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The genomic landscape of cohesin-associated chromatin interactions
Open accessAbstract
Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2264 SMC1A interactions, of which 1491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue-specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin-associated interactions in the genome and highlight their role in establishing the regulatory architecture of development.
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“Enhancer-bound proteins are constrained such that they tend to interact only with genes within these CTCF-CTCF loops.”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as DeMare et al., 2013
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“In the models that emerge from these data, each chromosome contains thousands of DNA loops, formed by the interaction of two CTCF molecules bound to different sites, and reinforced by a cohesin molecule (Figure 2A).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as DeMare et al., 2013
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Metadata
- Authors
- DeMare, L. E., Leng, J., Cotney, J., Reilly, S. K., Yin, J., Sarro, R., & Noonan, J. P.
- Affiliations
- Yale University (US)
- Corresponding author
- Noonan, James P.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2013-05-23
- Volume
- 23
- Issue
- 8
- Pages
- 1224-1234
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3730097
- OpenAlex
- W2024640399
- Cited by
- 114
- References
- 63
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 2 · 2023: 5 · 2022: 4 · 2021: 2 · 2020: 10 · 2019: 6 · 2018: 3 · 2017: 20 · 2016: 12 · 2015: 19 · 2014: 18 · 2013: 9
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Edward Mallinckrodt, Jr. Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (T32GM007223, GM094780, R01GM094780)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (T32HD007149)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- cohesin, SMC1A, CTCF, chromatin interactions, enhancer-promoter interactions, insulator proteins, tissue-specific gene regulation, limb development, embryonic stem cells, chromatin looping, regulatory architecture, mouse embryo
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Structural Maintenance of Chromosome Protein 1, Animals, Binding Sites, Chromatin, Chromosomal Proteins, Non-Histone, Enhancer Elements, Genetic, Histones, Mice, Inbred C57BL, Organ Specificity, Promoter Regions, Genetic, Repressor Proteins, Genome, Gene Expression Regulation, Developmental, Cell Cycle Proteins, Limb Buds, Protein Subunits, Chromatin Immunoprecipitation, Mice
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