1
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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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2
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Subramanian S, Thoms JAI, Huang Y, Cornejo-Páramo P, Koch FC, Jacquelin S, Shen S, Song E, Joshi S, Brownlee C, Woll PS, Chacon-Fajardo D, Beck D, Curtis DJ, Yehson K, Antonenas V, O'Brien T, Trickett A, Powell JA, Lewis ID, Pitson SM, Gandhi MK, Lane SW, Vafaee F, Wong ES, Göttgens B, Alinejad-Rokny H, Wong JWH, Pimanda JE. Genome-wide transcription factor-binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs. Blood 2023; 142:1448-1462. [PMID: 37595278 PMCID: PMC10651876 DOI: 10.1182/blood.2023021120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay among transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs (FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2) bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remains unknown. We mapped genome-wide chromatin contacts (HiC, H3K27ac, HiChIP), chromatin modifications (H3K4me3, H3K27ac, H3K27me3) and 10 TF binding profiles (heptad, PU.1, CTCF, STAG2) in HSPC subsets (stem/multipotent progenitors plus common myeloid, granulocyte macrophage, and megakaryocyte erythrocyte progenitors) and found TF occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. Furthermore, heptad-occupied regions in HSPCs were subsequently bound by lineage-defining TFs, including PU.1 and GATA1, suggesting that heptad factors may prime regulatory elements for use in mature cell types. We also found that enhancers with cell-type-specific heptad occupancy shared a common grammar with respect to TF binding motifs, suggesting that combinatorial binding of TF complexes was at least partially regulated by features encoded in DNA sequence motifs. Taken together, this study comprehensively characterizes the gene regulatory landscape in rare subpopulations of human HSPCs. The accompanying data sets should serve as a valuable resource for understanding adult hematopoiesis and a framework for analyzing aberrant regulatory networks in leukemic cells.
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Affiliation(s)
- Shruthi Subramanian
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Julie A. I. Thoms
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Yizhou Huang
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | | | - Forrest C. Koch
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | | | - Sylvie Shen
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Emma Song
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Swapna Joshi
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Chris Brownlee
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Petter S. Woll
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Diego Chacon-Fajardo
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Dominik Beck
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - David J. Curtis
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Kenneth Yehson
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology, Westmead, NSW, Australia
| | - Vicki Antonenas
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology, Westmead, NSW, Australia
| | | | - Annette Trickett
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Jason A. Powell
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Ian D. Lewis
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Stuart M. Pitson
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Maher K. Gandhi
- Blood Cancer Research Group, Mater Research, The University of Queensland, Brisbane, QLD, Australia
| | - Steven W. Lane
- Cancer Program, QIMR Berghofer Medical Research, Brisbane, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, Australia
| | - Emily S. Wong
- Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - John E. Pimanda
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- Haematology Department, Prince of Wales Hospital, Sydney, Australia
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3
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Sun Z, Fan J, Dang Y, Zhao Y. Enhancer in cancer pathogenesis and treatment. Genet Mol Biol 2023; 46:e20220313. [PMID: 37548349 PMCID: PMC10405138 DOI: 10.1590/1678-4685-gmb-2022-0313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Enhancers are essential cis-acting regulatory elements that determine cell identity and tumor progression. Enhancer function is dependent on the physical interaction between the enhancer and its target promoter inside its local chromatin environment. Enhancer reprogramming is an important mechanism in cancer pathogenesis and can be driven by both cis and trans factors. Super enhancers are acquired at oncogenes in numerous cancer types and represent potential targets for cancer treatment. BET and CDK inhibitors act through mechanisms of enhancer function and have shown promising results in therapy for various types of cancer. Genome editing is another way to reprogram enhancers in cancer treatment. The relationship between enhancers and cancer has been revised by several authors in the past few years, which mainly focuses on the mechanisms by which enhancers can impact cancer. Here, we emphasize SE's role in cancer pathogenesis and the new therapies involving epigenetic regulators (BETi and CDKi). We suggest that understanding mechanisms of activity would aid clinical success for these anti-cancer agents.
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Affiliation(s)
- Zhuo Sun
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
| | - Jinbo Fan
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
| | - Yixiong Dang
- Xi’an Medical University, School of Public Health, Weiyang District, Xi’an, 710021 Shaanxi, China
| | - Yufeng Zhao
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
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4
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Tu J, Yu S, Li J, Ren M, Zhang Y, Luo J, Sun K, Lv Y, Han Y, Huang Y, Ren X, Jiang T, Tang Z, Williams MTS, Lu Q, Liu M. Dhx38 is required for the maintenance and differentiation of erythro-myeloid progenitors and hematopoietic stem cells by alternative splicing. Development 2022; 149:276218. [DOI: 10.1242/dev.200450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/21/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Mutations that occur in RNA-splicing machinery may contribute to hematopoiesis-related diseases. How splicing factor mutations perturb hematopoiesis, especially in the differentiation of erythro-myeloid progenitors (EMPs), remains elusive. Dhx38 is a pre-mRNA splicing-related DEAH box RNA helicase, for which the physiological functions and splicing mechanisms during hematopoiesis currently remain unclear. Here, we report that Dhx38 exerts a broad effect on definitive EMPs as well as the differentiation and maintenance of hematopoietic stem and progenitor cells (HSPCs). In dhx38 knockout zebrafish, EMPs and HSPCs were found to be arrested in mitotic prometaphase, accompanied by a ‘grape’ karyotype, owing to the defects in chromosome alignment. Abnormal alternatively spliced genes related to chromosome segregation, the microtubule cytoskeleton, cell cycle kinases and DNA damage were present in the dhx38 mutants. Subsequently, EMPs and HSPCs in dhx38 mutants underwent P53-dependent apoptosis. This study provides novel insights into alternative splicing regulated by Dhx38, a process that plays a crucial role in the proliferation and differentiation of fetal EMPs and HSPCs.
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Affiliation(s)
- Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Shanshan Yu
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology 2 , Wuhan, Hubei 430065 , P.R. China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mengmeng Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yangjun Zhang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology 3 , Wuhan 430030 , P.R. China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mark Thomas Shaw Williams
- Charles Oakley Laboratories 4 , Department of Biological and Biomedical Sciences , , Glasgow G4 0BA , UK
- Glasgow Caledonian University 4 , Department of Biological and Biomedical Sciences , , Glasgow G4 0BA , UK
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
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5
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Rothenberg EV, Göttgens B. How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson. Curr Opin Hematol 2021; 28:1-10. [PMID: 33229891 PMCID: PMC7755131 DOI: 10.1097/moh.0000000000000628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW This historical perspective reviews how work of Eric H. Davidson was a catalyst and exemplar for explaining haematopoietic cell fate determination through gene regulation. RECENT FINDINGS Researchers studying blood and immune cells pioneered many of the early mechanistic investigations of mammalian gene regulatory processes. These efforts included the characterization of complex gene regulatory sequences exemplified by the globin and T-cell/B-cell receptor gene loci, as well as the identification of many key regulatory transcription factors through the fine mapping of chromosome translocation breakpoints in leukaemia patients. As the repertoire of known regulators expanded, assembly into gene regulatory network models became increasingly important, not only to account for the truism that regulatory genes do not function in isolation but also to devise new ways of extracting biologically meaningful insights from even more complex information. Here we explore how Eric H. Davidson's pioneering studies of gene regulatory network control in nonvertebrate model organisms have had an important and lasting impact on research into blood and immune cell development. SUMMARY The intellectual framework developed by Davidson continues to contribute to haematopoietic research, and his insistence on demonstrating logic and causality still challenges the frontier of research today.
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Affiliation(s)
- Ellen V. Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Berthold Göttgens
- Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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6
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Sauta E, Demartini A, Vitali F, Riva A, Bellazzi R. A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. BMC Bioinformatics 2020; 21:219. [PMID: 32471360 PMCID: PMC7257163 DOI: 10.1186/s12859-020-3510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number of interacting variables and the noise in the available heterogeneous experimental sources of information. RESULTS In this work, we propose a data fusion approach that exploits the integration of complementary omics-data as prior knowledge within a Bayesian framework, in order to learn and model large-scale transcriptional networks. We develop a hybrid structure-learning algorithm able to jointly combine TFs ChIP-Sequencing data and gene expression compendia to reconstruct TRNs in a genome-wide perspective. Applying our method to high-throughput data, we verified its ability to deal with the complexity of a genomic TRN, providing a snapshot of the synergistic TFs regulatory activity. Given the noisy nature of data-driven prior knowledge, which potentially contains incorrect information, we also tested the method's robustness to false priors on a benchmark dataset, comparing the proposed approach to other regulatory network reconstruction algorithms. We demonstrated the effectiveness of our framework by evaluating structural commonalities of our learned genomic network with other existing networks inferred by different DNA binding information-based methods. CONCLUSIONS This Bayesian omics-data fusion based methodology allows to gain a genome-wide picture of the transcriptional interplay, helping to unravel key hierarchical transcriptional interactions, which could be subsequently investigated, and it represents a promising learning approach suitable for multi-layered genomic data integration, given its robustness to noisy sources and its tailored framework for handling high dimensional data.
