1
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Chi C, Roland TJ, Song K. Differentiation of Pluripotent Stem Cells for Disease Modeling: Learning from Heart Development. Pharmaceuticals (Basel) 2024; 17:337. [PMID: 38543122 PMCID: PMC10975450 DOI: 10.3390/ph17030337] [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: 01/13/2024] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
Heart disease is a pressing public health problem and the leading cause of death worldwide. The heart is the first organ to gain function during embryogenesis in mammals. Heart development involves cell determination, expansion, migration, and crosstalk, which are orchestrated by numerous signaling pathways, such as the Wnt, TGF-β, IGF, and Retinoic acid signaling pathways. Human-induced pluripotent stem cell-based platforms are emerging as promising approaches for modeling heart disease in vitro. Understanding the signaling pathways that are essential for cardiac development has shed light on the molecular mechanisms of congenital heart defects and postnatal heart diseases, significantly advancing stem cell-based platforms to model heart diseases. This review summarizes signaling pathways that are crucial for heart development and discusses how these findings improve the strategies for modeling human heart disease in vitro.
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Affiliation(s)
- Congwu Chi
- Heart Institute, University of South Florida, Tampa, FL 33602, USA; (C.C.); (T.J.R.)
- Department of Internal Medicine, University of South Florida, Tampa, FL 33602, USA
- Center for Regenerative Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Truman J. Roland
- Heart Institute, University of South Florida, Tampa, FL 33602, USA; (C.C.); (T.J.R.)
- Department of Internal Medicine, University of South Florida, Tampa, FL 33602, USA
- Center for Regenerative Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Kunhua Song
- Heart Institute, University of South Florida, Tampa, FL 33602, USA; (C.C.); (T.J.R.)
- Department of Internal Medicine, University of South Florida, Tampa, FL 33602, USA
- Center for Regenerative Medicine, University of South Florida, Tampa, FL 33602, USA
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2
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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3
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Wang C, Zong X, Wu F, Leung RWT, Hu Y, Qin J. DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia. Front Mol Biosci 2022; 9:920492. [PMID: 36052164 PMCID: PMC9425088 DOI: 10.3389/fmolb.2022.920492] [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: 04/14/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
DNA- and RNA-binding proteins (DRBPs) typically possess multiple functions to bind both DNA and RNA and regulate gene expression from more than one level. They are controllers for post-transcriptional processes, such as splicing, polyadenylation, transportation, translation, and degradation of RNA transcripts in eukaryotic organisms, as well as regulators on the transcriptional level. Although DRBPs are reported to play critical roles in various developmental processes and diseases, it is still unclear how they work with DNAs and RNAs simultaneously and regulate genes at the transcriptional and post-transcriptional levels. To investigate the functional mechanism of DRBPs, we collected data from a variety of databases and literature and identified 118 DRBPs, which function as both transcription factors (TFs) and splicing factors (SFs), thus called DRBP-SF. Extensive investigations were conducted on four DRBP-SFs that were highly expressed in chronic myeloid leukemia (CML), heterogeneous nuclear ribonucleoprotein K (HNRNPK), heterogeneous nuclear ribonucleoprotein L (HNRNPL), non-POU domain–containing octamer–binding protein (NONO), and TAR DNA-binding protein 43 (TARDBP). By integrating and analyzing ChIP-seq, CLIP-seq, RNA-seq, and shRNA-seq data in K562 using binding and expression target analysis and Statistical Utility for RBP Functions, we discovered a two-layer regulatory network system centered on these four DRBP-SFs and proposed three possible regulatory models where DRBP-SFs can connect transcriptional and alternative splicing regulatory networks cooperatively in CML. The exploration of the identified DRBP-SFs provides new ideas for studying DRBP and regulatory networks, holding promise for further mechanistic discoveries of the two-layer gene regulatory system that may play critical roles in the occurrence and development of CML.
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Affiliation(s)
- Chuhui Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xueqing Zong
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Fanjie Wu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Ricky Wai Tak Leung
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- College of Professional and Continuing Education, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yaohua Hu
- Shenzhen Key Laboratory of Advanced Machine Learning and Applications, College of Mathematics and Statistics, Shenzhen University, Shenzhen, China
- *Correspondence: Yaohua Hu, ; Jing Qin,
| | - Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yaohua Hu, ; Jing Qin,
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4
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Coda DM, Patel H, Gori I, Gaarenstroom TE, Song OR, Howell M, Hill CS. A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses. J Cell Sci 2022; 135:jcs259972. [PMID: 35302162 PMCID: PMC9080556 DOI: 10.1242/jcs.259972] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
SMAD2, an effector of the NODAL/Activin signalling pathway, regulates developmental processes by sensing distinct chromatin states and interacting with different transcriptional partners. However, the network of factors that controls SMAD2 chromatin binding and shapes its transcriptional programme over time is poorly characterised. Here, we combine ATAC-seq with computational footprinting to identify temporal changes in chromatin accessibility and transcription factor activity upon NODAL/Activin signalling. We show that SMAD2 binding induces chromatin opening genome wide. We discover footprints for FOXI3, FOXO3 and ZIC3 at the SMAD2-bound enhancers of the early response genes, Pmepa1 and Wnt3, respectively, and demonstrate their functionality. Finally, we determine a mechanism by which NODAL/Activin signalling induces delayed gene expression, by uncovering a self-enabling transcriptional cascade whereby activated SMADs, together with ZIC3, induce the expression of Wnt3. The resultant activated WNT pathway then acts together with the NODAL/Activin pathway to regulate expression of delayed target genes in prolonged NODAL/Activin signalling conditions. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Davide M. Coda
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Tessa E. Gaarenstroom
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Caroline S. Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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5
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Figiel DM, Elsayed R, Nelson AC. Investigating the molecular guts of endoderm formation using zebrafish. Brief Funct Genomics 2021:elab013. [PMID: 33754635 DOI: 10.1093/bfgp/elab013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The vertebrate endoderm makes major contributions to the respiratory and gastrointestinal tracts and all associated organs. Zebrafish and humans share a high degree of genetic homology and strikingly similar endodermal organ systems. Combined with a multitude of experimental advantages, zebrafish are an attractive model organism to study endoderm development and disease. Recent functional genomics studies have shed considerable light on the gene regulatory programs governing early zebrafish endoderm development, while advances in biological and technological approaches stand to further revolutionize our ability to investigate endoderm formation, function and disease. Here, we discuss the present understanding of endoderm specification in zebrafish compared to other vertebrates, how current and emerging methods will allow refined and enhanced analysis of endoderm formation, and how integration with human data will allow modeling of the link between non-coding sequence variants and human disease.
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Affiliation(s)
- Daniela M Figiel
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
| | - Randa Elsayed
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
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6
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Yi S, Huang X, Zhou S, Zhou Y, Anderson MK, Zúñiga-Pflücker JC, Luan Q, Li Y. E2A regulates neural ectoderm fate specification in human embryonic stem cells. Development 2020; 147:dev.190298. [PMID: 33144398 DOI: 10.1242/dev.190298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022]
Abstract
E protein transcription factors are crucial for many cell fate decisions. However, the roles of E proteins in the germ-layer specification of human embryonic stem cells (hESCs) are poorly understood. We disrupted the TCF3 gene locus to delete the E protein E2A in hESCs. E2A knockout (KO) hESCs retained key features of pluripotency, but displayed decreased neural ectoderm coupled with enhanced mesoendoderm outcomes. Genome-wide analyses showed that E2A directly regulates neural ectoderm and Nodal pathway genes. Accordingly, inhibition of Nodal or E2A overexpression partially rescued the neural ectoderm defect in E2A KO hESCs. Loss of E2A had little impact on the epigenetic landscape of hESCs, whereas E2A KO neural precursors displayed increased accessibility of the gene locus encoding the Nodal agonist CRIPTO. Double-deletion of both E2A and HEB (TCF12) resulted in a more severe neural ectoderm defect. Therefore, this study reveals critical context-dependent functions for E2A in human neural ectoderm fate specification.
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Affiliation(s)
- Siqi Yi
- Department of Periodontology, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China.,Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Xiaotian Huang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Shixin Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Michele K Anderson
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | | | - Qingxian Luan
- Department of Periodontology, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
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7
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Rao C, Malaguti M, Mason JO, Lowell S. The transcription factor E2A drives neural differentiation in pluripotent cells. Development 2020; 147:dev184093. [PMID: 32487737 PMCID: PMC7328008 DOI: 10.1242/dev.184093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
The intrinsic mechanisms that link extracellular signalling to the onset of neural differentiation are not well understood. In pluripotent mouse cells, BMP blocks entry into the neural lineage via transcriptional upregulation of inhibitor of differentiation (Id) factors. We have previously identified the major binding partner of Id proteins in pluripotent cells as the basic helix-loop-helix (bHLH) transcription factor (TF) E2A. Id1 can prevent E2A from forming heterodimers with bHLH TFs or from forming homodimers. Here, we show that overexpression of a forced E2A homodimer is sufficient to drive robust neural commitment in pluripotent cells, even under non-permissive conditions. Conversely, we find that E2A null cells display a defect in their neural differentiation capacity. E2A acts as an upstream activator of neural lineage genes, including Sox1 and Foxd4, and as a repressor of Nodal signalling. Our results suggest a crucial role for E2A in establishing neural lineage commitment in pluripotent cells.
