Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin.
BACKGROUND The cohesin complex organizes the genome-forming dynamic chromatin loops that impact on all DNA-mediated processes. There are two different cohesin complexes in vertebrate somatic cells, carrying the STAG1 or STAG2 subunit, and two versions of the regulatory subunit PDS5, PDS5A and PDS5B....
| Autores: | ; ; ; ; ; ; |
|---|---|
| Tipo de documento: | Artículo |
| Fecha de publicación: | 2022 |
| País: | España |
| Institución: | Instituto de Salud Carlos III (ISCIII) |
| Repositorio: | Repisalud |
| Lenguaje: | Inglés |
| OAI Identifier: | oai:repisalud.isciii.es:20.500.12105/17655 |
| Acceso en línea: | http://hdl.handle.net/20.500.12105/17655 |
| Nivel de acceso: | Acceso abierto |
| Palabra clave: | Chromosomal Proteins, Non-Histone Cell Cycle Proteins Mice Animals Chromatin Genome Carrier Proteins Mammals Cohesins |
| _version_ | 1878733722529824769 |
|---|---|
| author | Cuadrado, Ana |
| author2 | Giménez-Llorente, Daniel De Koninck, Magali Ruiz-Torres, Miguel Kojic, Aleksandar Rodríguez-Corsino, Miriam Losada, Ana |
| author2_role | author author author author author author |
| author_browse | Cuadrado, Ana De Koninck, Magali Giménez-Llorente, Daniel Kojic, Aleksandar Losada, Ana Rodríguez-Corsino, Miriam Ruiz-Torres, Miguel |
| author_facet | Cuadrado, Ana Giménez-Llorente, Daniel De Koninck, Magali Ruiz-Torres, Miguel Kojic, Aleksandar Rodríguez-Corsino, Miriam Losada, Ana |
| author_role | author |
| collection | Repisalud |
| description | BACKGROUND The cohesin complex organizes the genome-forming dynamic chromatin loops that impact on all DNA-mediated processes. There are two different cohesin complexes in vertebrate somatic cells, carrying the STAG1 or STAG2 subunit, and two versions of the regulatory subunit PDS5, PDS5A and PDS5B. Mice deficient for any of the variant subunits are embryonic lethal, which indicates that they are not functionally redundant. However, their specific behavior at the molecular level is not fully understood. RESULTS The genome-wide distribution of cohesin provides important information with functional consequences. Here, we have characterized the distribution of cohesin subunits and regulators in mouse embryo fibroblasts (MEFs) either wild type or deficient for cohesin subunits and regulators by chromatin immunoprecipitation and deep sequencing. We identify non-CTCF cohesin-binding sites in addition to the commonly detected CTCF cohesin sites and show that cohesin-STAG2 is the preferred variant at these positions. Moreover, this complex has a more dynamic association with chromatin as judged by fluorescence recovery after photobleaching (FRAP), associates preferentially with WAPL and is more easily extracted from chromatin with salt than cohesin-STAG1. We observe that both PDS5A and PDS5B are exclusively located at cohesin-CTCF positions and that ablation of a single paralog has no noticeable consequences for cohesin distribution while double knocked out cells show decreased accumulation of cohesin at all its binding sites. With the exception of a fraction of cohesin positions in which we find binding of all regulators, including CTCF and WAPL, the presence of NIPBL and PDS5 is mutually exclusive, consistent with our immunoprecipitation analyses in mammalian cell extracts and previous results in yeast. CONCLUSION Our findings support the idea that non-CTCF cohesin-binding sites represent sites of cohesin loading or pausing and are preferentially occupied by the more dynamic cohesin-STAG2. PDS5 proteins redundantly contribute to arrest cohesin at CTCF sites, possibly by preventing binding of NIPBL, but are not essential for this arrest. These results add important insights towards understanding how cohesin regulates genome folding and the specific contributions of the different variants that coexist in the cell. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | ES_5bb459ef31cf8ce80f5ccf634dd0b2cb |
| institution | Instituto de Salud Carlos III (ISCIII) |
| instname_str | Instituto de Salud Carlos III (ISCIII) |
| language | eng |
| network_acronym_str | ES |
| network_name_str | España |
| oai_identifier_str | oai:repisalud.isciii.es:20.500.12105/17655 |
| publishDate | 2022 |
| publishDateSort | 2022 |
| publisher | BioMed Central (BMC) |
| publisherStr | BioMed Central (BMC) |
| reponame_str | Repisalud |
| spelling | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. Cuadrado, Ana Giménez-Llorente, Daniel De Koninck, Magali Ruiz-Torres, Miguel Kojic, Aleksandar Rodríguez-Corsino, Miriam Losada, Ana Chromosomal Proteins, Non-Histone Cell Cycle Proteins Mice Animals Chromatin Genome Carrier Proteins Mammals Cohesins BACKGROUND The cohesin complex organizes the genome-forming dynamic chromatin loops that impact on all DNA-mediated processes. There are two different cohesin complexes in vertebrate somatic cells, carrying the STAG1 or STAG2 subunit, and two versions of the regulatory subunit PDS5, PDS5A and PDS5B. Mice deficient for any of the variant subunits are embryonic lethal, which indicates that they are not functionally redundant. However, their specific behavior at the molecular level is not fully understood. RESULTS The genome-wide distribution of cohesin provides important information with functional consequences. Here, we have characterized the distribution of cohesin subunits and regulators in mouse embryo fibroblasts (MEFs) either wild type or deficient for cohesin subunits and regulators by chromatin immunoprecipitation and deep sequencing. We identify non-CTCF cohesin-binding sites in addition to the commonly detected CTCF cohesin sites and show that cohesin-STAG2 is the preferred variant at these positions. Moreover, this complex has a more dynamic association with chromatin as judged by fluorescence recovery after photobleaching (FRAP), associates preferentially with WAPL and is more easily extracted from chromatin with salt than cohesin-STAG1. We observe that both PDS5A and PDS5B are exclusively located at cohesin-CTCF positions and that ablation of a single paralog has no noticeable consequences for cohesin distribution while double knocked out cells show decreased accumulation of cohesin at all its binding sites. With the exception of a fraction of cohesin positions in which we find binding of all regulators, including CTCF and WAPL, the presence of NIPBL and PDS5 is mutually exclusive, consistent with our immunoprecipitation analyses in mammalian cell extracts and previous results in yeast. CONCLUSION Our findings support the idea that non-CTCF cohesin-binding sites represent sites of cohesin loading or pausing and are preferentially occupied by the more dynamic cohesin-STAG2. PDS5 proteins redundantly contribute to arrest cohesin at CTCF sites, possibly by preventing binding of NIPBL, but are not essential for this arrest. These results add important insights towards understanding how cohesin regulates genome folding and the specific contributions of the different variants that coexist in the cell. BioMed Central (BMC) http://hdl.handle.net/20.500.12105/17655 |
| spellingShingle | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. Cuadrado, Ana Chromosomal Proteins, Non-Histone Cell Cycle Proteins Mice Animals Chromatin Genome Carrier Proteins Mammals Cohesins |
| title | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. |
| title_full | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. |
| title_fullStr | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. |
| title_full_unstemmed | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. |
| title_short | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. |
| title_sort | Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin. |
| topic | Chromosomal Proteins, Non-Histone Cell Cycle Proteins Mice Animals Chromatin Genome Carrier Proteins Mammals Cohesins |
| topic_facet | Chromosomal Proteins, Non-Histone Cell Cycle Proteins Mice Animals Chromatin Genome Carrier Proteins Mammals Cohesins |
| url | http://hdl.handle.net/20.500.12105/17655 |