PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome [RNA-seq]

Purpose: Cohesin is an important structural regulator of the genome. Whether cohesin HEAT repeat accessory proteins PDS5A and PDS5B differentially contribute to cohesin function remains unclear. The purpose of this study is to interrogate how PDS5A and PDS5B affect cohesin localization and gene expression in mouse embronic stem cells (mESCs) Method: The role of PDS5A and PDS5B in gene regulation was assessed by performing RNA-seq in wildtype and CRISPR-Cas9 genome edited PDS5 knockout mouse embryonic stem cells (mESCs). The redundancy of the PDS5s was addressed by using siRNA against PDS5B in a PDS5A-knockout background. Whether PDS5 and STAG proteins have selective roles in gene expression was addressed by using siRNA against STAG1 and STAG2 in a PDS5A-KO background RNA-seq was performed in wild type mESCs, PDS5-knockout CRISPR-Cas9 genome edited mESCs, and PDS5A-knockout mESCs with siRNA depletion of PDS5B, STAG1, or STAG2, all in triplicate.