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Affiliation(s)
- Elisabetta Sauta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.
| | - Andrea Demartini
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Francesca Vitali
- Center for Biomedical Informatics and Biostatistics, Dept. of Medicine, The University of Arizona Health Sciences, 1230 Cherry Ave, Tucson, AZ, 85719, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
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7
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Peter IS. The function of architecture and logic in developmental gene regulatory networks. Curr Top Dev Biol 2020; 139:267-295. [PMID: 32450963 DOI: 10.1016/bs.ctdb.2020.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An important contribution of systems biology is the insight that biological systems depend on the function of molecular interactions and not just on individual molecules. System level mechanisms are particularly important in the development of animals and plants which depends not just on transcription factors and signaling molecules, but also on regulatory circuits and gene regulatory networks (GRNs). However, since GRNs consist of transcription factors, it can be challenging to assess the function of regulatory circuits independently of the function of regulatory factors. The comparison of different GRNs offers a way to do so and leads to several observations. First, similar regulatory circuits operate in various developmental contexts and in different species, and frequently, these circuits are associated with similar developmental functions. Second, given regulatory circuits are often used at particular positions within the GRN hierarchy. Third, in some GRNs, regulatory circuits are organized in a particular order in respect to each other. And fourth, the evolution of GRNs occurs not just by co-option of regulatory genes but also by rewiring of regulatory linkages between conserved regulatory genes, indicating that the organization of interactions is important. Thus, even though in most instances the function of regulatory circuits remains to be discovered, it becomes evident that the architecture and logic of GRNs are functionally important for the control of genome activity and for the specification of the body plan.
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Affiliation(s)
- Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
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8
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Pijuan-Sala B, Wilson NK, Xia J, Hou X, Hannah RL, Kinston S, Calero-Nieto FJ, Poirion O, Preissl S, Liu F, Göttgens B. Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis. Nat Cell Biol 2020; 22:487-497. [PMID: 32231307 PMCID: PMC7145456 DOI: 10.1038/s41556-020-0489-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/20/2020] [Indexed: 11/29/2022]
Abstract
During mouse embryonic development, pluripotent cells rapidly divide and diversify, yet the regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes during early organogenesis, we mapped chromatin accessibility in 19,453 single nuclei from mouse embryos at 8.25 days post-fertilization. Identification of cell-type-specific regions of open chromatin pinpointed two TAL1-bound endothelial enhancers, which we validated using transgenic mouse assays. Integrated gene expression and transcription factor motif enrichment analyses highlighted cell-type-specific transcriptional regulators. Subsequent in vivo experiments in zebrafish revealed a role for the ETS factor FEV in endothelial identity downstream of ETV2 (Etsrp in zebrafish). Concerted in vivo validation experiments in mouse and zebrafish thus illustrate how single-cell open chromatin maps, representative of a mammalian embryo, provide access to the regulatory blueprint for mammalian organogenesis.
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Affiliation(s)
- Blanca Pijuan-Sala
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jun Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Rebecca L Hannah
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sarah Kinston
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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9
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Genomic Alterations of Non-Coding Regions Underlie Human Cancer: Lessons from T-ALL. Trends Mol Med 2016; 22:1035-1046. [PMID: 28240214 DOI: 10.1016/j.molmed.2016.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 12/31/2022]
Abstract
It has been appreciated for decades that somatic genomic alterations that change coding sequences of proto-oncogenes, translocate enhancers/promoters near proto-oncogenes, or create fusion oncogenes can drive cancer by inducing oncogenic activities. An explosion of genome-wide technologies over the past decade has fueled discoveries of the roles of three-dimensional chromosome structure and powerful cis-acting elements (super-enhancers) in regulating gene transcription. In recent years, studies of human T cell acute lymphoblastic leukemia (T-ALL) using genome-wide technologies have provided paradigms for how non-coding genomic region alterations can disrupt 3D chromosome architecture or establish super-enhancers to activate oncogenic transcription of proto-oncogenes. These studies raise important issues to consider with the objective of leveraging basic knowledge into new diagnostic and therapeutic opportunities for cancer patients.
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10
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Stem Cell Leukemia: how a TALented actor can go awry on the hematopoietic stage. Leukemia 2016; 30:1968-1978. [DOI: 10.1038/leu.2016.169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 02/06/2023]
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11
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Lelieveld SH, Schütte J, Dijkstra MJJ, Bawono P, Kinston SJ, Göttgens B, Heringa J, Bonzanni N. ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites. Nucleic Acids Res 2016; 44:e72. [PMID: 26721389 PMCID: PMC4856970 DOI: 10.1093/nar/gkv1518] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal. While multiple sequence alignment (MSA) is a potent tool to detect the phylogenetic signal, the current MSA implementations are optimized to align the maximum number of identical nucleotides. This approach might result in the omission of conserved motifs that contain interchangeable nucleotides such as the ETS motif (IUPAC code: GGAW). Here, we introduce ConBind, a novel method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved TFBSs by improving the alignment accuracy of TFBS families within orthologous DNA sequences. Functional validation of the Gfi1b + 13 enhancer reveals that ConBind identifies additional functionally important ETS binding sites that were missed by all other tested alignment tools. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Judith Schütte
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK Klinik für Hämatologie, Universitätsklinik Essen 45147, Germany
| | - Maurits J J Dijkstra
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Punto Bawono
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Sarah J Kinston
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Jaap Heringa
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Nicola Bonzanni
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands ENPICOM, Eindhoven 5632 CW, The Netherlands
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12
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Schütte J, Wang H, Antoniou S, Jarratt A, Wilson NK, Riepsaame J, Calero-Nieto FJ, Moignard V, Basilico S, Kinston SJ, Hannah RL, Chan MC, Nürnberg ST, Ouwehand WH, Bonzanni N, de Bruijn MF, Göttgens B. An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability. eLife 2016; 5:e11469. [PMID: 26901438 PMCID: PMC4798972 DOI: 10.7554/elife.11469] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/12/2016] [Indexed: 12/12/2022] Open
Abstract
Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes.
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Affiliation(s)
- Judith Schütte
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Huange Wang
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stella Antoniou
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew Jarratt
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Joey Riepsaame
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Basilico
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Kinston
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca L Hannah
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mun Chiang Chan
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sylvia T Nürnberg
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NHS Blood and Transplant, Cambridge, United Kingdom
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NHS Blood and Transplant, Cambridge, United Kingdom
| | - Nicola Bonzanni
- IBIVU Centre for Integrative Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands.,Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marella Ftr de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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13
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Hewitt KJ, Johnson KD, Gao X, Keles S, Bresnick EH. The Hematopoietic Stem and Progenitor Cell Cistrome: GATA Factor-Dependent cis-Regulatory Mechanisms. Curr Top Dev Biol 2016; 118:45-76. [PMID: 27137654 PMCID: PMC8572122 DOI: 10.1016/bs.ctdb.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Transcriptional regulators mediate the genesis and function of the hematopoietic system by binding complex ensembles of cis-regulatory elements to establish genetic networks. While thousands to millions of any given cis-element resides in a genome, how transcriptional regulators select these sites and how site attributes dictate functional output is not well understood. An instructive system to address this problem involves the GATA family of transcription factors that control vital developmental and physiological processes and are linked to multiple human pathologies. Although GATA factors bind DNA motifs harboring the sequence GATA, only a very small subset of these abundant motifs are occupied in genomes. Mechanistic studies revealed a unique configuration of a GATA factor-regulated cis-element consisting of an E-box and a downstream GATA motif separated by a short DNA spacer. GATA-1- or GATA-2-containing multiprotein complexes at these composite elements control transcription of genes critical for hematopoietic stem cell emergence in the mammalian embryo, hematopoietic progenitor cell regulation, and erythroid cell maturation. Other constituents of the complex include the basic helix-loop-loop transcription factor Scl/TAL1, its heterodimeric partner E2A, and the Lim domain proteins LMO2 and LDB1. This chapter reviews the structure/function of E-box-GATA composite cis-elements, which collectively constitute an important sector of the hematopoietic stem and progenitor cell cistrome.