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Affiliation(s)
- Chandrika Rao
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Mattias Malaguti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - John O Mason
- Centre for Discovery Brain Sciences, University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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8
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Gilchrist MJ, Cho KWY, Veenstra GJC. Genomics Methods for Xenopus Embryos and Tissues. Cold Spring Harb Protoc 2020; 2020:097915. [PMID: 32123020 DOI: 10.1101/pdb.top097915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
High-throughput sequencing methods have created exciting opportunities to explore the regulatory landscape of the entire genome. Here we introduce methods to characterize the genomic locations of bound proteins, open chromatin, and sites of DNA-DNA contact in Xenopus embryos. These methods include chromatin immunoprecipitation followed by sequencing (ChIP-seq), a combination of DNase I digestion and sequencing (DNase-seq), the assay for transposase-accessible chromatin and sequencing (ATAC-seq), and the use of proximity-based DNA ligation followed by sequencing (Hi-C).
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Affiliation(s)
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697;
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, 6525GA Nijmegen, The Netherlands
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9
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Fu L, Wang H, Liao Y, Zhou P, Xu Y, Zhao Y, Xie S, Zhao S, Li X. miR-208b modulating skeletal muscle development and energy homoeostasis through targeting distinct targets. RNA Biol 2020; 17:743-754. [PMID: 32037961 DOI: 10.1080/15476286.2020.1728102] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Embryonic and neonatal skeletal muscles grow via the proliferation and fusion of myogenic cells, whereas adult skeletal muscle adapts largely by remodelling pre-existing myofibers and optimizing metabolic balance. It has been reported that miRNAs played key roles during skeletal muscle development through targeting different genes at post-transcriptional level. In this study, we show that a single miRNA (miR-208b) can modulate both the myogenesis and homoeostasis of skeletal muscle by distinct targets. As results, miR-208b accelerates the proliferation and inhibits the differentiation of myogenic cells by targeting the E-protein family member transcription factor 12 (TCF12). Also, miR-208b can stimulate fast-to-slow fibre conversion and oxidative metabolism programme through targeting folliculin interacting protein 1 (FNIP1) but not TCF12 gene. Further, miR-208b could active the AMPK/PGC-1a signalling and mitochondrial biogenesis through targeting FNIP1. Thus, miR-208b could mediate skeletal muscle development and homoeostasis through specifically targeting of TCF12 and FNIP1.
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Affiliation(s)
- Liangliang Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Heng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Yinlong Liao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Peng Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Yueyuan Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P. R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
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10
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TGF-β orchestrates fibrogenic and developmental EMTs via the RAS effector RREB1. Nature 2020; 577:566-571. [PMID: 31915377 DOI: 10.1038/s41586-019-1897-5] [Citation(s) in RCA: 279] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/05/2019] [Indexed: 12/15/2022]
Abstract
Epithelial-to-mesenchymal transitions (EMTs) are phenotypic plasticity processes that confer migratory and invasive properties to epithelial cells during development, wound-healing, fibrosis and cancer1-4. EMTs are driven by SNAIL, ZEB and TWIST transcription factors5,6 together with microRNAs that balance this regulatory network7,8. Transforming growth factor β (TGF-β) is a potent inducer of developmental and fibrogenic EMTs4,9,10. Aberrant TGF-β signalling and EMT are implicated in the pathogenesis of renal fibrosis, alcoholic liver disease, non-alcoholic steatohepatitis, pulmonary fibrosis and cancer4,11. TGF-β depends on RAS and mitogen-activated protein kinase (MAPK) pathway inputs for the induction of EMTs12-19. Here we show how these signals coordinately trigger EMTs and integrate them with broader pathophysiological processes. We identify RAS-responsive element binding protein 1 (RREB1), a RAS transcriptional effector20,21, as a key partner of TGF-β-activated SMAD transcription factors in EMT. MAPK-activated RREB1 recruits TGF-β-activated SMAD factors to SNAIL. Context-dependent chromatin accessibility dictates the ability of RREB1 and SMAD to activate additional genes that determine the nature of the resulting EMT. In carcinoma cells, TGF-β-SMAD and RREB1 directly drive expression of SNAIL and fibrogenic factors stimulating myofibroblasts, promoting intratumoral fibrosis and supporting tumour growth. In mouse epiblast progenitors, Nodal-SMAD and RREB1 combine to induce expression of SNAIL and mesendoderm-differentiation genes that drive gastrulation. Thus, RREB1 provides a molecular link between RAS and TGF-β pathways for coordinated induction of developmental and fibrogenic EMTs. These insights increase our understanding of the regulation of epithelial plasticity and its pathophysiological consequences in development, fibrosis and cancer.
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11
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The subcellular localization of bHLH transcription factor TCF4 is mediated by multiple nuclear localization and nuclear export signals. Sci Rep 2019; 9:15629. [PMID: 31666615 PMCID: PMC6821749 DOI: 10.1038/s41598-019-52239-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/11/2019] [Indexed: 01/10/2023] Open
Abstract
Transcription factor 4 (TCF4) is a class I basic helix-loop-helix (bHLH) transcription factor which regulates the neurogenesis and specialization of cells. TCF4 also plays an important role in the development and functioning of the immune system. Additionally, TCF4 regulates the development of Sertoli cells and pontine nucleus neurons, myogenesis, melanogenesis and epithelial-mesenchymal transition. The ability of transcription factors to fulfil their function often depends on their intracellular trafficking between the nucleus and cytoplasm of the cell. The trafficking is regulated by specific sequences, i.e. the nuclear localization signal (NLS) and the nuclear export signal (NES). We performed research on the TCF4 trafficking regulating sequences by mapping and detailed characterization of motifs potentially acting as the NLS or NES. We demonstrate that the bHLH domain of TCF4 contains an NLS that overlaps two NESs. The results of in silico analyses show high conservation of the sequences, especially in the area of the NLS and NESs. This high conservation is not only between mouse and human TCF4, but also between TCF4 and other mammalian E proteins, indicating the importance of these sequences for the functioning of bHLH class I transcription factors.
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12
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Gentsch GE, Spruce T, Owens NDL, Smith JC. Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals. Nat Commun 2019; 10:4269. [PMID: 31537794 PMCID: PMC6753111 DOI: 10.1038/s41467-019-12263-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.
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Affiliation(s)
- George E Gentsch
- Developmental Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Thomas Spruce
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, 08003, Barcelona, Spain
| | - Nick D L Owens
- Department of Stem Cell and Developmental Biology, Pasteur Institute, 75015, Paris, France
| | - James C Smith
- Developmental Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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13
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Song S, Cui H, Chen S, Liu Q, Jiang R. EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0175-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3. Sci Rep 2018; 8:14954. [PMID: 30297839 PMCID: PMC6175831 DOI: 10.1038/s41598-018-33235-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/25/2018] [Indexed: 11/08/2022] Open
Abstract
Zic3 encodes a zinc finger protein essential for the development of meso-ectodermal tissues. In mammals, Zic3 has important roles in the development of neural tube, axial skeletons, left-right body axis, and in maintaining pluripotency of ES cells. Here we characterized cis-regulatory elements required for Zic3 expression. Enhancer activities of human-chicken-conserved noncoding sequences around Zic1 and Zic3 were screened using chick whole-embryo electroporation. We identified enhancers for meso-ectodermal tissues. Among them, a mesodermal enhancer (Zic3-ME) in distant 3' flanking showed robust enhancement of reporter gene expression in the mesodermal tissue of chicken and mouse embryos, and was required for mesodermal Zic3 expression in mice. Zic3-ME minimal core region is included in the DNase hypersensitive region of ES cells, mesoderm, and neural progenitors, and was bound by T (Brachyury), Eomes, Lef1, Nanog, Oct4, and Zic2. Zic3-ME is derived from an ancestral sequence shared with a sequence encoding a mitochondrial enzyme. These results indicate that Zic3-ME is an integrated cis-regulatory element essential for the proper expression of Zic3 in vertebrates, serving as a hub for a gene regulatory network including Zic3.
