High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion
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 co...
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-57775-w |
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| author | Corriene E. Sept Y. Esther Tak Viraat Goel Mital S. Bhakta Christian G. Cerda-Smith Haley M. Hutchinson Marco Blanchette Christine E. Eyler Sarah E. Johnstone J. Keith Joung Anders S. Hansen Martin J. Aryee |
| author_facet | Corriene E. Sept Y. Esther Tak Viraat Goel Mital S. Bhakta Christian G. Cerda-Smith Haley M. Hutchinson Marco Blanchette Christine E. Eyler Sarah E. Johnstone J. Keith Joung Anders S. Hansen Martin J. Aryee |
| author_sort | Corriene E. Sept |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-8d38a3dc406e43fbae20dce22e90127f |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-8d38a3dc406e43fbae20dce22e90127f2025-08-20T01:51:38ZengNature PortfolioNature Communications2041-17232025-05-0116111410.1038/s41467-025-57775-wHigh-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusionCorriene E. Sept0Y. Esther Tak1Viraat Goel2Mital S. Bhakta3Christian G. Cerda-Smith4Haley M. Hutchinson5Marco Blanchette6Christine E. Eyler7Sarah E. Johnstone8J. Keith Joung9Anders S. Hansen10Martin J. Aryee11Department of Biostatistics, Harvard T.H. Chan School of Public HealthMolecular Pathology Unit, Massachusetts General HospitalBroad Institute of MIT and HarvardDovetail Genomics, Cantata Bio LLCDepartment of Pharmacology and Cancer Biology, Duke University School of MedicineDepartment of Pharmacology and Cancer Biology, Duke University School of MedicineLiftoff BiosolutionDepartment of Radiation Oncology, Duke University School of MedicineBroad Institute of MIT and HarvardMolecular Pathology Unit, Massachusetts General HospitalBroad Institute of MIT and HarvardDepartment of Biostatistics, Harvard T.H. Chan School of Public HealthAbstract 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.https://doi.org/10.1038/s41467-025-57775-w |
| spellingShingle | Corriene E. Sept Y. Esther Tak Viraat Goel Mital S. Bhakta Christian G. Cerda-Smith Haley M. Hutchinson Marco Blanchette Christine E. Eyler Sarah E. Johnstone J. Keith Joung Anders S. Hansen Martin J. Aryee High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion Nature Communications |
| title | High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion |
| title_full | High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion |
| title_fullStr | High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion |
| title_full_unstemmed | High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion |
| title_short | High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion |
| title_sort | high resolution ctcf footprinting reveals impact of chromatin state on cohesin extrusion |
| url | https://doi.org/10.1038/s41467-025-57775-w |
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