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Affiliation(s)
- Kyle J. Hewitt
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Kirby D. Johnson
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Xin Gao
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health
| | - Emery H. Bresnick
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program,Corresponding author:
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14
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Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16:144-54. [PMID: 25650801 PMCID: PMC4517609 DOI: 10.1038/nrm3949] [Citation(s) in RCA: 653] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
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Affiliation(s)
| | | | | | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, UC San Diego
- Department of Medicine, UC San Diego
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15
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The ets transcription factor Fli-1 in development, cancer and disease. Oncogene 2014; 34:2022-31. [PMID: 24909161 PMCID: PMC5028196 DOI: 10.1038/onc.2014.162] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/03/2014] [Accepted: 05/04/2014] [Indexed: 12/13/2022]
Abstract
Friend Leukemia Virus Induced erythroleukemia-1 (Fli-1), an ETS transcription factor, was isolated a quarter century ago through a retrovirus mutagenesis screen. Fli-1 has since been recognized to play critical roles in normal development and homeostasis. For example, it transcriptionally regulates genes that drive normal hematopoiesis and vasculogenesis. Indeed, Fli-1 is one of 10 key regulators of hematopoietic stem/progenitor cell maintenance and differentiation. Aberrant expression of Fli-1 also underlies a number of virally induced leukemias, including Friend virus-induced erythroleukemia and various types of human cancers, and it is the target of chromosomal translocations in childhood Ewing’s sarcoma. Abnormal expression of Fli-1 is important in the aetiology of auto-immune diseases such as Systemic Lupus Erythematosus (SLE) and Systemic Sclerosis (SSc). These studies establish Fli-1 as a strong candidate for drug development. Despite difficulties in targeting transcription factors, recent studies identified small molecule inhibitors for Fli-1. Here we review past and ongoing research on Fli-1 with emphasis on its mechanistic function in autoimmune disease and malignant transformation. The significance of identifying Fli-1 inhibitors and their clinical applications for treatment of disease and cancer with deregulated Fli-1 expression are discussed.
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16
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Patel B, Kang Y, Cui K, Litt M, Riberio MSJ, Deng C, Salz T, Casada S, Fu X, Qiu Y, Zhao K, Huang S. Aberrant TAL1 activation is mediated by an interchromosomal interaction in human T-cell acute lymphoblastic leukemia. Leukemia 2014; 28:349-61. [PMID: 23698277 PMCID: PMC10921969 DOI: 10.1038/leu.2013.158] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/09/2013] [Accepted: 05/16/2013] [Indexed: 01/21/2023]
Abstract
Long-range chromatin interactions control metazoan gene transcription. However, the involvement of intra- and interchromosomal interactions in development and oncogenesis remains unclear. TAL1/SCL is a critical transcription factor required for the development of all hematopoietic lineages; yet, aberrant TAL1 transcription often occurs in T-cell acute lymphoblastic leukemia (T-ALL). Here, we report that oncogenic TAL1 expression is regulated by different intra- and interchromosomal loops in normal hematopoietic and leukemic cells, respectively. These intra- and interchromosomal loops alter the cell-type-specific enhancers that interact with the TAL1 promoter. We show that human SET1 (hSET1)-mediated H3K4 methylations promote a long-range chromatin loop, which brings the +51 enhancer in close proximity to TAL1 promoter 1 in erythroid cells. The CCCTC-binding factor (CTCF) facilitates this long-range enhancer/promoter interaction of the TAL1 locus in erythroid cells while blocking the same enhancer/promoter interaction of the TAL1 locus in human T-cell leukemia. In human T-ALL, a T-cell-specific transcription factor c-Maf-mediated interchromosomal interaction brings the TAL1 promoter into close proximity with a T-cell-specific regulatory element located on chromosome 16, activating aberrant TAL1 oncogene expression. Thus, our study reveals a novel molecular mechanism involving changes in three-dimensional chromatin interactions that activate the TAL1 oncogene in human T-cell leukemia.
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Affiliation(s)
- B Patel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
- These authors contributed equally to this work
| | - Y Kang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
- College of Life Science, Jilin University, Changchun, China
- These authors contributed equally to this work
| | - K Cui
- Center for System Biology, NHLBI, National Institute of Health, Bethesda, MD, USA
| | - M Litt
- Medical Education Center, Ball State University, Muncie, IN, USA
| | - MSJ Riberio
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - C Deng
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - T Salz
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - S Casada
- Medical Education Center, Ball State University, Muncie, IN, USA
| | - X Fu
- College of Life Science, Jilin University, Changchun, China
| | - Y Qiu
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL, USA
- Shands Cancer Center, College of Medicine, University of Florida, Gainesville, FL, USA
| | - K Zhao
- Center for System Biology, NHLBI, National Institute of Health, Bethesda, MD, USA
| | - S Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
- Shands Cancer Center, College of Medicine, University of Florida, Gainesville, FL, USA
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17
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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 2014; 46:205-12. [PMID: 24413732 DOI: 10.1038/ng.2871] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/12/2013] [Indexed: 12/19/2022]
Abstract
Gene expression during development and differentiation is regulated in a cell- and stage-specific manner by complex networks of intergenic and intragenic cis-regulatory elements whose numbers and representation in the genome far exceed those of structural genes. Using chromosome conformation capture, it is now possible to analyze in detail the interaction between enhancers, silencers, boundary elements and promoters at individual loci, but these techniques are not readily scalable. Here we present a high-throughput approach (Capture-C) to analyze cis interactions, interrogating hundreds of specific interactions at high resolution in a single experiment. We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. In addition, we show how Capture-C will expedite identification of the target genes and functional effects of SNPs that are associated with complex diseases, which most frequently lie in intergenic cis-acting regulatory elements.
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18
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Bonzanni N, Garg A, Feenstra KA, Schütte J, Kinston S, Miranda-Saavedra D, Heringa J, Xenarios I, Göttgens B. Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinformatics 2013; 29:i80-8. [PMID: 23813012 PMCID: PMC3694641 DOI: 10.1093/bioinformatics/btt243] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Motivation: Combinatorial interactions of transcription factors with cis-regulatory elements control the dynamic progression through successive cellular states and thus underpin all metazoan development. The construction of network models of cis-regulatory elements, therefore, has the potential to generate fundamental insights into cellular fate and differentiation. Haematopoiesis has long served as a model system to study mammalian differentiation, yet modelling based on experimentally informed cis-regulatory interactions has so far been restricted to pairs of interacting factors. Here, we have generated a Boolean network model based on detailed cis-regulatory functional data connecting 11 haematopoietic stem/progenitor cell (HSPC) regulator genes. Results: Despite its apparent simplicity, the model exhibits surprisingly complex behaviour that we charted using strongly connected components and shortest-path analysis in its Boolean state space. This analysis of our model predicts that HSPCs display heterogeneous expression patterns and possess many intermediate states that can act as ‘stepping stones’ for the HSPC to achieve a final differentiated state. Importantly, an external perturbation or ‘trigger’ is required to exit the stem cell state, with distinct triggers characterizing maturation into the various different lineages. By focusing on intermediate states occurring during erythrocyte differentiation, from our model we predicted a novel negative regulation of Fli1 by Gata1, which we confirmed experimentally thus validating our model. In conclusion, we demonstrate that an advanced mammalian regulatory network model based on experimentally validated cis-regulatory interactions has allowed us to make novel, experimentally testable hypotheses about transcriptional mechanisms that control differentiation of mammalian stem cells. Contact:j.heringa@vu.nl or ioannis.xenarios@isb-sib.ch or bg200@cam.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicola Bonzanni
- IBIVU Centre for Integrative Bioinformatics, VU University Amsterdam, AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, De Boelelaan 1081, NKI-AVL The Netherlands
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19
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Chromatin looping defines expression of TAL1, its flanking genes, and regulation in T-ALL. Blood 2013; 122:4199-209. [PMID: 24200685 DOI: 10.1182/blood-2013-02-483875] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
TAL1 is an important regulator of hematopoiesis and its expression is tightly controlled despite complexities in its genomic organization. It is frequently misregulated in T-cell acute lymphoblastic leukemia (T-ALL), often due to deletions between TAL1 and the neighboring STIL gene. To better understand the events that lead to TAL1 expression in hematopoiesis and in T-ALL, we studied looping interactions at the TAL1 locus. In TAL1-expressing erythroid cells, the locus adopts a looping "hub" which brings into close physical proximity all known TAL1 cis-regulatory elements including CTCF-bound insulators. Loss of GATA1 results in disassembly of the hub and loss of CTCF/RAD21 from one of its insulators. Genes flanking TAL1 are partly dependent on hub integrity for their transcriptional regulation. We identified looping patterns unique to TAL1-expressing T-ALL cells, and, intriguingly, loops occurring between the TAL1 and STIL genes at the common TAL1/STIL breakpoints found in T-ALL. These findings redefine how TAL1 and neighboring genes communicate within the nucleus, and indicate that looping facilitates both normal and aberrant TAL1 expression and may predispose to structural rearrangements in T-ALL. We also propose that GATA1-dependent looping mechanisms may facilitate the conservation of TAL1 regulation despite cis-regulatory remodeling during vertebrate evolution.
