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Determining cellular CTCF and cohesin abundances to constrain 3D genome models

View ORCID ProfileClaudia Cattoglio, Iryna Pustova, View ORCID ProfileNike Walther, Jaclyn J. Ho, View ORCID ProfileMerle Hantsche-Grininger, Carla J. Inouye, View ORCID ProfileM. Julius Hossain, Gina M. Dailey, View ORCID ProfileJan Ellenberg, View ORCID ProfileXavier Darzacq, View ORCID ProfileRobert Tjian, View ORCID ProfileAnders S. Hansen
doi: https://doi.org/10.1101/370650
Claudia Cattoglio
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
2Howard Hughes Medical Institute, Berkeley, CA 94720, USA
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Iryna Pustova
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
2Howard Hughes Medical Institute, Berkeley, CA 94720, USA
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Nike Walther
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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Jaclyn J. Ho
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
2Howard Hughes Medical Institute, Berkeley, CA 94720, USA
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Merle Hantsche-Grininger
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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  • ORCID record for Merle Hantsche-Grininger
Carla J. Inouye
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
2Howard Hughes Medical Institute, Berkeley, CA 94720, USA
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M. Julius Hossain
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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  • ORCID record for M. Julius Hossain
Gina M. Dailey
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
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Jan Ellenberg
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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  • ORCID record for Jan Ellenberg
Xavier Darzacq
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
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Robert Tjian
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
2Howard Hughes Medical Institute, Berkeley, CA 94720, USA
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Anders S. Hansen
1Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
2Howard Hughes Medical Institute, Berkeley, CA 94720, USA
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  • For correspondence: anders.sejr.hansen@berkeley.edu
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Abstract

Achieving a quantitative and predictive understanding of 3D genome architecture remains a major challenge, as it requires quantitative measurements of the key proteins involved. Here we report the quantification of CTCF and cohesin, two causal regulators of topologically associating domains (TADs) in mammalian cells. Extending our previous imaging studies (Hansen et al., 2017), we estimate bounds on the density of putatively DNA loop-extruding cohesin complexes and CTCF binding site occupancy. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) suggest the presence of cohesin dimers and/or oligomers. Finally, based on our cell lines with accurately measured protein abundances, we report a method to conveniently determine the number of molecules of any Halo-tagged protein in the cell. We anticipate that our results and the established tool for measuring cellular protein abundances will advance a more quantitative understanding of 3D genome organization, and facilitate protein quantification, key to comprehend diverse biological processes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 24, 2019.
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Determining cellular CTCF and cohesin abundances to constrain 3D genome models
Claudia Cattoglio, Iryna Pustova, Nike Walther, Jaclyn J. Ho, Merle Hantsche-Grininger, Carla J. Inouye, M. Julius Hossain, Gina M. Dailey, Jan Ellenberg, Xavier Darzacq, Robert Tjian, Anders S. Hansen
bioRxiv 370650; doi: https://doi.org/10.1101/370650
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Determining cellular CTCF and cohesin abundances to constrain 3D genome models
Claudia Cattoglio, Iryna Pustova, Nike Walther, Jaclyn J. Ho, Merle Hantsche-Grininger, Carla J. Inouye, M. Julius Hossain, Gina M. Dailey, Jan Ellenberg, Xavier Darzacq, Robert Tjian, Anders S. Hansen
bioRxiv 370650; doi: https://doi.org/10.1101/370650

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