CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention
| Autor: | Alexander L. Kovalchuk, Alexander V. Strunnikov, Gabriel E. Zentner, Sungyun Kang, Tajmul, Victor V. Lobanenkov, Naoki Kubo, Dmitri Loukinov, Elena M. Pugacheva, Bing Ren |
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| Rok vydání: | 2020 |
| Předmět: |
CCCTC-Binding Factor
Cohesin complex Chromosomal Proteins Non-Histone cohesin Breast Neoplasms Cell Cycle Proteins 03 medical and health sciences 0302 clinical medicine Protein Domains BORIS 3D genome organization Tumor Cells Cultured Humans Binding site 030304 developmental biology Zinc finger 0303 health sciences Binding Sites Multidisciplinary Cohesin Genome Human Chemistry DNA Neoplasm Cell Biology Biological Sciences CTCF Chromatin Cell biology DNA-Binding Proteins DNA binding site 030220 oncology & carcinogenesis Female Chromatin Loop biological phenomena cell phenomena and immunity Protein Binding |
| Zdroj: | Proceedings of the National Academy of Sciences of the United States of America |
| ISSN: | 1091-6490 0027-8424 |
| DOI: | 10.1073/pnas.1911708117 |
| Popis: | Significance The DNA-binding protein CCCTC-binding factor (CTCF) and the cohesin complex function together to establish chromatin loops and regulate gene expression in mammalian cells. It has been proposed that the cohesin complex moving bidirectionally along DNA extrudes the chromatin fiber and generates chromatin loops when it pauses at CTCF binding sites. To date, the mechanisms by which cohesin localizes at CTCF binding sites remain unclear. In the present study we define two short segments within the CTCF protein that are essential for localization of cohesin complexes at CTCF binding sites. Based on our data, we propose that the N-terminus of CTCF and 3D geometry of the CTCF–DNA complex act as a roadblock constraining cohesin movement and establishing long-range chromatin loops. The DNA-binding protein CCCTC-binding factor (CTCF) and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. Here, we demonstrate that a 79-aa region within the CTCF N terminus is essential for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N terminus of CTCF fused to artificial zinc fingers was not sufficient to redirect cohesin to non-CTCF binding sites, indicating a lack of an autonomously functioning domain in CTCF responsible for cohesin positioning. BORIS (CTCFL), a germline-specific paralog of CTCF, was unable to anchor cohesin to CTCF DNA binding sites. Furthermore, CTCF–BORIS chimeric constructs provided evidence that, besides the N terminus of CTCF, the first two CTCF zinc fingers, and likely the 3D geometry of CTCF–DNA complexes, are also involved in cohesin retention. Based on this knowledge, we were able to convert BORIS into CTCF with respect to cohesin positioning, thus providing additional molecular details of the ability of CTCF to retain cohesin. Taken together, our data provide insight into the process by which DNA-bound CTCF constrains cohesin movement to shape spatiotemporal genome organization. |
| Databáze: | OpenAIRE |
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