PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes

Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heterochromatic compartments. Cohesin can also bind PDS5A or PDS5B, which do not support loop extrusion but are required for the formation of CTCF boundaries. How PDS5 proteins perform this function is unknown. Here we show by in vitro single-molecule imaging that PDS5 proteins stop loop extrusion by facilitating the dissociation of NIPBL from cohesin. Hi-C experiments suggest that this function is required for the establishment of CTCF boundaries in cells. In silico modelling indicates that PDS5 proteins enable the separation between compartments by limiting cohesin’s velocity and chromatin-residence time. The degree of this compartmentalization depends on the frequency with which chromatin is extruded relative to the time it takes for compartments to form. These results identify PDS5 proteins as key regulators of genome organization.

黏连蛋白（Cohesin）与NIPBL复合物可将基因组DNA挤出形成环状结构，该结构受CTCF边界（CTCF）约束。此过程具备重要的调控功能，同时会削弱常染色质与异染色质区室之间的分隔。黏连蛋白还可结合PDS5A或PDS5B，这类蛋白虽无法支持环挤出（loop extrusion）过程，但却是CTCF边界形成所必需的。目前学界尚未明确PDS5蛋白如何行使该功能。本研究通过体外单分子成像实验证实，PDS5蛋白可通过促进NIPBL从黏连蛋白上解离，从而终止环挤出过程。Hi-C实验结果表明，该功能对于细胞内CTCF边界的建立不可或缺。计算机模拟建模显示，PDS5蛋白通过限制黏连蛋白的移动速度与染色质驻留时间，促成区室之间的分隔。该种区室化程度取决于染色质被挤出的频率与区室形成所需时长的相对比例。上述研究结果证实PDS5蛋白是基因组三维组织结构的关键调控因子。