Absolute quantification of cohesin, CTCF and their regulators in human cells
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 cohesi...
| 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/46269 |
| _version_ | 1811181116468494336 |
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| author | Johann Holzmann Antonio Z Politi Kota Nagasaka Merle Hantsche-Grininger Nike Walther Birgit Koch Johannes Fuchs Gerhard Dürnberger Wen Tang Rene Ladurner Roman R Stocsits Georg A Busslinger Béla Novák Karl Mechtler Iain Finley Davidson Jan Ellenberg Jan-Michael Peters |
| author_facet | Johann Holzmann Antonio Z Politi Kota Nagasaka Merle Hantsche-Grininger Nike Walther Birgit Koch Johannes Fuchs Gerhard Dürnberger Wen Tang Rene Ladurner Roman R Stocsits Georg A Busslinger Béla Novák Karl Mechtler Iain Finley Davidson Jan Ellenberg Jan-Michael Peters |
| author_sort | Johann Holzmann |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T09:14:12Z |
| format | Article |
| id | doaj.art-b4dd695cfba54d39a1aacd86fcfa079a |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:14:12Z |
| publishDate | 2019-06-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-b4dd695cfba54d39a1aacd86fcfa079a2022-12-22T04:32:25ZengeLife Sciences Publications LtdeLife2050-084X2019-06-01810.7554/eLife.46269Absolute quantification of cohesin, CTCF and their regulators in human cellsJohann Holzmann0Antonio Z Politi1https://orcid.org/0000-0003-4788-0933Kota Nagasaka2https://orcid.org/0000-0003-0765-638XMerle Hantsche-Grininger3https://orcid.org/0000-0002-5137-1616Nike Walther4https://orcid.org/0000-0002-7591-5251Birgit Koch5Johannes Fuchs6Gerhard Dürnberger7Wen Tang8Rene Ladurner9Roman R Stocsits10Georg A Busslinger11Béla Novák12https://orcid.org/0000-0002-6961-1366Karl Mechtler13Iain Finley Davidson14https://orcid.org/0000-0003-4945-6415Jan Ellenberg15https://orcid.org/0000-0001-5909-701XJan-Michael Peters16https://orcid.org/0000-0003-2820-3195Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria; Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, AustriaCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, AustriaCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria; Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, AustriaResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria; Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, AustriaResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, AustriaResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, AustriaResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, AustriaResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, AustriaDepartment of Biochemistry, University of Oxford, Oxford, United KingdomResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria; Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, AustriaResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, AustriaCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria; Medical University of Vienna, Vienna, AustriaThe 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.https://elifesciences.org/articles/46269cohesinCTCFgenome organizationsister chromatid cohesionmass spectrometryfluorescence-correlation spectroscopy |
| spellingShingle | Johann Holzmann Antonio Z Politi Kota Nagasaka Merle Hantsche-Grininger Nike Walther Birgit Koch Johannes Fuchs Gerhard Dürnberger Wen Tang Rene Ladurner Roman R Stocsits Georg A Busslinger Béla Novák Karl Mechtler Iain Finley Davidson Jan Ellenberg Jan-Michael Peters Absolute quantification of cohesin, CTCF and their regulators in human cells eLife cohesin CTCF genome organization sister chromatid cohesion mass spectrometry fluorescence-correlation spectroscopy |
| title | Absolute quantification of cohesin, CTCF and their regulators in human cells |
| title_full | Absolute quantification of cohesin, CTCF and their regulators in human cells |
| title_fullStr | Absolute quantification of cohesin, CTCF and their regulators in human cells |
| title_full_unstemmed | Absolute quantification of cohesin, CTCF and their regulators in human cells |
| title_short | Absolute quantification of cohesin, CTCF and their regulators in human cells |
| title_sort | absolute quantification of cohesin ctcf and their regulators in human cells |
| topic | cohesin CTCF genome organization sister chromatid cohesion mass spectrometry fluorescence-correlation spectroscopy |
| url | https://elifesciences.org/articles/46269 |
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