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
-
Nuclear organization and dynamics of CTCF and cohesinPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE90994).
-
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).
-
CTCF-Mediated Functional Chromatin Interactome in Pluripotent CellsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE28247).
-
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.
Reviewing Editor
- David Sherratt, University of Oxford, United Kingdom
Version history
- Received: February 6, 2017
- Accepted: April 30, 2017
- Accepted Manuscript published: May 3, 2017 (version 1)
- Version of Record published: May 26, 2017 (version 2)
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.
Metrics
-
- 19,715
- views
-
- 3,049
- downloads
-
- 486
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
eLife 6:e25776.
https://doi.org/10.7554/eLife.25776
Further reading
-
- Structural Biology and Molecular Biophysics
The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation rate remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags can influence substrate degradation. Fat10 is upregulated during inflammation, and its substrates undergo rapid proteasomal degradation. We report that the degradation rate of Fat10 substrates critically depends on the structural plasticity of Fat10. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate. Our results suggest significantly lower thermodynamic stability and faster mechanical unfolding in Fat10 compared to ubiquitin. Long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate, which correlated excellently to Fat10-substrate contacts, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tags.
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
The articles in this special issue highlight how modern cellular, biochemical, biophysical and computational techniques are allowing deeper and more detailed studies of allosteric kinase regulation.
