CTCF and cohesin regulate chromatin loop stability with distinct dynamics
- University of California, Berkeley, United States
Abstract
Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining genomic and biochemical approaches we show that CTCF and cohesin co-occupy the same sites and physically interact as a biochemically stable complex. However, using single-molecule imaging we find that CTCF binds chromatin much more dynamically than cohesin (~1-2 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin for which the search process is long (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging "dynamic complex" rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops are dynamic and constantly break and reform throughout the cell cycle.
Data availability
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Nuclear organization and dynamics of CTCF and cohesinPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE90994).
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he Cohesin Complex Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell IdentityPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE24030).
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CTCF-Mediated Functional Chromatin Interactome in Pluripotent CellsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE28247).
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A draft map of cis-regulatory sequences in the mouse genome [ChIP-Seq]Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE29218).
Article and author information
Author details
Funding
Siebel Stem Cell Institute (NA)
- Anders S Hansen
Howard Hughes Medical Institute (3061)
- Robert Tjian
California Institute of Regenerative Medicine (LA1-08013)
- Xavier Darzacq
National Institutes of Health (UO1-EB021236 U54-DK107980)
- Xavier Darzacq
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Hansen et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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CTCF and cohesin regulate chromatin loop stability with distinct dynamics
eLife 6:e25776.
https://doi.org/10.7554/eLife.25776
Further reading
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- Chromosomes and Gene Expression
- Structural Biology and Molecular Biophysics
Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
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