The following study was conducted by Scientists from National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda; University of California San Diego; Indiana University; Indiana University Melvin and Bren Simon Cancer Center, Indiana University–Purdue University, Indianapolis, USA; Guangzhou Institutes of Biomedicine and Health, Science Park, Guangzhou, China. Study is published in Proceedings of the National Academy of Sciences Journal as detailed below.
Proceedings of the National Academy of Sciences 117(4): 2020-2031
CTCF Mediates Chromatin Looping via N-terminal Domain-Dependent Cohesin Retention
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.
Abstract
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.
Source:
Proceedings of the National Academy of Sciences
URL: https://www.pnas.org/content/early/2020/01/13/1911708117
Citation:
Pugacheva, E. M., N. Kubo, et al. (2020). “CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention.” Proceedings of the National Academy of Sciences 117(4): 2020-2031.