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15
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Xu X, Zheng L, Yuan Q, Zhen G, Crane JL, Zhou X, Cao X. Transforming growth factor-β in stem cells and tissue homeostasis. Bone Res 2018; 6:2. [PMID: 29423331 PMCID: PMC5802812 DOI: 10.1038/s41413-017-0005-4] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/12/2017] [Accepted: 11/15/2017] [Indexed: 02/05/2023] Open
Abstract
TGF-β 1-3 are unique multi-functional growth factors that are only expressed in mammals, and mainly secreted and stored as a latent complex in the extracellular matrix (ECM). The biological functions of TGF-β in adults can only be delivered after ligand activation, mostly in response to environmental perturbations. Although involved in multiple biological and pathological processes of the human body, the exact roles of TGF-β in maintaining stem cells and tissue homeostasis have not been well-documented until recent advances, which delineate their functions in a given context. Our recent findings, along with data reported by others, have clearly shown that temporal and spatial activation of TGF-β is involved in the recruitment of stem/progenitor cell participation in tissue regeneration/remodeling process, whereas sustained abnormalities in TGF-β ligand activation, regardless of genetic or environmental origin, will inevitably disrupt the normal physiology and lead to pathobiology of major diseases. Modulation of TGF-β signaling with different approaches has proven effective pre-clinically in the treatment of multiple pathologies such as sclerosis/fibrosis, tumor metastasis, osteoarthritis, and immune disorders. Thus, further elucidation of the mechanisms by which TGF-β is activated in different tissues/organs and how targeted cells respond in a context-dependent way can likely be translated with clinical benefits in the management of a broad range of diseases with the involvement of TGF-β.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Gehua Zhen
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Janet L. Crane
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD USA
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xu Cao
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
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16
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Burdine RD, Grimes DT. Antagonistic interactions in the zebrafish midline prior to the emergence of asymmetric gene expression are important for left-right patterning. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0402. [PMID: 27821532 DOI: 10.1098/rstb.2015.0402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2016] [Indexed: 12/16/2022] Open
Abstract
Left-right (L-R) asymmetry of the internal organs of vertebrates is presaged by domains of asymmetric gene expression in the lateral plate mesoderm (LPM) during somitogenesis. Ciliated L-R coordinators (LRCs) are critical for biasing the initiation of asymmetrically expressed genes, such as nodal and pitx2, to the left LPM. Other midline structures, including the notochord and floorplate, are then required to maintain these asymmetries. Here we report an unexpected role for the zebrafish EGF-CFC gene one-eyed pinhead (oep) in the midline to promote pitx2 expression in the LPM. Late zygotic oep (LZoep) mutants have strongly reduced or absent pitx2 expression in the LPM, but this expression can be rescued to strong levels by restoring oep in midline structures only. Furthermore, removing midline structures from LZoep embryos can rescue pitx2 expression in the LPM, suggesting the midline is a source of an LPM pitx2 repressor that is itself inhibited by oep Reducing lefty1 activity in LZoep embryos mimics removal of the midline, implicating lefty1 in the midline-derived repression. Together, this suggests a model where Oep in the midline functions to overcome a midline-derived repressor, involving lefty1, to allow for the expression of left side-specific genes in the LPM.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.
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Affiliation(s)
- Rebecca D Burdine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Daniel T Grimes
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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17
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Liu JX, Xu QH, Li S, Yu X, Liu W, Ouyang G, Zhang T, Chen LL. Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1103-1116. [DOI: 10.1016/j.bbagrm.2017.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/11/2023]
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18
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Zhao H, Choi K. A CRISPR screen identifies genes controlling Etv2 threshold expression in murine hemangiogenic fate commitment. Nat Commun 2017; 8:541. [PMID: 28912455 PMCID: PMC5599515 DOI: 10.1038/s41467-017-00667-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/17/2017] [Indexed: 01/08/2023] Open
Abstract
The ETS transcription factor Etv2 is necessary and sufficient for the generation of hematopoietic and endothelial cells. However, upstream regulators of Etv2 in hemangiogenesis, generation of hematopoietic and endothelial cells, have not been clearly addressed. Here we track the developmental route of hemangiogenic progenitors from mouse embryonic stem cells, perform genome-wide CRISPR screening, and transcriptome analysis of en route cell populations by utilizing Brachyury, Etv2, or Scl reporter embryonic stem cell lines to further understand the mechanisms that control hemangiogenesis. We identify the forkhead transcription factor Foxh1, in part through Eomes, to be critical for the formation of FLK1+ mesoderm, from which the hemangiogenic fate is specified. Importantly, hemangiogenic fate is specified not simply by the onset of Etv2 expression, but by a threshold-dependent mechanism, in which VEGF-FLK1 signaling plays an instructive role by promoting Etv2 threshold expression. These studies reveal comprehensive cellular and molecular pathways governing the hemangiogenic cell lineage development. How haematopoietic and endothelial cell lineages are specified is unclear. Here, the authors identify the forkhead transcription factor Foxh1 as regulating FLK1+ mesoderm formation in mouse embryonic stem cells, which in turn specifies hemangiogenic fate via Etv2.
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Affiliation(s)
- Haiyong Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Developmental, Regenerative, and Stem Cell Biology Program, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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19
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Cunningham TJ, Yu MS, McKeithan WL, Spiering S, Carrette F, Huang CT, Bushway PJ, Tierney M, Albini S, Giacca M, Mano M, Puri PL, Sacco A, Ruiz-Lozano P, Riou JF, Umbhauer M, Duester G, Mercola M, Colas AR. Id genes are essential for early heart formation. Genes Dev 2017; 31:1325-1338. [PMID: 28794185 PMCID: PMC5580654 DOI: 10.1101/gad.300400.117] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Deciphering the fundamental mechanisms controlling cardiac specification is critical for our understanding of how heart formation is initiated during embryonic development and for applying stem cell biology to regenerative medicine and disease modeling. Using systematic and unbiased functional screening approaches, we discovered that the Id family of helix-loop-helix proteins is both necessary and sufficient to direct cardiac mesoderm formation in frog embryos and human embryonic stem cells. Mechanistically, Id proteins specify cardiac cell fate by repressing two inhibitors of cardiogenic mesoderm formation-Tcf3 and Foxa2-and activating inducers Evx1, Grrp1, and Mesp1. Most importantly, CRISPR/Cas9-mediated ablation of the entire Id (Id1-4) family in mouse embryos leads to failure of anterior cardiac progenitor specification and the development of heartless embryos. Thus, Id proteins play a central and evolutionarily conserved role during heart formation and provide a novel means to efficiently produce cardiovascular progenitors for regenerative medicine and drug discovery applications.
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Affiliation(s)
- Thomas J Cunningham
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Michael S Yu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA
| | - Wesley L McKeithan
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA.,Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA
| | - Sean Spiering
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Florent Carrette
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Paul J Bushway
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA
| | - Matthew Tierney
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Sonia Albini
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Miguel Mano
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Istituti di Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, 00179 Rome, Italy
| | - Alessandra Sacco
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Pilar Ruiz-Lozano
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Regencor, Inc., Los Altos, California 94022, USA
| | - Jean-Francois Riou
- UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France
| | - Muriel Umbhauer
- UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France
| | - Gregg Duester
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Mark Mercola
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA
| | - Alexandre R Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
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20
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Lu AQ, Popova EY, Barnstable CJ. Activin Signals through SMAD2/3 to Increase Photoreceptor Precursor Yield during Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:838-852. [PMID: 28781074 PMCID: PMC5599185 DOI: 10.1016/j.stemcr.2017.06.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 01/23/2023] Open
Abstract
In vitro differentiation of mouse embryonic stem cells (ESCs) into retinal fates can be used to study the roles of exogenous factors acting through multiple signaling pathways during retina development. Application of activin A during a specific time frame that corresponds to early embryonic retinogenesis caused increased generation of CRX+ photoreceptor precursors and decreased PAX6+ retinal progenitor cells (RPCs). Following activin A treatment, SMAD2/3 was activated in RPCs and bound to promoter regions of key RPC and photoreceptor genes. The effect of activin on CRX expression was repressed by pharmacological inhibition of SMAD2/3 phosphorylation. Activin signaling through SMAD2/3 in RPCs regulates expression of transcription factors involved in cell type determination and promotes photoreceptor lineage specification. Our findings can contribute to the production of photoreceptors for cell replacement therapy.
