Absolute quantification of cohesin, CTCF and their regulators in human cells
- Research Institute of Molecular Pathology, Austria
- European Molecular Biology Laboratory, Germany
- University of Oxford, United Kingdom
Abstract
The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase there are ~250,000 nuclear cohesin complexes, of which ~160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion.
Data availability
Mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD012712. Sequencing data have been deposited in GEO (GSE126990.
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ChIP-seq data from Absolute quantification of cohesin, CTCF and their regulators in human cellsNCBI Gene Expression Omnibus, GSE126990.
Article and author information
Author details
Iain Finley Davidson
Jan-Michael Peters
Funding
Boehringer Ingelheim
- Johann Holzmann
- Kota Nagasaka
- Johannes Fuchs
- Gerhard Dürnberger
- Wen Tang
- Rene Ladurner
- Georg A Busslinger
- Karl Mechtler
- Iain Finley Davidson
- Jan-Michael Peters
European Molecular Biology Laboratory
- Antonio Z Politi
- Merle Hantsche-Grininger
- Nike Walther
- Birgit Koch
- Jan Ellenberg
National Institutes of Health (Common Fund 4D Nucleome Program (U01 EB021223 / U01 DA047728))
- Jan Ellenberg
Paul G. Allen Frontiers Group (Allen Distinguished Investigator Program)
- Jan Ellenberg
EMBL International PhD Programme
- Nike Walther
Austrian Research Promotion Agency (FFG-852936)
- Jan-Michael Peters
Austrian Research Promotion Agency (Laura Bassi Centre for Optimized Structural Studies grant FFG-840283)
- Jan-Michael Peters
Austrian Science Fund (Wittgenstein award Z196-B20)
- Jan-Michael Peters
Horizon 2020 Framework Programme (653706)
- Jan Ellenberg
Horizon 2020 Framework Programme (823839)
- Karl Mechtler
Austrian Science Fund (I 3686-B25 MEIOREC - ERA-CAPS)
- Karl Mechtler
Austrian Science Fund (FWF special research program SFB F34)
- Jan-Michael Peters
Austrian Research Promotion Agency (FFG-834223)
- Jan-Michael Peters
Vienna Science and Technology Fund (WWTF LS09-13)
- Jan-Michael Peters
Seventh Framework Programme (241548 (MitoSys))
- Jan Ellenberg
- Jan-Michael Peters
Horizon 2020 Framework Programme (693949)
- Jan-Michael Peters
Sixth Framework Programme (503464 (MitoCheck))
- Jan-Michael Peters
European Molecular Biology Organization (ALTF 1335-2016)
- Kota Nagasaka
Human Frontier Science Program (LT001527/2017)
- Kota Nagasaka
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- David J Sherratt, University of Oxford, United Kingdom
Version history
- Received: February 20, 2019
- Accepted: June 13, 2019
- Accepted Manuscript published: June 17, 2019 (version 1)
- Version of Record published: July 2, 2019 (version 2)
- Version of Record updated: July 22, 2019 (version 3)
Copyright
© 2019, Holzmann 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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Absolute quantification of cohesin, CTCF and their regulators in human cells
eLife 8:e46269.
https://doi.org/10.7554/eLife.46269
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