Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin

作者：Ana Cuadrado, Daniel Giménez-Llorente, Magali De Koninck, Miguel Ruiz‐Torres, Aleksandar Kojic, Miriam Rodríguez-Corsino, Ana Losada · 发表于：Epigenetics & Chromatin · 年份：2022 · DOI：10.1186/s13072-022-00469-0 · 被引用次数：21 · 研究领域：Genomics and Chromatin Dynamics、Developmental Biology and Gene Regulation、Chromosomal and Genetic Variations

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 acc...