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Affiliation(s)
- Amy Q Lu
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Evgenya Y Popova
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Colin J Barnstable
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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21
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Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KWY. Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program. Dev Cell 2017; 40:595-607.e4. [PMID: 28325473 PMCID: PMC5434453 DOI: 10.1016/j.devcel.2017.02.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/24/2016] [Accepted: 02/16/2017] [Indexed: 12/14/2022]
Abstract
The interplay between transcription factors and chromatin dictates gene regulatory network activity. Germ layer specification is tightly coupled with zygotic gene activation and, in most metazoans, is dependent upon maternal factors. We explore the dynamic genome-wide interactions of Foxh1, a maternal transcription factor that mediates Nodal/TGF-β signaling, with cis-regulatory modules (CRMs) during mesendodermal specification. Foxh1 marks CRMs during cleavage stages and recruits the co-repressor Tle/Groucho in the early blastula. We highlight a population of CRMs that are continuously occupied by Foxh1 and show that they are marked by H3K4me1, Ep300, and Fox/Sox/Smad motifs, suggesting interplay between these factors in gene regulation. We also propose a molecular "hand-off" between maternal Foxh1 and zygotic Foxa at these CRMs to maintain enhancer activation. Our findings suggest that Foxh1 functions at the top of a hierarchy of interactions by marking developmental genes for activation, beginning with the onset of zygotic gene expression.
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Affiliation(s)
- Rebekah M Charney
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Elmira Forouzmand
- Department of Computer Science, Donald Bren School of Information & Computer Sciences, University of California, Irvine, CA 92697, USA
| | - Jin Sun Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Shuji Takahashi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8526, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ira L Blitz
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Xiaohui Xie
- Department of Computer Science, Donald Bren School of Information & Computer Sciences, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA.
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22
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Charney RM, Paraiso KD, Blitz IL, Cho KWY. A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs. Semin Cell Dev Biol 2017; 66:12-24. [PMID: 28341363 DOI: 10.1016/j.semcdb.2017.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 02/08/2023]
Abstract
Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied extensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN). We highlight regulatory connections conserved between frog, fish, mouse, and human endodermal lineages. Especially prominent is the conserved role and regulatory targets of the Nodal signaling pathway and the T-box transcription factors, Vegt and Eomes. Additionally, we highlight network topologies and motifs, and speculate on their possible roles in development.
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Affiliation(s)
- Rebekah M Charney
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA.
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23
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Lattanzi W, Barba M, Di Pietro L, Boyadjiev SA. Genetic advances in craniosynostosis. Am J Med Genet A 2017; 173:1406-1429. [PMID: 28160402 DOI: 10.1002/ajmg.a.38159] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/30/2016] [Accepted: 01/06/2017] [Indexed: 12/22/2022]
Abstract
Craniosynostosis, the premature ossification of one or more skull sutures, is a clinically and genetically heterogeneous congenital anomaly affecting approximately one in 2,500 live births. In most cases, it occurs as an isolated congenital anomaly, that is, nonsyndromic craniosynostosis (NCS), the genetic, and environmental causes of which remain largely unknown. Recent data suggest that, at least some of the midline NCS cases may be explained by two loci inheritance. In approximately 25-30% of patients, craniosynostosis presents as a feature of a genetic syndrome due to chromosomal defects or mutations in genes within interconnected signaling pathways. The aim of this review is to provide a detailed and comprehensive update on the genetic and environmental factors associated with NCS, integrating the scientific findings achieved during the last decade. Focus on the neurodevelopmental, imaging, and treatment aspects of NCS is also provided.
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Affiliation(s)
- Wanda Lattanzi
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy.,Latium Musculoskeletal Tıssue Bank, Rome, Italy
| | - Marta Barba
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorena Di Pietro
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Simeon A Boyadjiev
- Division of Genomic Medicine, Department of Pediatrics, Davis Medical Center, University of California, Sacramento, California
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24
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Yi S, Yu M, Yang S, Miron RJ, Zhang Y. Tcf12, A Member of Basic Helix-Loop-Helix Transcription Factors, Mediates Bone Marrow Mesenchymal Stem Cell Osteogenic Differentiation In Vitro and In Vivo. Stem Cells 2017; 35:386-397. [PMID: 27574032 DOI: 10.1002/stem.2491] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/05/2016] [Accepted: 07/29/2016] [Indexed: 01/12/2023]
Abstract
Several basic Helix-Loop-Helix transcription factors have recently been identified to regulate mesenchymal stem cell (MSC) differentiation. In the present study, Tcf12 was investigated for its involvement in the osteoblastic cell commitment of MSCs. Tcf12 was found highly expressed in undifferentiated MSCs whereas its expression decreased following osteogenic culture differentiation. Interestingly, Tcf12 endogenous silencing using shRNA lentivirus significantly promoted the differentiation ability of MSCs evaluated by alkaline phosphatase staining, alizarin red staining and expression of osteoblast-specific markers by real-time PCR. Conversely, overexpression of Tcf12 in MSCs suppressed osteoblast differentiation. It was further found that silencing of Tcf12 activated bone morphogenetic protein (BMP) signaling and extracellular signal-regulated kinase (Erk)1/2 signaling pathway activity and upregulated the expression of phospho-SMAD1 and phospho-Erk1/2. A BMP inhibitor (LDN-193189) and Erk1/2 signaling pathway inhibitor (U0126) reduced these findings in the Tcf12 silencing group. Following these in vitro results, a poly-L-lactic acid/Hydroxyappatite scaffold carrying Tcf12 silencing lentivirus was utilized to investigate the repair of bone defects in vivo. The use of Tcf12 silencing lentivirus significantly promoted new bone formation in 3-mm mouse calvarial defects as assessed by micro-CT and histological examination whereas overexpression of Tcf12 inhibited new bone formation. Collectively, these data indicate that Tcf12 is a transcription factor highly expressed in the nuclei of stem cells and its downregulation plays an essential role in osteoblast differentiation partially via BMP and Erk1/2 signaling pathways. Stem Cells 2017;35:386-397.
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Affiliation(s)
- Siqi Yi
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
- Medical Research Institute, Wuhan University, Wuhan, People's Republic of China
| | - Miao Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Shuang Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Richard J Miron
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
- Department of Periodontology, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
- Department of Preventive, Restorative and Pediatric Dentistry, School of Dental Medicine, University of Bern, Switzerland
| | - Yufeng Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
- Medical Research Institute, Wuhan University, Wuhan, People's Republic of China
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25
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Cooperation Between T-Box Factors Regulates the Continuous Segregation of Germ Layers During Vertebrate Embryogenesis. Curr Top Dev Biol 2017; 122:117-159. [DOI: 10.1016/bs.ctdb.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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Wang Q, Zou Y, Nowotschin S, Kim SY, Li QV, Soh CL, Su J, Zhang C, Shu W, Xi Q, Huangfu D, Hadjantonakis AK, Massagué J. The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells. Cell Stem Cell 2016; 20:70-86. [PMID: 27889317 DOI: 10.1016/j.stem.2016.10.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/07/2016] [Accepted: 10/02/2016] [Indexed: 01/01/2023]
Abstract
In this study, we outline a regulatory network that involves the p53 tumor suppressor family and the Wnt pathway acting together with the TGF-β pathway in mesendodermal differentiation of mouse and human embryonic stem cells. Knockout of all three members, p53, p63, and p73, shows that the p53 family is essential for mesendoderm specification during exit from pluripotency in embryos and in culture. Wnt3 and its receptor Fzd1 are direct p53 family target genes in this context, and induction of Wnt signaling by p53 is critical for activation of mesendodermal differentiation genes. Globally, Wnt3-activated Tcf3 and nodal-activated Smad2/3 transcription factors depend on each other for co-occupancy of target enhancers associated with key differentiation loci. Our results therefore highlight an unanticipated role for p53 family proteins in a regulatory network that integrates essential Wnt-Tcf and nodal-Smad inputs in a selective and interdependent way to drive mesendodermal differentiation of pluripotent cells.
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Affiliation(s)
- Qiong Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yilong Zou
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sonja Nowotschin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sang Yong Kim
- Rodent Genetic Engineering Core, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Qing V Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Chew-Li Soh
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jie Su
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chao Zhang
- Department of Medicine and Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Weiping Shu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qiaoran Xi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Danwei Huangfu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Joan Massagué
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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27
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Baillon L, Pierron F, Pannetier P, Normandeau E, Couture P, Labadie P, Budzinski H, Lambert P, Bernatchez L, Baudrimont M. Gene transcription profiling in wild and laboratory-exposed eels: Effect of captivity and in situ chronic exposure to pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:92-102. [PMID: 27470668 DOI: 10.1016/j.scitotenv.2016.07.131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
Aquatic ecosystems are subjected to a variety of man-induced stressors but also vary spatially and temporally due to variation in natural factors. In such complex environments, it remains difficult to detect, dissociate and evaluate the effects of contaminants in wild organisms. In this context, the aim of this study was to test whether the hepatic transcriptome profile of fish may be used to detect in situ exposure to a particular contaminant. Transcriptomic profiles from laboratory-exposed and wild eels sampled along a contamination gradient were compared. During laboratory experiments, fish were exposed during 45days to different pollutants (Hg, PCBs, OCPs or Cd) or natural factors (temperature, salinity or low food supply) at levels close to those found in the sampling sites. A strong difference was observed between the transcriptomic profiles obtained from wild and laboratory-exposed animals (whatever the sites or experimental conditions), suggesting a general stress induced by captivity in the laboratory. Among the biological functions that were up-regulated in laboratory eels in comparison to wild eels, histone modification was the most represented. This finding suggests that laboratory conditions could affect the epigenome of fish and thus modulate the transcriptional responses developed by fish in response to pollutant exposure. Among experimental conditions, only the transcription profiles of laboratory animals exposed to cold temperature were correlated with those obtained from wild fish, and more significantly with fish from contaminated sites. Common regulated genes were mainly involved in cell differentiation and liver development, suggesting that stem/progenitor liver cells could be involved in the adaptive response developed by fish chronically exposed to pollutant mixtures.