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20
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Joseph C, Quach J, Walkley C, Lane S, Lo Celso C, Purton L. Deciphering Hematopoietic Stem Cells in Their Niches: A Critical Appraisal of Genetic Models, Lineage Tracing, and Imaging Strategies. Cell Stem Cell 2013; 13:520-33. [DOI: 10.1016/j.stem.2013.10.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Wilkinson AC, Goode DK, Cheng YH, Dickel DE, Foster S, Sendall T, Tijssen MR, Sanchez MJ, Pennacchio LA, Kirkpatrick AM, Göttgens B. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses. Biol Open 2013; 2:1229-38. [PMID: 24244860 PMCID: PMC3828770 DOI: 10.1242/bio.20136296] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/09/2013] [Indexed: 01/05/2023] Open
Abstract
Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.
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Affiliation(s)
- Adam C Wilkinson
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge , Hills Road, Cambridge CB2 0XY , UK
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22
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Transcriptional regulation of haematopoietic stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 786:187-212. [PMID: 23696358 DOI: 10.1007/978-94-007-6621-1_11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Haematopoietic stem cells (HSCs) are a rare cell population found in the bone marrow of adult mammals and are responsible for maintaining the entire haematopoietic system. Definitive HSCs are produced from mesoderm during embryonic development, from embryonic day 10 in the mouse. HSCs seed the foetal liver before migrating to the bone marrow around the time of birth. In the adult, HSCs are largely quiescent but have the ability to divide to self-renew and expand, or to proliferate and differentiate into any mature haematopoietic cell type. Both the specification of HSCs during development and their cellular choices once formed are tightly controlled at the level of transcription. Numerous transcriptional regulators of HSC specification, expansion, homeostasis and differentiation have been identified, primarily from analysis of mouse gene knockout experiments and transplantation assays. These include transcription factors, epigenetic modifiers and signalling pathway effectors. This chapter reviews the current knowledge of these HSC transcriptional regulators, predominantly focusing on the transcriptional regulation of mouse HSCs, although transcriptional regulation of human HSCs is also mentioned where relevant. Due to the breadth and maturity of this field, we have prioritised recently identified examples of HSC transcriptional regulators. We go on to highlight additional layers of control that regulate expression and activity of HSC transcriptional regulators and discuss how chromosomal translocations that result in fusion proteins of these HSC transcriptional regulators commonly drive leukaemias through transcriptional dysregulation.
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23
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Abstract
Bcl11b is a T-cell specific gene in hematopoiesis that begins expression during T-lineage commitment and is required for this process. Aberrant expression of BCL11B or proto-oncogene translocation to the vicinity of BCL11B can be a contributing factor in human T-ALL. To identify the mechanism that controls its distinctive T-lineage expression, we corrected the identified Bcl11b transcription start site and mapped a cell-type-specific differentially methylated region bracketing the Bcl11b promoter. We identified a 1.9-kb region 850 kb downstream of Bcl11b, "Major Peak," distinguished by its dynamic histone marking pattern in development that mirrors the pattern at the Bcl11b promoter. Looping interactions between promoter-proximal elements including the differentially methylated region and downstream elements in the Major Peak are required to recapitulate the T-cell specific expression of Bcl11b in stable reporter assays. Functional dissection of the Major Peak sequence showed distinct subregions, in which TCF-1 sites and a conserved element were required for T-lineage-specific activation and silencing in non-T cells. A bacterial artificial chromosome encompassing the full Bcl11b gene still required the addition of the Major Peak to exhibit T-cell specific expression. Thus, promoter-proximal and Major Peak sequences are cis-regulatory elements that interact over 850 kb to control expression of Bcl11b in hematopoietic cells.
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24
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Zeng X, Sanalkumar R, Bresnick EH, Li H, Chang Q, Keleş S. jMOSAiCS: joint analysis of multiple ChIP-seq datasets. Genome Biol 2013; 14:R38. [PMID: 23844871 PMCID: PMC4053760 DOI: 10.1186/gb-2013-14-4-r38] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 04/12/2013] [Accepted: 04/29/2013] [Indexed: 12/20/2022] Open
Abstract
The ChIP-seq technique enables genome-wide mapping of in vivo protein-DNA interactions and chromatin states. Current analytical approaches for ChIP-seq analysis are largely geared towards single-sample investigations, and have limited applicability in comparative settings that aim to identify combinatorial patterns of enrichment across multiple datasets. We describe a novel probabilistic method, jMOSAiCS, for jointly analyzing multiple ChIP-seq datasets. We demonstrate its usefulness with a wide range of data-driven computational experiments and with a case study of histone modifications on GATA1-occupied segments during erythroid differentiation. jMOSAiCS is open source software and can be downloaded from Bioconductor 1.
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Affiliation(s)
- Xin Zeng
- Department of Statistics, University of Wisconsin-Madison, 1220 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706, USA
| | - Rajendran Sanalkumar
- Wisconsin Institutes for Medical Research, University of Wisconsin-Madison Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, 325 Services Memorial Institute, 1300 University Avenue, Madison, WI 53706, USA
| | - Emery H Bresnick
- Wisconsin Institutes for Medical Research, University of Wisconsin-Madison Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, 325 Services Memorial Institute, 1300 University Avenue, Madison, WI 53706, USA
| | - Hongda Li
- Genetics Training Program, Waisman Center, University of Wisconsin-Madison, 1500 Highland Avenue, Madison, WI 53705-2280, USA
| | - Qiang Chang
- Genetics Training Program, Waisman Center, University of Wisconsin-Madison, 1500 Highland Avenue, Madison, WI 53705-2280, USA
- Department of Genetics and Neurology, University of Wisconsin-Madison, 425 Henry Mall Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, 1220 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, K6/446 Clinical Sciences Center, 600 Highland Avenue, Madison, WI 53792-4675, USA
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25
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Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression. Mol Cell Biol 2013; 33:1254-66. [PMID: 23319051 DOI: 10.1128/mcb.01525-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Scl (Tal1) gene encodes a helix-loop-helix transcription factor essential for hematopoietic stem cell and erythroid development. The Scl +40 enhancer is situated downstream of Map17, the 3' flanking gene of Scl, and is active in transgenic mice during primitive and definitive erythropoiesis. To analyze the in vivo function of the Scl +40 enhancer within the Scl/Map17 transcriptional domain, we deleted this element in the germ line. Scl(Δ40/Δ40) mice were viable with reduced numbers of erythroid CFU in both bone marrow and spleen yet displayed a normal response to stress hematopoiesis. Analysis of Scl(Δ40/Δ40) embryonic stem (ES) cells revealed impaired erythroid differentiation, which was accompanied by a failure to upregulate Scl when erythropoiesis was initiated. Map17 expression was also reduced in hematopoietic tissues and differentiating ES cells, and the Scl +40 element was able to enhance activity of the Map17 promoter. However, only Scl but not Map17 could rescue the Scl(Δ40/Δ40) ES phenotype. Together, these data demonstrate that the Scl +40 enhancer is an erythroid cell-specific enhancer that regulates the expression of both Scl and Map17. Moreover, deletion of the +40 enhancer causes a novel erythroid phenotype, which can be rescued by ectopic expression of Scl but not Map17.
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26
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Wareing S, Mazan A, Pearson S, Göttgens B, Lacaud G, Kouskoff V. The Flk1-Cre-mediated deletion of ETV2 defines its narrow temporal requirement during embryonic hematopoietic development. Stem Cells 2012; 30:1521-31. [PMID: 22570122 DOI: 10.1002/stem.1115] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During embryonic development, the emergence of hematopoiesis and vasculogenesis is tightly associated, with many transcription factors implicated in both developmental processes. Among those factors, ETV2 acts at the top of the hierarchy and controls the formation of both lineages. However, it is not known at which stage of mesoderm development ETV2 is acting and whether ETV2 activity is further required once mesodermal precursors have been specified to the hematopoietic and endothelial fates. In this study, we characterize the developmental window during which ETV2 expression is required for hematopoietic and endothelial development. Using cre-mediated deletion of ETV2, we demonstrate that ETV2 is acting prior to or at the time of FLK1 expression in mesodermal precursors to initiate the hematopoietic and endothelial program. Using the in vitro differentiation of embryonic stem cells as a model system, we further show that ETV2 re-expression in Etv2(-/-) Flk1-negative precursors drives hematopoiesis specification and switches on the expression of most genes known to be implicated in hematopoietic and endothelial development. Among the downstream targets of ETV2, we identify the transcription factors SCL, GATA2, and FLI1 known to operate a recursive loop controlling hematopoietic development. Surprisingly, SCL re-expression in Etv2(-/-) cells fully rescues hematopoiesis, while the re-expression of FLI1 or GATA2 promotes only a very limited rescue. Altogether, our data establish that ETV2 is required very transiently to specify mesodermal precursors to hematopoiesis and vasculogenesis and that SCL is one of the key downstream targets of ETV2 in controlling hematopoietic specification.
