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Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res 2020; 30:472-484. [PMID: 32132109 PMCID: PMC7111515 DOI: 10.1101/gr.255760.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/21/2020] [Indexed: 01/29/2023]
Abstract
Thousands of epigenomic data sets have been generated in the past decade, but it is difficult for researchers to effectively use all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for validated systematic integration of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By using IDEAS as our integrative and discriminative epigenome annotation system, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of more than 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website to aid research in genomics and hematopoiesis.
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Affiliation(s)
- Guanjue Xiang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elisabeth Heuston
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Lin An
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alexander Q Wixom
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael E G Sauria
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Kathryn Weaver
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Jens Lichtenberg
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Qunhua Li
- Department of Statistics, Program in Bioinformatics and Genomics, Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David Bodine
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - James Taylor
- Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, Maryland 20218, USA
| | - Gerd A Blobel
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Jim Hughes
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Yu Zhang
- Department of Statistics, Program in Bioinformatics and Genomics, Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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