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Reilly SK, Gosai SJ, Gutierrez A, Mackay-Smith A, Ulirsch JC, Kanai M, Mouri K, Berenzy D, Kales S, Butler GM, Gladden-Young A, Bhuiyan RM, Stitzel ML, Finucane HK, Sabeti PC, Tewhey R. Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH. Nat Genet 2021; 53:1166-1176. [PMID: 34326544 PMCID: PMC8925018 DOI: 10.1038/s41588-021-00900-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/23/2021] [Indexed: 12/26/2022]
Abstract
Effective interpretation of genome function and genetic variation requires a shift from epigenetic mapping of cis-regulatory elements (CREs) to characterization of endogenous function. We developed hybridization chain reaction fluorescence in situ hybridization coupled with flow cytometry (HCR-FlowFISH), a broadly applicable approach to characterize CRISPR-perturbed CREs via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity. Across >325,000 perturbations, we provide evidence that CREs can regulate multiple genes, skip over the nearest gene and display activating and/or silencing effects. At the cholesterol-level-associated FADS locus, we combine endogenous screens with reporter assays to exhaustively characterize multiple genome-wide association signals, functionally nominate causal variants and, importantly, identify their target genes.
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Affiliation(s)
- Steven K Reilly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Sager J Gosai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
| | | | | | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Gina M Butler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Redwan M Bhuiyan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
- Institute of Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Ryan Tewhey
- The Jackson Laboratory, Bar Harbor, ME, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA.
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Beisaw A, Tsaytler P, Koch F, Schmitz SU, Melissari MT, Senft AD, Wittler L, Pennimpede T, Macura K, Herrmann BG, Grote P. BRACHYURY directs histone acetylation to target loci during mesoderm development. EMBO Rep 2017; 19:118-134. [PMID: 29141987 DOI: 10.15252/embr.201744201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/19/2017] [Accepted: 10/25/2017] [Indexed: 12/24/2022] Open
Abstract
T-box transcription factors play essential roles in multiple aspects of vertebrate development. Here, we show that cooperative function of BRACHYURY (T) with histone-modifying enzymes is essential for mouse embryogenesis. A single point mutation (TY88A) results in decreased histone 3 lysine 27 acetylation (H3K27ac) at T target sites, including the T locus, suggesting that T autoregulates the maintenance of its expression and functions by recruiting permissive chromatin modifications to putative enhancers during mesoderm specification. Our data indicate that T mediates H3K27ac recruitment through a physical interaction with p300. In addition, we determine that T plays a prominent role in the specification of hematopoietic and endothelial cell types. Hematopoietic and endothelial gene expression programs are disrupted in TY88A mutant embryos, leading to a defect in the differentiation of hematopoietic progenitors. We show that this role of T is mediated, at least in part, through activation of a distal Lmo2 enhancer.
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Affiliation(s)
- Arica Beisaw
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.,Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Pavel Tsaytler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Frederic Koch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria-Theodora Melissari
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna D Senft
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Karol Macura
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical Genetics, Charité-University Medicine Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Phillip Grote
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany .,Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
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