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Affiliation(s)
- Sarah Wareing
- Cancer Research UK Stem Cell Hematopoiesis Group, Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, United Kingdom
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27
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Spensberger D, Kotsopoulou E, Ferreira R, Broccardo C, Scott LM, Fourouclas N, Ottersbach K, Green AR, Göttgens B. Deletion of the Scl +19 enhancer increases the blood stem cell compartment without affecting the formation of mature blood lineages. Exp Hematol 2012; 40:588-598.e1. [PMID: 22401818 PMCID: PMC3387379 DOI: 10.1016/j.exphem.2012.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/11/2012] [Accepted: 02/15/2012] [Indexed: 11/29/2022]
Abstract
The stem cell leukemia (Scl)/Tal1 gene is essential for normal blood and endothelial development, and is expressed in hematopoietic stem cells (HSCs), progenitors, erythroid, megakaryocytic, and mast cells. The Scl +19 enhancer is active in HSCs and progenitor cells, megakaryocytes, and mast cells, but not mature erythroid cells. Here we demonstrate that in vivo deletion of the Scl +19 enhancer (Scl(Δ19/Δ19)) results in viable mice with normal Scl expression in mature hematopoietic lineages. By contrast, Scl expression is reduced in the stem/progenitor compartment and flow cytometry analysis revealed that the HSC and megakaryocyte-erythroid progenitor populations are enlarged in Scl(Δ19/Δ19) mice. The increase in HSC numbers contributed to enhanced expansion in bone marrow transplantation assays, but did not affect multilineage repopulation or stress responses. These results affirm that the Scl +19 enhancer plays a key role in the development of hematopoietic stem/progenitor cells, but is not necessary for mature hematopoietic lineages. Moreover, active histone marks across the Scl locus were significantly reduced in Scl(Δ19/Δ19) fetal liver cells without major changes in steady-state messenger RNA levels, suggesting post-transcriptional compensation for loss of a regulatory element, a result that might be widely relevant given the frequent observation of mild phenotypes after deletion of regulatory elements.
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Affiliation(s)
| | | | | | | | | | | | | | - Anthony R. Green
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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Curtis DJ, Salmon JM, Pimanda JE. Concise Review: Blood Relatives: Formation and regulation of hematopoietic stem cells by the basic helix-loop-helix transcription factors stem cell leukemia and lymphoblastic leukemia-derived sequence 1. Stem Cells 2012; 30:1053-8. [DOI: 10.1002/stem.1093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Follows GA, Ferreira R, Janes ME, Spensberger D, Cambuli F, Chaney AF, Kinston SJ, Landry JR, Green AR, Göttgens B. Mapping and functional characterisation of a CTCF-dependent insulator element at the 3' border of the murine Scl transcriptional domain. PLoS One 2012; 7:e31484. [PMID: 22396734 PMCID: PMC3291548 DOI: 10.1371/journal.pone.0031484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 01/09/2012] [Indexed: 11/18/2022] Open
Abstract
The Scl gene encodes a transcription factor essential for haematopoietic development. Scl transcription is regulated by a panel of cis-elements spread over 55 kb with the most distal 3′ element being located downstream of the neighbouring gene Map17, which is co-regulated with Scl in haematopoietic cells. The Scl/Map17 domain is flanked upstream by the ubiquitously expressed Sil gene and downstream by a cluster of Cyp genes active in liver, but the mechanisms responsible for delineating the domain boundaries remain unclear. Here we report identification of a DNaseI hypersensitive site at the 3′ end of the Scl/Map17 domain and 45 kb downstream of the Scl transcription start site. This element is located at the boundary of active and inactive chromatin, does not function as a classical tissue-specific enhancer, binds CTCF and is both necessary and sufficient for insulator function in haematopoietic cells in vitro. Moreover, in a transgenic reporter assay, tissue-specific expression of the Scl promoter in brain was increased by incorporation of 350 bp flanking fragments from the +45 element. Our data suggests that the +45 region functions as a boundary element that separates the Scl/Map17 and Cyp transcriptional domains, and raise the possibility that this element may be useful for improving tissue-specific expression of transgenic constructs.
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Affiliation(s)
- George A Follows
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.
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30
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Schütte J, Moignard V, Göttgens B. Establishing the stem cell state: insights from regulatory network analysis of blood stem cell development. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:285-95. [PMID: 22334489 DOI: 10.1002/wsbm.1163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Transcription factors (TFs) have long been recognized as powerful regulators of cell-type identity and differentiation. As TFs function as constituents of regulatory networks, identification and functional characterization of key interactions within these wider networks will be required to understand how TFs exert their powerful biological functions. The formation of blood cells (hematopoiesis) represents a widely used model system for the study of cellular differentiation. Moreover, specific TFs or groups of TFs have been identified to control the various cell fate choices that must be made when blood stem cells differentiate into more than a dozen distinct mature blood lineages. Because of the relative ease of accessibility, the hematopoietic system represents an attractive experimental system for the development of regulatory network models. Here, we review the modeling efforts carried out to date, which have already provided new insights into the molecular control of blood cell development. We also explore potential areas of future study such as the need for new high-throughput technologies and a focus on studying dynamic cellular systems. Many leukemias arise as the result of mutations that cause transcriptional dysregulation, thus suggesting that a better understanding of transcriptional control mechanisms in hematopoiesis is of substantial biomedical relevance. Moreover, lessons learned from regulatory network analysis in the hematopoietic system are likely to inform research on less experimentally tractable tissues.
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Affiliation(s)
- Judith Schütte
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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Wilson NK, Calero-Nieto FJ, Ferreira R, Göttgens B. Transcriptional regulation of haematopoietic transcription factors. Stem Cell Res Ther 2011; 2:6. [PMID: 21345252 PMCID: PMC3092146 DOI: 10.1186/scrt47] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The control of differential gene expression is central to all metazoan biology. Haematopoiesis represents one of the best understood developmental systems where multipotent blood stem cells give rise to a range of phenotypically distinct mature cell types, all characterised by their own distinctive gene expression profiles. Small combinations of lineage-determining transcription factors drive the development of specific mature lineages from multipotent precursors. Given their powerful regulatory nature, it is imperative that the expression of these lineage-determining transcription factors is under tight control, a fact underlined by the observation that their misexpression commonly leads to the development of leukaemia. Here we review recent studies on the transcriptional control of key haematopoietic transcription factors, which demonstrate that gene loci contain multiple modular regulatory regions within which specific regulatory codes can be identified, that some modular elements cooperate to mediate appropriate tissue-specific expression, and that long-range approaches will be necessary to capture all relevant regulatory elements. We also explore how changes in technology will impact on this area of research in the future.
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Affiliation(s)
- Nicola K Wilson
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
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Abstract
Development progresses through a sequence of cellular identities which are determined by the activities of networks of transcription factor genes. Alterations in cis-regulatory elements of these genes play a major role in evolutionary change, but little is known about the mechanisms responsible for maintaining conserved patterns of gene expression. We have studied the evolution of cis-regulatory mechanisms controlling the SCL gene, which encodes a key transcriptional regulator of blood, vasculature, and brain development and exhibits conserved function and pattern of expression throughout vertebrate evolution. SCL cis-regulatory elements are conserved between frog and chicken but accrued alterations at an accelerated rate between 310 and 200 million years ago, with subsequent fixation of a new cis-regulatory pattern at the beginning of the mammalian radiation. As a consequence, orthologous elements shared by mammals and lower vertebrates exhibit functional differences and binding site turnover between widely separated cis-regulatory modules. However, the net effect of these alterations is constancy of overall regulatory inputs and of expression pattern. Our data demonstrate remarkable cis-regulatory remodelling across the SCL locus and indicate that stable patterns of expression can mask extensive regulatory change. These insights illuminate our understanding of vertebrate evolution.