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Affiliation(s)
- Lucie Baillon
- Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France
| | - Fabien Pierron
- Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France.
| | - Pauline Pannetier
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (Québec) G1V 0A6, Canada
| | - Patrice Couture
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Pierre Labadie
- Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France
| | - Hélène Budzinski
- Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France
| | - Patrick Lambert
- Irtsea, UR EABX, 50 avenue de Verdun-Gazinet, 33612 Cestas, France
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (Québec) G1V 0A6, Canada
| | - Magalie Baudrimont
- Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France
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Wang W, Song B, Anbarchian T, Shirazyan A, Sadik JE, Lyons KM. Smad2 and Smad3 Regulate Chondrocyte Proliferation and Differentiation in the Growth Plate. PLoS Genet 2016; 12:e1006352. [PMID: 27741240 PMCID: PMC5065210 DOI: 10.1371/journal.pgen.1006352] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/08/2016] [Indexed: 12/30/2022] Open
Abstract
TGFβs act through canonical and non-canonical pathways, and canonical signals are transduced via Smad2 and Smad3. However, the contribution of canonical vs. non-canonical pathways in cartilage is unknown because the role of Smad2 in chondrogenesis has not been investigated in vivo. Therefore, we analyzed mice in which Smad2 is deleted in cartilage (Smad2CKO), global Smad3-/- mutants, and crosses of these strains. Growth plates at birth from all mutant strains exhibited expanded columnar and hypertrophic zones, linked to increased proliferation in resting chondrocytes. Defects were more severe in Smad2CKO and Smad2CKO;Smad3-/-(Smad2/3) mutant mice than in Smad3-/- mice, demonstrating that Smad2 plays a role in chondrogenesis. Increased levels of Ihh RNA, a key regulator of chondrocyte proliferation and differentiation, were seen in prehypertrophic chondrocytes in the three mutant strains at birth. In accordance, TGFβ treatment decreased Ihh RNA levels in primary chondrocytes from control (Smad2fx/fx) mice, but inhibition was impaired in cells from mutants. Consistent with the skeletal phenotype, the impact on TGFβ-mediated inhibition of Ihh RNA expression was more severe in Smad2CKO than in Smad3-/- cells. Putative Smad2/3 binding elements (SBEs) were identified in the proximal Ihh promoter. Mutagenesis demonstrated a role for three of them. ChIP analysis suggested that Smad2 and Smad3 have different affinities for these SBEs, and that the repressors SnoN and Ski were differentially recruited by Smad2 and Smad3, respectively. Furthermore, nuclear localization of the repressor Hdac4 was decreased in growth plates of Smad2CKO and double mutant mice. TGFβ induced association of Hdac4 with Smad2, but not with Smad3, on the Ihh promoter. Overall, these studies revealed that Smad2 plays an essential role in the development of the growth plate, that both Smads 2 and 3 inhibit Ihh expression in the neonatal growth plate, and suggested they accomplish this by binding to distinct SBEs, mediating assembly of distinct repressive complexes. The cartilage growth plate regulates the size and shape of nearly every skeletal element in the body. TGFβs are potent inducers of cartilage formation, but the mechanisms by which they transduce their signals in cartilage during development are poorly understood. Similarly, there is strong evidence that dysregulation of the TGFβ pathway increases the risk for osteoarthritis (OA) in humans, but the underlying mechanisms are unknown. TGFβs transduce their signals through a canonical pathway involving Smad2 and Smad3, and through several non-canonical pathways. However, the roles of canonical vs. noncanonical signaling are unknown in cartilage because the combined roles of Smad2 and Smad3 have not been determined. We generated mice lacking both Smad2 and Smad3 in cartilage in order to determine the role of canonical TGFβ signaling during embryonic development. We determined that Smad2 has a more prominent role than Smad3 in non-hypertrophic chondrocytes in the growth plate, and identified elevated levels of Ihh RNA in neonatal cartilage in Smad2 and Smad3 mutants. These findings may be important because Ihh is a vital regulator of cartilage proliferation and differentiation during cartilage development. More generally, the studies identify how Smad2 and Smad3 can regulate a common target gene through distinct mechanisms.
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Affiliation(s)
- Weiguang Wang
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Buer Song
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Teni Anbarchian
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Anna Shirazyan
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Joshua E. Sadik
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Karen M. Lyons
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Abstract
The transforming growth factor-β (TGF-β) family of ligands elicit their biological effects by initiating new programs of gene expression. The best understood signal transducers for these ligands are the SMADs, which essentially act as transcription factors that are activated in the cytoplasm and then accumulate in the nucleus in response to ligand induction where they bind to enhancer/promoter sequences in the regulatory regions of target genes to either activate or repress transcription. This review focuses on the mechanisms whereby the SMADs achieve this and the functional implications. The SMAD complexes have weak affinity for DNA and limited specificity and, thus, they cooperate with other site-specific transcription factors that act either to actively recruit the SMAD complexes or to stabilize their DNA binding. In some situations, these cooperating transcription factors function to integrate the signals from TGF-β family ligands with environmental cues or with information about cell lineage. Activated SMAD complexes regulate transcription via remodeling of the chromatin template. Consistent with this, they recruit a variety of coactivators and corepressors to the chromatin, which either directly or indirectly modify histones and/or modulate chromatin structure.
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Affiliation(s)
- Caroline S Hill
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom
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Faial T, Bernardo AS, Mendjan S, Diamanti E, Ortmann D, Gentsch GE, Mascetti VL, Trotter MWB, Smith JC, Pedersen RA. Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells. Development 2015; 142:2121-35. [PMID: 26015544 PMCID: PMC4483767 DOI: 10.1242/dev.117838] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Abstract
The transcription factor brachyury (T, BRA) is one of the first markers of gastrulation and lineage specification in vertebrates. Despite its wide use and importance in stem cell and developmental biology, its functional genomic targets in human cells are largely unknown. Here, we use differentiating human embryonic stem cells to study the role of BRA in activin A-induced endoderm and BMP4-induced mesoderm progenitors. We show that BRA has distinct genome-wide binding landscapes in these two cell populations, and that BRA interacts and collaborates with SMAD1 or SMAD2/3 signalling to regulate the expression of its target genes in a cell-specific manner. Importantly, by manipulating the levels of BRA in cells exposed to different signalling environments, we demonstrate that BRA is essential for mesoderm but not for endoderm formation. Together, our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context dependent. Our study reinforces the importance of analysing the functions of a transcription factor in different cellular and signalling environments.
