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Sept CE, Tak YE, Goel V, Bhakta MS, Cerda-Smith CG, Hutchinson HM, Blanchette M, Eyler CE, Johnstone SE, Joung JK, Hansen AS, Aryee MJ. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion. Nat Commun 2025; 16:4506. [PMID: 40374602 PMCID: PMC12081859 DOI: 10.1038/s41467-025-57775-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/03/2025] [Indexed: 05/17/2025] Open
Abstract
Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription.
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Affiliation(s)
- Corriene E Sept
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Y Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Viraat Goel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Mital S Bhakta
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA, 95066, USA
| | - Christian G Cerda-Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | | | - Christine E Eyler
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sarah E Johnstone
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anders S Hansen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Arena Bioworks, Cambridge, MA, 02141, USA.
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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 PMCID: PMC11574175 DOI: 10.1038/s41580-024-00710-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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Sept CE, Tak YE, Cerda-Smith CG, Hutchinson HM, Goel V, Blanchette M, Bhakta MS, Hansen AS, Joung JK, Johnstone S, Eyler CE, Aryee MJ. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563340. [PMID: 37961446 PMCID: PMC10634716 DOI: 10.1101/2023.10.20.563340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
DNA looping is vital for establishing many enhancer-promoter interactions. While CTCF is known to anchor many cohesin-mediated loops, the looped chromatin fiber appears to predominantly exist in a poorly characterized actively extruding state. To better characterize extruding chromatin loop structures, we used CTCF MNase HiChIP data to determine both CTCF binding at high resolution and 3D contact information. Here we present FactorFinder, a tool that identifies CTCF binding sites at near base-pair resolution. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics, and find that active enhancers and RNA Pol II impede cohesin extrusion, facilitating an enrichment of enhancer-promoter contacts in the partially extruded loop state. We propose a model of topological regulation whereby the transient, partially extruded states play active roles in transcription.
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Affiliation(s)
- Corriene E Sept
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Y Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital; Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02115, USA
| | - Christian G Cerda-Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Viraat Goel
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA 02139, USA
| | - Marco Blanchette
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA 95066, USA
| | - Mital S Bhakta
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA 95066, USA
| | - Anders S Hansen
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA 02139, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital; Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02115, USA
| | - Sarah Johnstone
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Pathology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Christine E Eyler
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
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