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A previously unrecognized promoter of LMO2 forms part of a transcriptional regulatory circuit mediating LMO2 expression in a subset of T-acute lymphoblastic leukaemia patients. Oncogene 2010; 29:5796-808. [PMID: 20676125 DOI: 10.1038/onc.2010.320] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The T-cell oncogene Lim-only 2 (LMO2) critically influences both normal and malignant haematopoiesis. LMO2 is not normally expressed in T cells, yet ectopic expression is seen in the majority of T-acute lymphoblastic leukaemia (T-ALL) patients with specific translocations involving LMO2 in only a subset of these patients. Ectopic lmo2 expression in thymocytes of transgenic mice causes T-ALL, and retroviral vector integration into the LMO2 locus was implicated in the development of clonal T-cell disease in patients undergoing gene therapy. Using array-based chromatin immunoprecipitation, we now demonstrate that in contrast to B-acute lymphoblastic leukaemia, human T-ALL samples largely use promoter elements with little influence from distal enhancers. Active LMO2 promoter elements in T-ALL included a previously unrecognized third promoter, which we demonstrate to be active in cell lines, primary T-ALL patients and transgenic mice. The ETS factors ERG and FLI1 previously implicated in lmo2-dependent mouse models of T-ALL bind to the novel LMO2 promoter in human T-ALL samples, while in return LMO2 binds to blood stem/progenitor enhancers in the FLI1 and ERG gene loci. Moreover, LMO2, ERG and FLI1 all regulate the +1 enhancer of HHEX/PRH, which was recently implicated as a key mediator of early progenitor expansion in LMO2-driven T-ALL. Our data therefore suggest that a self-sustaining triad of LMO2/ERG/FLI1 stabilizes the expression of important mediators of the leukaemic phenotype such as HHEX/PRH.
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Calero-Nieto FJ, Wood AD, Wilson NK, Kinston S, Landry JR, Göttgens B. Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation. Nucleic Acids Res 2010; 38:6363-74. [PMID: 20525788 PMCID: PMC2965225 DOI: 10.1093/nar/gkq490] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ets transcription factors play important roles during the development and maintenance of the haematopoietic system. One such factor, Elf-1 (E74-like factor 1) controls the expression of multiple essential haematopoietic regulators including Scl/Tal1, Lmo2 and PU.1. However, to integrate Elf-1 into the wider regulatory hierarchies controlling haematopoietic development and differentiation, regulatory elements as well as upstream regulators of Elf-1 need to be identified. Here, we have used locus-wide comparative genomic analysis coupled with chromatin immunoprecipitation (ChIP-chip) assays which resulted in the identification of five distinct regulatory regions directing expression of Elf-1. Further, ChIP-chip assays followed by functional validation demonstrated that the key haematopoietic transcription factor PU.1 is a major upstream regulator of Elf-1. Finally, overexpression studies in a well-characterized erythroid differentiation assay from primary murine fetal liver cells demonstrated that Elf-1 downregulation is necessary for terminal erythroid differentiation. Given the known activation of PU.1 by Elf-1 and our newly identified reciprocal activation of Elf-1 by PU.1, identification of an inhibitory role for Elf-1 has significant implications for our understanding of how PU.1 controls myeloid-erythroid differentiation. Our findings therefore not only represent the first report of Elf-1 regulation but also enhance our understanding of the wider regulatory networks that control haematopoiesis.
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Affiliation(s)
- Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Hills Road, Cambridge CB2 0XY, UK.
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35
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Dhami P, Bruce AW, Jim JH, Dillon SC, Hall A, Cooper JL, Bonhoure N, Chiang K, Ellis PD, Langford C, Andrews RM, Vetrie D. Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus. PLoS One 2010; 5:e9059. [PMID: 20140202 PMCID: PMC2816701 DOI: 10.1371/journal.pone.0009059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 01/14/2010] [Indexed: 01/25/2023] Open
Abstract
The SCL (TAL1) transcription factor is a critical regulator of haematopoiesis and its expression is tightly controlled by multiple cis-acting regulatory elements. To elaborate further the DNA elements which control its regulation, we used genomic tiling microarrays covering 256 kb of the human SCL locus to perform a concerted analysis of chromatin structure and binding of regulatory proteins in human haematopoietic cell lines. This approach allowed us to characterise further or redefine known human SCL regulatory elements and led to the identification of six novel elements with putative regulatory function both up and downstream of the SCL gene. They bind a number of haematopoietic transcription factors (GATA1, E2A LMO2, SCL, LDB1), CTCF or components of the transcriptional machinery and are associated with relevant histone modifications, accessible chromatin and low nucleosomal density. Functional characterisation shows that these novel elements are able to enhance or repress SCL promoter activity, have endogenous promoter function or enhancer-blocking insulator function. Our analysis opens up several areas for further investigation and adds new layers of complexity to our understanding of the regulation of SCL expression.
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Affiliation(s)
- Pawandeep Dhami
- The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Johanna H. Jim
- The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Shane C. Dillon
- The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Amanda Hall
- The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Nicolas Bonhoure
- Section of Pathology and Gene Regulation, Division of Cancer Sciences and Molecular Pathology, University of Glasgow, Glasgow, United Kingdom
| | - Kelly Chiang
- Section of Pathology and Gene Regulation, Division of Cancer Sciences and Molecular Pathology, University of Glasgow, Glasgow, United Kingdom
| | - Peter D. Ellis
- The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | | | - David Vetrie
- The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Section of Pathology and Gene Regulation, Division of Cancer Sciences and Molecular Pathology, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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36
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Ottersbach K, Smith A, Wood A, Göttgens B. Ontogeny of haematopoiesis: recent advances and open questions. Br J Haematol 2009; 148:343-55. [PMID: 19863543 DOI: 10.1111/j.1365-2141.2009.07953.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unravelling the embryonic origins of the haematopoietic system has been the subject of sustained research for more than a century. Nevertheless, many important questions are still either unanswered or remain a matter of intense debate. Recent progress in mouse and embryonic stem cell model systems as well as imaging and post-genomic technologies has provided new insights into many of these open questions. Here we place into context recent reports on the anatomical site of blood stem cell emergence and, using red blood cells as an example, illustrate how the development of stem cells and the other blood lineages is both temporally and spatially decoupled. In addition, we outline how embryonic stem cell assays are increasingly used as a powerful surrogate for studying lineage relationships and developmental potential of early embryonic blood progenitors. Finally, we review how recent progress in the reconstruction of transcriptional regulatory networks is beginning to define the connectivity between key regulators that control early blood development. In light of these rapid recent advances, research into the embryonic origins of the haematopoietic system should remain one of the most vibrant disciplines within the wider field of haematology for the foreseeable future.
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Affiliation(s)
- Katrin Ottersbach
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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37
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Bockamp E, Antunes C, Liebner S, Schmitt S, Cabezas-Wallscheid N, Heck R, Ohnngemach S, Oesch-Bartlomowicz B, Rickert C, Sanchez MJ, Hengstler J, Kaina B, Wilson A, Trumpp A, Eshkind L. In vivo fate mapping with SCL regulatory elements identifies progenitors for primitive and definitive hematopoiesis in mice. Mech Dev 2009; 126:863-72. [DOI: 10.1016/j.mod.2009.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/13/2009] [Accepted: 07/17/2009] [Indexed: 12/01/2022]
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38
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Foster SD, Oram SH, Wilson NK, Göttgens B. From genes to cells to tissues--modelling the haematopoietic system. MOLECULAR BIOSYSTEMS 2009; 5:1413-20. [PMID: 19763334 DOI: 10.1039/b907225j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Haematopoiesis (or blood formation) in general and haematopoietic stem cells more specifically represent some of the best studied mammalian developmental systems. Sophisticated purification protocols coupled with powerful biological assays permit functional analysis of highly purified cell populations both in vitro and in vivo. However, despite several decades of intensive research, the sheer complexity of the haematopoietic system means that many important questions remain unanswered or even unanswerable with current experimental tools. Scientists have therefore increasingly turned to modelling to tackle complexity at multiple levels ranging from networks of genes to the behaviour of cells and tissues. Early modelling attempts of gene regulatory networks have focused on core regulatory circuits but have more recently been extended to genome-wide datasets such as expression profiling and ChIP-sequencing data. Modelling of haematopoietic cells and tissues has provided insight into the importance of phenotypic heterogeneity for the differentiation of normal progenitor cells as well as a greater understanding of treatment response for particular pathologies such as chronic myeloid leukaemia. Here we will review recent progress in attempts to reconstruct segments of the haematopoietic system. A variety of modelling strategies will be covered from small-scale, protein-DNA or protein-protein interactions to large scale reconstructions. Also discussed will be examples of how stochastic modelling may be applied to multi cell systems such as those seen in normal and malignant haematopoiesis.
