PreprintCited by 114Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

The genomic landscape of cohesin-associated chromatin interactions

Open access
DeMare, Laura E., Leng, Jing, Cotney, Justin, Reilly, Steven K., Yin, Jun, Sarro, Richard, Noonan, James P.·2013·Genome Research

Abstract

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/gr.156570.113

Cites

62 of 62 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Enhancer-bound proteins tend to interact only with genes within CTCF-CTCF loops.

    “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

  • 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.

    “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

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

1 of the 63 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

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
Published
2013-05-23
Volume
23
Issue
8
Pages
1224-1234
ISSN
1088-9051 (ISSN-L)
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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review