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Affiliation(s)
- Tiago Faial
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andreia S Bernardo
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sasha Mendjan
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Evangelia Diamanti
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK
| | - Daniel Ortmann
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - George E Gentsch
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria L Mascetti
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Matthew W B Trotter
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
| | - James C Smith
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Roger A Pedersen
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
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31
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Dubrulle J, Jordan BM, Akhmetova L, Farrell JA, Kim SH, Solnica-Krezel L, Schier AF. Response to Nodal morphogen gradient is determined by the kinetics of target gene induction. eLife 2015; 4. [PMID: 25869585 PMCID: PMC4395910 DOI: 10.7554/elife.05042] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/02/2015] [Indexed: 12/24/2022] Open
Abstract
Morphogen gradients expose cells to different signal concentrations and induce target genes with different ranges of expression. To determine how the Nodal morphogen gradient induces distinct gene expression patterns during zebrafish embryogenesis, we measured the activation dynamics of the signal transducer Smad2 and the expression kinetics of long- and short-range target genes. We found that threshold models based on ligand concentration are insufficient to predict the response of target genes. Instead, morphogen interpretation is shaped by the kinetics of target gene induction: the higher the rate of transcription and the earlier the onset of induction, the greater the spatial range of expression. Thus, the timing and magnitude of target gene expression can be used to modulate the range of expression and diversify the response to morphogen gradients. DOI:http://dx.doi.org/10.7554/eLife.05042.001 How a cell can tell where it is in a developing embryo has fascinated scientists for decades. The pioneering computer scientist and mathematical biologist Alan Turing was the first person to coin the term ‘morphogen’ to describe a protein that provides information about locations in the body. A morphogen is released from a group of cells (called the ‘source’) and as it moves away its activity (called the ‘signal’) declines gradually. Cells sense this signal gradient and use it to detect their position with respect to the source. Nodal is an important morphogen and is required to establish the correct identity of cells in the embryo; for example, it helps determine which cells should become a brain or heart or gut cell and so on. The zebrafish is a widely used model to study animal development, in part because its embryos are transparent; this allows cells and proteins to be easily observed under a microscope. When Nodal acts on cells, another protein called Smad2 becomes activated, moves into the cell's nucleus, and then binds to specific genes. This triggers the expression of these genes, which are first copied into mRNA molecules via a process known as transcription and are then translated into proteins. The protein products of these targeted genes control cell identity and movement. Several models have been proposed to explain how different concentrations of Nodal switch on the expression of different target genes; that is to say, to explain how a cell interprets the Nodal gradient. Dubrulle et al. have now measured factors that underlie how this gradient is interpreted. Individual cells in zebrafish embryos were tracked under a microscope, and Smad2 activation and gene expression were assessed. Dubrulle et al. found that, in contradiction to previous models, the amount of Nodal present on its own was insufficient to predict the target gene response. Instead, their analysis suggests that the size of each target gene's response depends on its rate of transcription and how quickly it is first expressed in response to Nodal. These findings of Dubrulle et al. suggest that timing and transcription rate are important in determining the appropriate response to Nodal. Further work will be now needed to find out whether similar mechanisms regulate other processes that rely on the activity of morphogens. DOI:http://dx.doi.org/10.7554/eLife.05042.002
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Affiliation(s)
- Julien Dubrulle
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Benjamin M Jordan
- Department of Mathematics, College of Science and Engineering, University of Minnesota, Minneapolis, United States
| | - Laila Akhmetova
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Jeffrey A Farrell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Seok-Hyung Kim
- Division of Medicine, Medical University of South Carolina, Charleston, United States
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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32
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E2a is necessary for Smad2/3-dependent transcription and the direct repression of lefty during gastrulation. Dev Cell 2015; 32:345-57. [PMID: 25669884 DOI: 10.1016/j.devcel.2014.11.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 09/24/2014] [Accepted: 11/25/2014] [Indexed: 11/20/2022]
Abstract
Transcription factor complexes have varied effects on cell fate and behavior, but how this diversification of function occurs is largely unknown. The Nodal signaling pathway has many biological functions that all converge on the transcription factors Smad2/3. Smad2/3 has many cofactors, and alternative usage of these may provide a mechanism for modulating Smad2/3 function. Here, we investigate how perturbation of the cofactor E2a affects global patterns of Smad2/3 binding and gene expression during gastrulation. We find that E2a regulates early development in two ways. E2a changes the position of Smad2/3 binding at the Nodal inhibitor lefty, resulting in direct repression of lefty that is critical for mesendoderm specification. Separately, E2a is necessary to drive transcription of Smad2/3 target genes, including critical regulators of dorsal cell fate and morphogenesis. Overall, we find that E2a functions as both a transcriptional repressor and activator to precisely regulate Nodal signaling.
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33
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HEB associates with PRC2 and SMAD2/3 to regulate developmental fates. Nat Commun 2015; 6:6546. [PMID: 25775035 DOI: 10.1038/ncomms7546] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/05/2015] [Indexed: 11/09/2022] Open
Abstract
In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.
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34
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Gentsch GE, Patrushev I, Smith JC. Genome-wide snapshot of chromatin regulators and states in Xenopus embryos by ChIP-Seq. J Vis Exp 2015. [PMID: 25742027 PMCID: PMC4354678 DOI: 10.3791/52535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The recruitment of chromatin regulators and the assignment of chromatin states to specific genomic loci are pivotal to cell fate decisions and tissue and organ formation during development. Determining the locations and levels of such chromatin features in vivo will provide valuable information about the spatio-temporal regulation of genomic elements, and will support aspirations to mimic embryonic tissue development in vitro. The most commonly used method for genome-wide and high-resolution profiling is chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq). This protocol outlines how yolk-rich embryos such as those of the frog Xenopus can be processed for ChIP-Seq experiments, and it offers simple command lines for post-sequencing analysis. Because of the high efficiency with which the protocol extracts nuclei from formaldehyde-fixed tissue, the method allows easy upscaling to obtain enough ChIP material for genome-wide profiling. Our protocol has been used successfully to map various DNA-binding proteins such as transcription factors, signaling mediators, components of the transcription machinery, chromatin modifiers and post-translational histone modifications, and for this to be done at various stages of embryogenesis. Lastly, this protocol should be widely applicable to other model and non-model organisms as more and more genome assemblies become available.
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Affiliation(s)
- George E Gentsch
- Division of Systems Biology, MRC National Institute for Medical Research;
| | - Ilya Patrushev
- Division of Systems Biology, MRC National Institute for Medical Research
| | - James C Smith
- Division of Systems Biology, MRC National Institute for Medical Research
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35
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Zebrafish Rnf111 is encoded by multiple transcripts and is required for epiboly progression and prechordal plate development. Differentiation 2015; 89:22-30. [PMID: 25619648 DOI: 10.1016/j.diff.2014.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 12/04/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022]
Abstract
Arkadia (also known as RING finger 111) encodes a nuclear E3 ubiquitin ligase that targets intracellular effectors and modulators of TGFβ/Nodal-related signaling for polyubiquitination and proteasome-dependent degradation. In the mouse, loss of Arkadia results in early embryonic lethality, with defects attributed to compromised Nodal signaling. Here, we report the isolation of zebrafish arkadia/rnf111, which is represented by 5 transcript variants. arkadia/rnf111 is broadly expressed during the blastula and gastrula stages, with eventual enrichment in the anterior mesendoderm, including the prechordal plate. Morpholino knockdown experiments reveal an unexpected role for Arkadia/Rnf111 in both early blastula organization and epiboly progression. Using a splice junction morpholino, we present additional evidence that arkadia/rnf111 transcript variants containing a 3' alternative exon are specifically required for epiboly progression in the late gastrula. This result suggests that arkadia/rnf111 transcript variants encode functionally relevant protein isoforms that provide additional intracellular flexibility and regulation to the Nodal signaling pathway.
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36
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Chiu WT, Charney Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, Cho KWY. Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program. Development 2014; 141:4537-47. [PMID: 25359723 DOI: 10.1242/dev.107227] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nodal/TGFβ signaling regulates diverse biological responses. By combining RNA-seq on Foxh1 and Nodal signaling loss-of-function embryos with ChIP-seq of Foxh1 and Smad2/3, we report a comprehensive genome-wide interaction between Foxh1 and Smad2/3 in mediating Nodal signaling during vertebrate mesendoderm development. This study significantly increases the total number of Nodal target genes regulated by Foxh1 and Smad2/3, and reinforces the notion that Foxh1-Smad2/3-mediated Nodal signaling directly coordinates the expression of a cohort of genes involved in the control of gene transcription, signaling pathway modulation and tissue morphogenesis during gastrulation. We also show that Foxh1 may function independently of Nodal signaling, in addition to its role as a transcription factor mediating Nodal signaling via Smad2/3. Finally, we propose an evolutionarily conserved interaction between Foxh1 and PouV, a mechanism observed in Pou5f1-mediated regulation of pluripotency in human embryonic stem and epiblast cells.
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Affiliation(s)
- William T Chiu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Rebekah Charney Le
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Margaret B Fish
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Yi Li
- Department of Computer Science, University of California, Irvine, CA 92697-2300, USA
| | - Jacob Biesinger
- Department of Computer Science, University of California, Irvine, CA 92697-2300, USA
| | - Xiaohui Xie
- Department of Computer Science, University of California, Irvine, CA 92697-2300, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
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37
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Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AEE, Wardle FC. Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biol 2014; 12:81. [PMID: 25277163 PMCID: PMC4206766 DOI: 10.1186/s12915-014-0081-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/27/2022] Open
Abstract
Background Nodal signalling is an absolute requirement for normal mesoderm and endoderm formation in vertebrate embryos, yet the transcriptional networks acting directly downstream of Nodal and the extent to which they are conserved is largely unexplored, particularly in vivo. Eomesodermin also plays a role in patterning mesoderm and endoderm in vertebrates, but its mechanisms of action and how it interacts with the Nodal signalling pathway are still unclear. Results Using a combination of expression analysis and chromatin immunoprecipitation with deep sequencing (ChIP-seq) we identify direct targets of Smad2, the effector of Nodal signalling in blastula stage zebrafish embryos, including many novel target genes. Through comparison of these data with published ChIP-seq data in human, mouse and Xenopus we show that the transcriptional network driven by Smad2 in mesoderm and endoderm is conserved in these vertebrate species. We also show that Smad2 and zebrafish Eomesodermin a (Eomesa) bind common genomic regions proximal to genes involved in mesoderm and endoderm formation, suggesting Eomesa forms a general component of the Smad2 signalling complex in zebrafish. Combinatorial perturbation of Eomesa and Smad2-interacting factor Foxh1 results in loss of both mesoderm and endoderm markers, confirming the role of Eomesa in endoderm formation and its functional interaction with Foxh1 for correct Nodal signalling. Finally, we uncover a novel role for Eomesa in repressing ectodermal genes in the early blastula. Conclusions Our data demonstrate that evolutionarily conserved developmental functions of Nodal signalling occur through maintenance of the transcriptional network directed by Smad2. This network is modulated by Eomesa in zebrafish which acts to promote mesoderm and endoderm formation in combination with Nodal signalling, whilst Eomesa also opposes ectoderm gene expression. Eomesa, therefore, regulates the formation of all three germ layers in the early zebrafish embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0081-5) contains supplementary material, which is available to authorized users.