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Affiliation(s)
- Samuel D Foster
- Haematopoietic Stem Cell Laboratory, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Rd, Cambridge, CB2 0XY
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39
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The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood 2009; 113:5456-65. [PMID: 19346495 DOI: 10.1182/blood-2009-01-200048] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The basic helix-loop-helix transcription factor Scl/Tal1 controls the development and subsequent differentiation of hematopoietic stem cells (HSCs). However, because few Scl target genes have been validated to date, the underlying mechanisms have remained largely unknown. In this study, we have used ChIP-Seq technology (coupling chromatin immunoprecipitation with deep sequencing) to generate a genome-wide catalog of Scl-binding events in a stem/progenitor cell line, followed by validation using primary fetal liver cells and comprehensive transgenic mouse assays. Transgenic analysis provided in vivo validation of multiple new direct Scl target genes and allowed us to reconstruct an in vivo validated network consisting of 17 factors and their respective regulatory elements. By coupling ChIP-Seq in model cell lines with in vivo transgenic validation and sophisticated bioinformatic analysis, we have identified a widely applicable strategy for the reconstruction of stem cell regulatory networks in which biologic material is otherwise limiting. Moreover, in addition to revealing multiple previously unrecognized links to known HSC regulators, as well as novel links to genes not previously implicated in HSC function, comprehensive transgenic analysis of regulatory elements provided substantial new insights into the transcriptional control of several important hematopoietic regulators, including Cbfa2t3h/Eto2, Cebpe, Nfe2, Zfpm1/Fog1, Erg, Mafk, Gfi1b, and Myb.
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40
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De Val S, Black BL. Transcriptional control of endothelial cell development. Dev Cell 2009; 16:180-95. [PMID: 19217421 DOI: 10.1016/j.devcel.2009.01.014] [Citation(s) in RCA: 256] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 01/26/2009] [Accepted: 01/26/2009] [Indexed: 12/14/2022]
Abstract
The transcription factors that regulate endothelial cell development have been a focus of active research for several years, and many players in the endothelial transcriptional program have been identified. This review discusses the function of several major regulators of endothelial transcription, including members of the Sox, Ets, Forkhead, GATA, and Kruppel-like families. This review also highlights recent developments aimed at unraveling the combinatorial mechanisms and transcription factor interactions that regulate endothelial cell specification and differentiation during vasculogenesis and angiogenesis.
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Affiliation(s)
- Sarah De Val
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, 94158, USA
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41
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Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors. Blood 2009; 113:5783-92. [PMID: 19171877 DOI: 10.1182/blood-2008-11-187757] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Lmo2 gene encodes a transcriptional cofactor critical for the development of hematopoietic stem cells. Ectopic LMO2 expression causes leukemia in T-cell acute lymphoblastic leukemia (T-ALL) patients and severe combined immunodeficiency patients undergoing retroviral gene therapy. Tightly controlled Lmo2 expression is therefore essential, yet no comprehensive analysis of Lmo2 regulation has been published so far. By comparative genomics, we identified 17 highly conserved noncoding elements, 9 of which revealed specific acetylation marks in chromatin-immunoprecipitation and microarray (ChIP-chip) assays performed across 250 kb of the Lmo2 locus in 11 cell types covering different stages of hematopoietic differentiation. All candidate regulatory regions were tested in transgenic mice. An extended LMO2 proximal promoter fragment displayed strong endothelial activity, while the distal promoter showed weak forebrain activity. Eight of the 15 distal candidate elements functioned as enhancers, which together recapitulated the full expression pattern of Lmo2, directing expression to endothelium, hematopoietic cells, tail, and forebrain. Interestingly, distinct combinations of specific distal regulatory elements were required to extend endothelial activity of the LMO2 promoter to yolk sac or fetal liver hematopoietic cells. Finally, Sfpi1/Pu.1, Fli1, Gata2, Tal1/Scl, and Lmo2 were shown to bind to and transactivate Lmo2 hematopoietic enhancers, thus identifying key upstream regulators and positioning Lmo2 within hematopoietic regulatory networks.
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42
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Liu F, Walmsley M, Rodaway A, Patient R. Fli1 acts at the top of the transcriptional network driving blood and endothelial development. Curr Biol 2008; 18:1234-40. [PMID: 18718762 DOI: 10.1016/j.cub.2008.07.048] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 07/09/2008] [Accepted: 07/10/2008] [Indexed: 01/27/2023]
Abstract
Blood and endothelium arise in close association during development, possibly from a common precursor, the hemangioblast [1-4]. Genes essential for blood and endothelial development contain functional ETS binding sites, and binding and expression data implicate the transcription factor, friend leukaemia integration 1 (Fli1) [5-10]. However, loss-of-function phenotypes in mice, although suffering both blood and endothelial defects, have thus far precluded the conclusion that Fli1 is essential for these two lineages [11, 12]. By using Xenopus and zebrafish embryos, we show that loss of Fli1 function results in a substantial reduction or absence of hemangioblasts, revealing an absolute requirement. TUNEL assays show that the cells are eventually lost by apoptosis, but only after the regulatory circuit has been disrupted by loss of Fli1. In addition, a constitutively active form of Fli1 is sufficient to induce expression of key hemangioblast genes, such as Scl/Tal1, Lmo2, Gata2, Etsrp, and Flk1. Epistasis assays show that Fli1 expression is induced by Bmp signaling or Cloche, depending on the hemangioblast population, and in both cases Fli1 acts upstream of Gata2, Scl, Lmo2, and Etsrp. Taken together, these results place Fli1 at the top of the transcriptional regulatory hierarchy for hemangioblast specification in vertebrate embryos.
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Affiliation(s)
- Feng Liu
- John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
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43
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Miranda-Saavedra D, Göttgens B. Transcriptional regulatory networks in haematopoiesis. Curr Opin Genet Dev 2008; 18:530-5. [PMID: 18838119 DOI: 10.1016/j.gde.2008.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 08/29/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
Abstract
The coordinated expression of genes lies at the heart of developmental programmes, with complex regulatory networks controlling the spatial and temporal aspects of gene expression. Haematopoiesis (blood formation) has long served as a model process for studying the specification and subsequent differentiation of stem cells and represents the best characterised adult stem cell system. In this review, we outline how the integration of experimental and computational approaches as applied to haematopoiesis has resulted in some of the most advanced models of transcriptional regulatory networks in mammals.
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Affiliation(s)
- Diego Miranda-Saavedra
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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44
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Abstract
In the lab, the cis-regulatory network seems to exhibit great functional redundancy. Many experiments testing enhancer activity of neighboring cis-regulatory elements show largely overlapping expression domains. Of recent interest, mice in which cis-regulatory ultraconserved elements were knocked out showed no obvious phenotype, further suggesting functional redundancy. Here, we present a global evolutionary analysis of mammalian conserved nonexonic elements (CNEs), and find strong evidence to the contrary. Given a set of CNEs conserved between several mammals, we characterize functional dispensability as the propensity for the ancestral element to be lost in mammalian species internal to the spanned species tree. We show that ultraconserved-like elements are over 300-fold less likely than neutral DNA to have been lost during rodent evolution. In fact, many thousands of noncoding loci under purifying selection display near uniform indispensability during mammalian evolution, largely irrespective of nucleotide conservation level. These findings suggest that many genomic noncoding elements possess functions that contribute noticeably to organism fitness in naturally evolving populations.
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Affiliation(s)
- Cory McLean
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
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45
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Sausville J, Molinolo AA, Cheng X, Frampton J, Takebe N, Gutkind JS, Feldman RA. RCAS/SCL-TVA animal model allows targeted delivery of polyoma middle T oncogene to vascular endothelial progenitors in vivo and results in hemangioma development. Clin Cancer Res 2008; 14:3948-55. [PMID: 18559617 DOI: 10.1158/1078-0432.ccr-07-5152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To recapitulate the generation of cancer stem cells in the context of an intact animal using a retroviral vector capable of in vivo delivery of oncogenes to primitive endothelial and hematopoietic stem cells. EXPERIMENTAL DESIGN Targeting of these progenitors was achieved using transgenic mice in which the avian TVA retroviral receptor was placed under the control of the stem cell leukemia (scl/tal-1) gene promoter and SCL +19 enhancer. RESULTS Injection of an avian retrovirus encoding polyoma middle T (PyMT), an oncogene that transforms endothelial cells, caused rapid lethality in all SCL-TVA mice but not in control TVA(-) littermates. The infected animals exhibited hemorrhagic foci in several organs. Histopathologic analysis confirmed the presence of hemangiomas and the endothelial origin of the PyMT-transformed cells. Surprisingly, the transformed endothelial cells contained readily detectable numbers of TVA(+) cells. By contrast, normal blood vessels had very few of these cells. The presence of TVA(+) cells in the lesions suggests that the cells originally infected by PyMT retained stem cell characteristics. Further analysis showed that the tumor cells exhibited activation of the phosphatidylinositol 3-kinase/Akt and S6/mammalian target of rapamycin pathways, suggesting a mechanism used by PyMT to transform endothelial progenitors in vivo. CONCLUSIONS We conclude that this experimental system can specifically deliver oncogenes to vascular endothelial progenitors in vivo and cause a fatal neoplastic disease. This animal model should allow the generation of endothelial cancer stem cells in the natural environment of an immunocompetent animal, thereby enabling the recapitulation of genetic alterations that are responsible for the initiation and progression of human malignancies of endothelial origin.
