters and poised enhancers are regulatory regions decorated with histone marks that are associated with both positive and negative transcriptional outcomes. These apparently contradictory signals are important for setting bivalent genes in a poised state, which is subsequently resolved during differentiation into either active or repressive states. We discuss the origins of bivalent promoters and the mechanisms implicated in their acquisition and maintenance. We further review how the presence of bivalent marks influences genome architecture. Finally, we highlight the potential link between bivalency and cancer which could drive biomedical research in disease etiology and treatment.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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38
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Cheutin T, Cavalli G. The multiscale effects of polycomb mechanisms on 3D chromatin folding. Crit Rev Biochem Mol Biol 2019; 54:399-417. [PMID: 31698957 DOI: 10.1080/10409238.2019.1679082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins silence master regulatory genes required to properly confer cell identity during the development of both Drosophila and mammals. They may act through chromatin compaction and higher-order folding of chromatin inside the cell nucleus. During the last decade, analysis on interphase chromosome architecture discovered self-interacting regions named topologically associated domains (TADs). TADs result from the 3D chromatin folding of a succession of transcribed and repressed epigenomic domains and from loop extrusion mediated by cohesin/CTCF in mammals. Polycomb silenced chromatin constitutes one type of repressed epigenomic domains which form compacted nano-compartments inside cell nuclei. Recruitment of canonical PcG proteins on chromatin relies on initial binding to discrete elements and further spreading into large chromatin domains covered with H3K27me3. Some of these discrete elements have a bivalent nature both in mammals and Drosophila and are dynamically regulated during development. Loops can occur between them, suggesting that their interaction plays both functional and structural roles. Formation of large chromatin domains covered by H3K27me3 seems crucial for PcG silencing and PcG proteins might exert their function through compaction of these domains in both mammals and flies, rather than by directly controlling the nucleosomal accessibility of discrete regulatory elements. In addition, PcG chromatin domains interact over long genomic distances, shaping a higher-order chromatin network. Therefore, PcG silencing might rely on multiscale chromatin folding to maintain cell identity during differentiation.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
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39
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Hemberger M, Hanna CW, Dean W. Mechanisms of early placental development in mouse and humans. Nat Rev Genet 2019; 21:27-43. [PMID: 31534202 DOI: 10.1038/s41576-019-0169-4] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
The importance of the placenta in supporting mammalian development has long been recognized, but our knowledge of the molecular, genetic and epigenetic requirements that underpin normal placentation has remained remarkably under-appreciated. Both the in vivo mouse model and in vitro-derived murine trophoblast stem cells have been invaluable research tools for gaining insights into these aspects of placental development and function, with recent studies starting to reshape our view of how a unique epigenetic environment contributes to trophoblast differentiation and placenta formation. These advances, together with recent successes in deriving human trophoblast stem cells, open up new and exciting prospects in basic and clinical settings that will help deepen our understanding of placental development and associated disorders of pregnancy.
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Affiliation(s)
- Myriam Hemberger
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada. .,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| | - Courtney W Hanna
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Wendy Dean
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada. .,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK. .,Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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40
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Tsuboi M, Hirabayashi Y, Gotoh Y. Diverse gene regulatory mechanisms mediated by Polycomb group proteins during neural development. Curr Opin Neurobiol 2019; 59:164-173. [PMID: 31398486 DOI: 10.1016/j.conb.2019.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/07/2019] [Indexed: 12/26/2022]
Abstract
While all the developmental genes are temporarily repressed for future activation in the pluripotent stem cells, non-neural genes become persistently repressed in the course of commitment to the neuronal lineage. Although Polycomb group proteins (PcG) are key factors for both temporary and persistent repression of the developmental genes, how the same group of proteins can differentially repress target genes remains unclarified. The identification of a variety of PcG complexes and activities sheds light on these issues. In this review, based on the recent findings including those with the use of interactome and Chromosome Conformation Capture (3C)-type analyses, we summarize the molecular mechanisms of PcG-mediated gene regulation and discuss how PcG regulates cell fate specification during neural development.
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Affiliation(s)
- Masafumi Tsuboi
- Graduate School of Engineering, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Yusuke Hirabayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo 113-0033, Japan
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41
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Schoenfelder S, Fraser P. Long-range enhancer–promoter contacts in gene expression control. Nat Rev Genet 2019; 20:437-455. [DOI: 10.1038/s41576-019-0128-0] [Citation(s) in RCA: 486] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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42
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Domsch K, Carnesecchi J, Disela V, Friedrich J, Trost N, Ermakova O, Polychronidou M, Lohmann I. The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila. eLife 2019; 8:42675. [PMID: 31050646 PMCID: PMC6513553 DOI: 10.7554/elife.42675] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/30/2019] [Indexed: 12/22/2022] Open
Abstract
During development cells become restricted in their differentiation potential by repressing alternative cell fates, and the Polycomb complex plays a crucial role in this process. However, how alternative fate genes are lineage-specifically silenced is unclear. We studied Ultrabithorax (Ubx), a multi-lineage transcription factor of the Hox class, in two tissue lineages using sorted nuclei and interfered with Ubx in mesodermal cells. We find that depletion of Ubx leads to the de-repression of genes normally expressed in other lineages. Ubx silences expression of alternative fate genes by retaining the Polycomb Group protein Pleiohomeotic at Ubx targeted genomic regions, thereby stabilizing repressive chromatin marks in a lineage-dependent manner. Our study demonstrates that Ubx stabilizes lineage choice by suppressing the multipotency encoded in the genome via its interaction with Pho. This mechanism may explain why the Hox code is maintained throughout the lifecycle, since it could set a block to transdifferentiation in adult cells.
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Affiliation(s)
- Katrin Domsch
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | | | - Vanessa Disela
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | - Jana Friedrich
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | - Nils Trost
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | - Olga Ermakova
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | | | - Ingrid Lohmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
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Todd CD, Deniz Ö, Taylor D, Branco MR. Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells. eLife 2019; 8:e44344. [PMID: 31012843 PMCID: PMC6544436 DOI: 10.7554/elife.44344] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/20/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that they play significant roles in gene regulation. Here we tested a set of long terminal repeat TE families for roles as enhancers in mouse embryonic and trophoblast stem cells. Epigenomic and transcriptomic data suggested that a large number of TEs helped to establish tissue-specific gene expression programmes. Genetic editing of individual TEs confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a subset of TEs are important for gene regulation in early mouse development, and highlight the importance of functional experiments when evaluating gene regulatory roles of TEs.
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Affiliation(s)
- Christopher D Todd
- Blizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUnited Kingdom
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUnited Kingdom
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Darren Taylor
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
| | - Miguel R Branco
- Centre for Genomic Health, Life Sciences InstituteQueen Mary University of LondonLondonUnited Kingdom
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