Determining cellular CTCF and cohesin abundances to constrain 3D genome models
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)...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2019-06-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/40164 |
| _version_ | 1811180544354942976 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Claudia Cattoglio |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T09:05:01Z |
| format | Article |
| id | doaj.art-823bc1e21a0d456c9e2681dbaa8ee00e |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:05:01Z |
| publishDate | 2019-06-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-823bc1e21a0d456c9e2681dbaa8ee00e2022-12-22T04:32:40ZengeLife Sciences Publications LtdeLife2050-084X2019-06-01810.7554/eLife.40164Determining cellular CTCF and cohesin abundances to constrain 3D genome modelsClaudia Cattoglio0https://orcid.org/0000-0001-6100-0491Iryna Pustova1Nike Walther2https://orcid.org/0000-0002-7591-5251Jaclyn J Ho3Merle Hantsche-Grininger4Carla J Inouye5M Julius Hossain6https://orcid.org/0000-0003-3303-5755Gina M Dailey7Jan Ellenberg8https://orcid.org/0000-0001-5909-701XXavier Darzacq9https://orcid.org/0000-0003-2537-8395Robert Tjian10https://orcid.org/0000-0003-0539-8217Anders S Hansen11https://orcid.org/0000-0001-7540-7858Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States; Howard Hughes Medical Institute, Berkeley, United StatesDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States; Howard Hughes Medical Institute, Berkeley, United StatesCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States; Howard Hughes Medical Institute, Berkeley, United StatesCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States; Howard Hughes Medical Institute, Berkeley, United StatesCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United StatesCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United StatesDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States; Howard Hughes Medical Institute, Berkeley, United StatesDepartment of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States; Howard Hughes Medical Institute, Berkeley, United StatesAchieving 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.https://elifesciences.org/articles/40164CTCFcohesinloop extrusionTADgenome organizationRad21 |
| spellingShingle | 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 Determining cellular CTCF and cohesin abundances to constrain 3D genome models eLife CTCF cohesin loop extrusion TAD genome organization Rad21 |
| title | Determining cellular CTCF and cohesin abundances to constrain 3D genome models |
| title_full | Determining cellular CTCF and cohesin abundances to constrain 3D genome models |
| title_fullStr | Determining cellular CTCF and cohesin abundances to constrain 3D genome models |
| title_full_unstemmed | Determining cellular CTCF and cohesin abundances to constrain 3D genome models |
| title_short | Determining cellular CTCF and cohesin abundances to constrain 3D genome models |
| title_sort | determining cellular ctcf and cohesin abundances to constrain 3d genome models |
| topic | CTCF cohesin loop extrusion TAD genome organization Rad21 |
| url | https://elifesciences.org/articles/40164 |
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