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Affiliation(s)
- Justin Sausville
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Smith AM, Sanchez MJ, Follows GA, Kinston S, Donaldson IJ, Green AR, Göttgens B. A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity. Genome Res 2008; 18:1422-32. [PMID: 18687876 PMCID: PMC2527711 DOI: 10.1101/gr.077008.108] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Altered cis-regulation is thought to underpin much of metazoan evolution, yet the underlying mechanisms remain largely obscure. The stem cell leukemia TAL1 (also known as SCL) transcription factor is essential for the normal development of blood stem cells and we have previously shown that the Tal1 +19 enhancer directs expression to hematopoietic stem cells, hematopoietic progenitors, and to endothelium. Here we demonstrate that an adjacent region 1 kb upstream (+18 element) is in an open chromatin configuration and carries active histone marks but does not function as an enhancer in transgenic mice. Instead, it boosts activity of the +19 enhancer both in stable transfection assays and during differentiation of embryonic stem (ES) cells carrying single-copy reporter constructs targeted to the Hprt locus. The +18 element contains a mammalian interspersed repeat (MIR) which is essential for the +18 function and which was transposed to the Tal1 locus approximately 160 million years ago at the time of the mammalian/marsupial branchpoint. Our data demonstrate a previously unrecognized mechanism whereby enhancer activity is modulated by a transposon exerting a "booster" function which would go undetected by conventional transgenic approaches.
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Affiliation(s)
- Aileen M Smith
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Cambridge CB2 2XY, United Kingdom
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47
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Abstract
Transcription factors such as Scl/Tal1, Lmo2, and Runx1 are essential for the development of hematopoietic stem cells (HSCs). However, the precise mechanisms by which these factors interact to form transcriptional networks, as well as the identity of the genes downstream of these regulatory cascades, remain largely unknown. To this end, we generated an Scl(-/-) yolk sac cell line to identify candidate Scl target genes by global expression profiling after reintroduction of a TAT-Scl fusion protein. Bioinformatics analysis resulted in the identification of 9 candidate Scl target transcription factor genes, including Runx1 and Runx3. Chromatin immunoprecipitation confirmed that both Runx genes are direct targets of Scl in the fetal liver and that Runx1 is also occupied by Scl in the yolk sac. Furthermore, binding of an Scl-Lmo2-Gata2 complex was demonstrated to occur on the regions flanking the conserved E-boxes of the Runx1 loci and was shown to transactivate the Runx1 element. Together, our data provide a key component of the transcriptional network of early hematopoiesis by identifying downstream targets of Scl that can explain key aspects of the early Scl(-/-) phenotype.
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Hochman E, Kinston S, Harmelin A, Göttgens B, Izraeli S. The SCL 3' enhancer responds to Hedgehog signaling during hemangioblast specification. Exp Hematol 2007; 34:1643-50. [PMID: 17157160 DOI: 10.1016/j.exphem.2006.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 06/27/2006] [Accepted: 07/31/2006] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The Hedgehog family of intercellular proteins has a crucial role in embryonic development. Recent experimental data suggests that the Hedgehog pathway may play a role in early hematopoiesis and angiogenesis. Stem cell leukemia (SCL), a basic helix-loop-helix (bHLH) transcription factor, is essential for the specification and function of the hemangioblast. SCL expression in early hematopoietic precursors and endothelium is directed by a 3' enhancer. We hypothesized that the SCL 3' enhancer is regulated by Hedgehog signaling during specification of mesoderm towards hemangioblastic fate. MATERIALS AND METHODS Whole embryos derived from transgenic mouse lines carrying reporter genes under the regulation of SCL 3' enhancer were cultured in the presence of active Hedgehog peptide. Hedgehog transcriptional regulation of SCL 3' enhancer was studied by in vitro and in vivo binding and reporter assays. RESULTS Hedgehog induced expansion of cells in which the SCL 3' enhancer was transcriptionally activated. A Gli-binding site within the 3' enhancer of SCL was identified and Gli1 was demonstrated to bind and transactivate this enhancer in a sequence-dependent manner. We further demonstrated that the core region of the SCL 3' enhancer is transcriptionally regulated by Hedgehog in-vivo and that the Gli-binding site located in this enhancer is essential for Hedgehog transcriptional regulation in vitro. CONCLUSION These findings suggest that SCL may be a direct target of Hedgehog signaling during hemangioblast specification.
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Affiliation(s)
- Eldar Hochman
- The Research Section of Pediatric Malignancies, The Sheba Cancer Research Center, Safra Children's Hospital, Sheba Medical Center and Faculty of Medicine, Tel-Aviv University, Tel Hashomer, Israel
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Dekel B, Metsuyanim S, Garcia AM, Quintero C, Sanchez MJ, Izraeli S. Organ-injury-induced reactivation of hemangioblastic precursor cells. Leukemia 2007; 22:103-13. [PMID: 17898790 DOI: 10.1038/sj.leu.2404941] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Early in mammalian development, the stem cell leukemia (SCL/TAL1) gene and its distinct 3' enhancer (SCL 3'En) specify bipotential progenitor cells that give rise to blood and endothelium, thus termed hemangioblasts. We have previously detected a minor population of SCL (+) cells in the postnatal kidney. Here, we demonstrate that cells expressing the SCL 3'En in the adult kidney are comprised of CD45+CD31- hematopoietic cells, CD45-CD31+ endothelial cells and CD45-CD31- interstitial cells. Creation of bone marrow chimeras of SCL 3'En transgenic mice into wild-type hosts shows that all three types of SCL 3'En-expressing cells in the adult kidney can originate from the bone marrow. Ischemia/reperfusion injury to the adult kidney of SCL 3'En transgenic mice results in the intrarenal elevation of SCL and FLK1 mRNA levels and of cells expressing hem-endothelial progenitor markers (CD45, CD34, c-Kit and FLK1). Furthermore, analysis of SCL 3'En in the ischemic kidneys reveals an increase in the abundance of SCL 3'En-expressing cells, predominantly within the CD45 (+) hematopoietic fraction and to a lesser extent in the CD45 (-) fraction. Our results suggest organ-injury-induced reactivation of bone marrow-derived hemangioblasts and possible local angioblastic progenitors expressing SCL and SCL 3'En.
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Affiliation(s)
- B Dekel
- Department of Pediatrics and Laboratory of Regenerative Nephrology, Edmond and Lili Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.
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Nottingham WT, Jarratt A, Burgess M, Speck CL, Cheng JF, Prabhakar S, Rubin EM, Li PS, Sloane-Stanley J, Kong-A-San J, de Bruijn MFTR. Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. Blood 2007; 110:4188-97. [PMID: 17823307 PMCID: PMC2234795 DOI: 10.1182/blood-2007-07-100883] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factor Runx1/AML1 is an important regulator of hematopoiesis and is critically required for the generation of the first definitive hematopoietic stem cells (HSCs) in the major vasculature of the mouse embryo. As a pivotal factor in HSC ontogeny, its transcriptional regulation is of high interest but is largely undefined. In this study, we used a combination of comparative genomics and chromatin analysis to identify a highly conserved 531-bp enhancer located at position + 23.5 in the first intron of the 224-kb mouse Runx1 gene. We show that this enhancer contributes to the early hematopoietic expression of Runx1. Transcription factor binding in vivo and analysis of the mutated enhancer in transient transgenic mouse embryos implicate Gata2 and Ets proteins as critical factors for its function. We also show that the SCL/Lmo2/Ldb-1 complex is recruited to the enhancer in vivo. Importantly, transplantation experiments demonstrate that the intronic Runx1 enhancer targets all definitive HSCs in the mouse embryo, suggesting that it functions as a crucial cis-regulatory element that integrates the Gata, Ets, and SCL transcriptional networks to initiate HSC generation.
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Affiliation(s)
- Wade T Nottingham
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
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