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38
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Gaarenstroom T, Hill CS. TGF-β signaling to chromatin: how Smads regulate transcription during self-renewal and differentiation. Semin Cell Dev Biol 2014; 32:107-18. [PMID: 24503509 DOI: 10.1016/j.semcdb.2014.01.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/29/2014] [Indexed: 12/20/2022]
Abstract
Ligands of the TGF-β superfamily (including the TGF-βs, Nodal and BMPs) play instructive roles during embryonic development. This is achieved by regulation of genes important for both maintaining pluripotency and germ layer specification and differentiation. Here we review how the TGF-β superfamily ligands signal to the chromatin to regulate transcription during development. The effectors of the pathway, the Smad transcription factors, are regulated in a combinatorial and spatiotemporal manner. This occurs via post-translational modifications affecting stability, localization and activity, as well as through interactions with other transcription factors and chromatin modifying enzymes, which occur on DNA. Expression profiling and Chromatin Immunoprecipitation have defined Smad target genes and binding sites on a genome-wide scale, which vary between cell types and differentiation stages. This has led to the insight that Smad-mediated transcriptional responses are influenced by the presence of master transcription factors, such as OCT4, SOX2 and NANOG in embryonic stem cells, interaction with other signal-induced factors, as well as by the general chromatin remodeling machinery. Interplay with transcriptional repressors and the polycomb group proteins also regulates the balance between expression of self-renewal and mesendoderm-specific genes in embryonic stem cells and during early development.
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Affiliation(s)
- Tessa Gaarenstroom
- Laboratory of Developmental Signalling, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
| | - Caroline S Hill
- Laboratory of Developmental Signalling, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom.
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39
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Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification. Nat Commun 2014; 5:4322. [PMID: 25005894 DOI: 10.1038/ncomms5322] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 06/06/2014] [Indexed: 12/11/2022] Open
Abstract
Head specification by the head-selector gene, orthodenticle (otx), is highly conserved among bilaterian lineages. However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we define two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and other head organizer TFs (for example, Lim1/Lhx1 (activator) or Goosecoid (repressor)) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.
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40
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Hough SR, Thornton M, Mason E, Mar JC, Wells CA, Pera MF. Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Reports 2014; 2:881-95. [PMID: 24936473 PMCID: PMC4050352 DOI: 10.1016/j.stemcr.2014.04.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells display significant heterogeneity in gene expression, but whether this diversity is an inherent feature of the pluripotent state remains unknown. Single-cell gene expression analysis in cell subsets defined by surface antigen expression revealed that human embryonic stem cell cultures exist as a continuum of cell states, even under defined conditions that drive self-renewal. The majority of the population expressed canonical pluripotency transcription factors and could differentiate into derivatives of all three germ layers. A minority subpopulation of cells displayed high self-renewal capacity, consistently high transcripts for all pluripotency-related genes studied, and no lineage priming. This subpopulation was characterized by its expression of a particular set of intercellular signaling molecules whose genes shared common regulatory features. Our data support a model of an inherently metastable self-renewing population that gives rise to a continuum of intermediate pluripotent states, which ultimately become primed for lineage specification. Single-cell transcript profiles characteristic of distinct substates of pluripotency Prospective isolation of substate with high self-renewal, no lineage priming Self-renewing subpopulation marked by expression of specific ligands and receptors
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Affiliation(s)
- Shelley R Hough
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA ; University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Matthew Thornton
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Elizabeth Mason
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, 4072 QLD, Australia
| | - Jessica C Mar
- Department of Systems and Computational Biology and Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christine A Wells
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, 4072 QLD, Australia
| | - Martin F Pera
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA ; University of Melbourne, Walter and Eliza Hall Institute of Medical Research, Florey Institute of Neuroscience and Mental Health, Melbourne, 3010 VIC, Australia
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41
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Abstract
ChIP-seq has become the primary method for identifying in vivo protein-DNA interactions on a genome-wide scale, with nearly 800 publications involving the technique appearing in PubMed as of December 2012. Individually and in aggregate, these data are an important and information-rich resource. However, uncertainties about data quality confound their use by the wider research community. Recently, the Encyclopedia of DNA Elements (ENCODE) project developed and applied metrics to objectively measure ChIP-seq data quality. The ENCODE quality analysis was useful for flagging datasets for closer inspection, eliminating or replacing poor data, and for driving changes in experimental pipelines. There had been no similarly systematic quality analysis of the large and disparate body of published ChIP-seq profiles. Here, we report a uniform analysis of vertebrate transcription factor ChIP-seq datasets in the Gene Expression Omnibus (GEO) repository as of April 1, 2012. The majority (55%) of datasets scored as being highly successful, but a substantial minority (20%) were of apparently poor quality, and another ∼25% were of intermediate quality. We discuss how different uses of ChIP-seq data are affected by specific aspects of data quality, and we highlight exceptional instances for which the metric values should not be taken at face value. Unexpectedly, we discovered that a significant subset of control datasets (i.e., no immunoprecipitation and mock immunoprecipitation samples) display an enrichment structure similar to successful ChIP-seq data. This can, in turn, affect peak calling and data interpretation. Published datasets identified here as high-quality comprise a large group that users can draw on for large-scale integrated analysis. In the future, ChIP-seq quality assessment similar to that used here could guide experimentalists at early stages in a study, provide useful input in the publication process, and be used to stratify ChIP-seq data for different community-wide uses.
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42
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Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Cario C, Di YPP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional genomic assessment of phosgene-induced acute lung injury in mice. Am J Respir Cell Mol Biol 2013; 49:368-83. [PMID: 23590305 DOI: 10.1165/rcmb.2012-0337oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In this study, a genetically diverse panel of 43 mouse strains was exposed to phosgene and genome-wide association mapping performed using a high-density single nucleotide polymorphism (SNP) assembly. Transcriptomic analysis was also used to improve the genetic resolution in the identification of genetic determinants of phosgene-induced acute lung injury (ALI). We prioritized the identified genes based on whether the encoded protein was previously associated with lung injury or contained a nonsynonymous SNP within a functional domain. Candidates were selected that contained a promoter SNP that could alter a putative transcription factor binding site and had variable expression by transcriptomic analyses. The latter two criteria also required that ≥10% of mice carried the minor allele and that this allele could account for ≥10% of the phenotypic difference noted between the strains at the phenotypic extremes. This integrative, functional approach revealed 14 candidate genes that included Atp1a1, Alox5, Galnt11, Hrh1, Mbd4, Phactr2, Plxnd1, Ptprt, Reln, and Zfand4, which had significant SNP associations, and Itga9, Man1a2, Mapk14, and Vwf, which had suggestive SNP associations. Of the genes with significant SNP associations, Atp1a1, Alox5, Plxnd1, Ptprt, and Zfand4 could be associated with ALI in several ways. Using a competitive electrophoretic mobility shift analysis, Atp1a1 promoter (rs215053185) oligonucleotide containing the minor G allele formed a major distinct faster-migrating complex. In addition, a gene with a suggestive SNP association, Itga9, is linked to transforming growth factor β1 signaling, which previously has been associated with the susceptibility to ALI in mice.
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Affiliation(s)
- George D Leikauf
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, PA 15219, USA.
