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.

The following data sets were generated

Article and author information

Author details

  1. Johann Holzmann

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  2. Antonio Z Politi

    Chemical Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4788-0933
  3. Kota Nagasaka

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0765-638X
  4. Merle Hantsche-Grininger

    Chemical Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Nike Walther

    Chemical Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7591-5251
  6. Birgit Koch

    Chemical Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Johannes Fuchs

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  8. Gerhard Dürnberger

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  9. Wen Tang

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  10. Rene Ladurner

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  11. Roman R Stocsits

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  12. Georg A Busslinger

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  13. Béla Novák

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6961-1366
  14. Karl Mechtler

    Research Institute of Molecular Pathology, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  15. Iain Finley Davidson

    Research Institute of Molecular Pathology, Vienna, Austria
    For correspondence
    davidson@imp.ac.at
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4945-6415
  16. Jan Ellenberg

    Chemical Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    For correspondence
    jan.ellenberg@embl.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5909-701X
  17. Jan-Michael Peters

    Research Institute of Molecular Pathology, Vienna, Austria
    For correspondence
    Jan-Michael.Peters@imp.ac.at
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2820-3195

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

  1. David J Sherratt, University of Oxford, United Kingdom

Version history

  1. Received: February 20, 2019
  2. Accepted: June 13, 2019
  3. Accepted Manuscript published: June 17, 2019 (version 1)
  4. Version of Record published: July 2, 2019 (version 2)
  5. 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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  1. Johann Holzmann
  2. Antonio Z Politi
  3. Kota Nagasaka
  4. Merle Hantsche-Grininger
  5. Nike Walther
  6. Birgit Koch
  7. Johannes Fuchs
  8. Gerhard Dürnberger
  9. Wen Tang
  10. Rene Ladurner
  11. Roman R Stocsits
  12. Georg A Busslinger
  13. Béla Novák
  14. Karl Mechtler
  15. Iain Finley Davidson
  16. Jan Ellenberg
  17. Jan-Michael Peters
(2019)
Absolute quantification of cohesin, CTCF and their regulators in human cells
eLife 8:e46269.
https://doi.org/10.7554/eLife.46269

Share this article

https://doi.org/10.7554/eLife.46269

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