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43
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Gentsch G, Owens N, Martin S, Piccinelli P, Faial T, Trotter M, Gilchrist M, Smith J. In vivo T-box transcription factor profiling reveals joint regulation of embryonic neuromesodermal bipotency. Cell Rep 2013; 4:1185-96. [PMID: 24055059 PMCID: PMC3791401 DOI: 10.1016/j.celrep.2013.08.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/11/2013] [Accepted: 08/06/2013] [Indexed: 01/30/2023] Open
Abstract
The design of effective cell replacement therapies requires detailed knowledge of how embryonic stem cells form primary tissues, such as mesoderm or neurectoderm that later become skeletal muscle or nervous system. Members of the T-box transcription factor family are key in the formation of these primary tissues, but their underlying molecular activities are poorly understood. Here, we define in vivo genome-wide regulatory inputs of the T-box proteins Brachyury, Eomesodermin, and VegT, which together maintain neuromesodermal stem cells and determine their bipotential fates in frog embryos. These T-box proteins are all recruited to the same genomic recognition sites, from where they activate genes involved in stem cell maintenance and mesoderm formation while repressing neurogenic genes. Consequently, their loss causes embryos to form an oversized neural tube with no mesodermal derivatives. This collaboration between T-box family members thus ensures the continuous formation of correctly proportioned neural and mesodermal tissues in vertebrate embryos during axial elongation.
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Affiliation(s)
- George E. Gentsch
- Division of Systems Biology, National Institute for Medical Research, London NW7 1AA, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Nick D.L. Owens
- Division of Systems Biology, National Institute for Medical Research, London NW7 1AA, UK
| | - Stephen R. Martin
- Division of Physical Biochemistry, National Institute for Medical Research, London NW7 1AA, UK
| | - Paul Piccinelli
- Division of Systems Biology, National Institute for Medical Research, London NW7 1AA, UK
| | - Tiago Faial
- Division of Systems Biology, National Institute for Medical Research, London NW7 1AA, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Anne McLaren Laboratory for Regenerative Medicine, Cambridge CB2 0SZ, UK
| | | | - Michael J. Gilchrist
- Division of Systems Biology, National Institute for Medical Research, London NW7 1AA, UK
| | - James C. Smith
- Division of Systems Biology, National Institute for Medical Research, London NW7 1AA, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis. Methods 2013; 66:410-21. [PMID: 24064036 DOI: 10.1016/j.ymeth.2013.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 06/24/2013] [Accepted: 09/12/2013] [Indexed: 11/24/2022] Open
Abstract
Chromatin immunoprecipitation and deep sequencing (ChIP-SEQ) represents a powerful tool for identifying the genomic targets of transcription factors, chromatin remodeling factors, and histone modifications. The frogs Xenopus laevis and Xenopus tropicalis have historically been outstanding model systems for embryology and cell biology, with emerging utility as highly accessible embryos for genome-wide studies. Here we focus on the particular strengths and limitations of Xenopus cell biology and genomics as they apply to ChIP-SEQ, and outline a methodology for ChIP-SEQ in both species, providing detailed strategies for sample preparation, antibody selection, quality control, sequencing library preparation, and basic analysis.
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45
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Webb AE, Pollina EA, Vierbuchen T, Urbán N, Ucar D, Leeman DS, Martynoga B, Sewak M, Rando TA, Guillemot F, Wernig M, Brunet A. FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis. Cell Rep 2013; 4:477-91. [PMID: 23891001 DOI: 10.1016/j.celrep.2013.06.035] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/11/2013] [Accepted: 06/25/2013] [Indexed: 12/16/2022] Open
Abstract
FOXO transcription factors are central regulators of longevity from worms to humans. FOXO3, the FOXO isoform associated with exceptional human longevity, preserves adult neural stem cell pools. Here, we identify FOXO3 direct targets genome-wide in primary cultures of adult neural progenitor cells (NPCs). Interestingly, FOXO3-bound sites are enriched for motifs for bHLH transcription factors, and FOXO3 shares common targets with the proneuronal bHLH transcription factor ASCL1/MASH1 in NPCs. Analysis of the chromatin landscape reveals that FOXO3 and ASCL1 are particularly enriched at the enhancers of genes involved in neurogenic pathways. Intriguingly, FOXO3 inhibits ASCL1-dependent neurogenesis in NPCs and direct neuronal conversion in fibroblasts. FOXO3 also restrains neurogenesis in vivo. Our study identifies a genome-wide interaction between the prolongevity transcription factor FOXO3 and the cell-fate determinant ASCL1 and raises the possibility that FOXO3's ability to restrain ASCL1-dependent neurogenesis may help preserve the neural stem cell pool.
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Affiliation(s)
- Ashley E Webb
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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46
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Malhotra N, Kang J. SMAD regulatory networks construct a balanced immune system. Immunology 2013; 139:1-10. [PMID: 23347175 DOI: 10.1111/imm.12076] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/10/2013] [Accepted: 01/17/2013] [Indexed: 12/17/2022] Open
Abstract
A balanced immune response requires combating infectious assaults while striving to maintain quiescence towards the self. One of the central players in this process is the pleiotropic cytokine transforming growth factor-β (TGF-β), whose deficiency results in spontaneous systemic autoimmunity in mice. The dominant function of TGF-β is to regulate the peripheral immune homeostasis, particularly in the microbe-rich and antigen-rich environment of the gut. To maintain intestinal integrity, the epithelial cells, myeloid cells and lymphocytes that inhabit the gut secrete TGF-β, which acts in both paracrine and autocrine fashions to activate its signal transducers, the SMAD transcription factors. The SMAD pathway regulates the production of IgA by B cells, maintains the protective mucosal barrier and promotes the balanced differentiation of CD4(+) T cells into inflammatory T helper type 17 cells and suppressive FOXP3(+) T regulatory cells. While encounters with pathogenic microbes activate SMAD proteins to evoke a protective inflammatory immune response, SMAD activation and synergism with immunoregulatory factors such as the vitamin A metabolite retinoic acid enforce immunosuppression toward commensal microbes and innocuous food antigens. Such complementary context-dependent functions of TGF-β are achieved by the co-operation of SMAD proteins with distinct dominant transcription activators and accessory chromatin modifiers. This review highlights recent advances in unravelling the molecular basis for the multi-faceted functions of TGF-β in the gut that are dictacted by fluid orchestrations of SMADs and their myriad partners.
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Affiliation(s)
- Nidhi Malhotra
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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47
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Abstract
A balanced immune response requires combating infectious assaults while striving to maintain quiescence towards the self. One of the central players in this process is the pleiotropic cytokine transforming growth factor-β (TGF-β), whose deficiency results in spontaneous systemic autoimmunity in mice. The dominant function of TGF-β is to regulate the peripheral immune homeostasis, particularly in the microbe-rich and antigen-rich environment of the gut. To maintain intestinal integrity, the epithelial cells, myeloid cells and lymphocytes that inhabit the gut secrete TGF-β, which acts in both paracrine and autocrine fashions to activate its signal transducers, the SMAD transcription factors. The SMAD pathway regulates the production of IgA by B cells, maintains the protective mucosal barrier and promotes the balanced differentiation of CD4(+) T cells into inflammatory T helper type 17 cells and suppressive FOXP3(+) T regulatory cells. While encounters with pathogenic microbes activate SMAD proteins to evoke a protective inflammatory immune response, SMAD activation and synergism with immunoregulatory factors such as the vitamin A metabolite retinoic acid enforce immunosuppression toward commensal microbes and innocuous food antigens. Such complementary context-dependent functions of TGF-β are achieved by the co-operation of SMAD proteins with distinct dominant transcription activators and accessory chromatin modifiers. This review highlights recent advances in unravelling the molecular basis for the multi-faceted functions of TGF-β in the gut that are dictacted by fluid orchestrations of SMADs and their myriad partners.
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Affiliation(s)
- Nidhi Malhotra
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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48
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Chuong EB, Rumi MAK, Soares MJ, Baker JC. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 2013; 45:325-9. [PMID: 23396136 PMCID: PMC3789077 DOI: 10.1038/ng.2553] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/11/2013] [Indexed: 01/30/2023]
Abstract
The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification1. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers between mouse and rat trophoblast stem cells (TSCs) and find that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific H3K4me1/H3K27ac-defined enhancers that functionally bind Cdx2, Eomes, and Elf5 - core factors that define the TSC regulatory network. Furthermore, we demonstrate that RLTR13D5 is capable of driving gene expression in rat placental cells. Comparison with other tissues revealed that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive to ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer cooption as a mechanism underlying the striking evolutionary diversification of placental development.
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Affiliation(s)
- Edward B Chuong
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
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49
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Synergistic roles of scleraxis and Smads in the regulation of collagen 1α2 gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1936-44. [DOI: 10.1016/j.bbamcr.2012.07.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 12/30/2022]
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50
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Abstract
The basic elements of the transforming growth factor-β (TGFβ) pathway were revealed more than a decade ago. Since then, the concept of how the TGFβ signal travels from the membrane to the nucleus has been enriched with additional findings, and its multifunctional nature and medical relevance have relentlessly come to light. However, an old mystery has endured: how does the context determine the cellular response to TGFβ? Solving this question is key to understanding TGFβ biology and its many malfunctions. Recent progress is pointing at answers.
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Affiliation(s)
- Joan Massagué
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
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