Cohesin-independent STAG proteins interact with RNA and R-loops and promote complex loading

Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA, and R-loops, even in the absence of cohesin. Our results place SA1 on chromatin upstream of the cohesin ring and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease. ; This work was supported by a Senior Research Fellowship from the Wellcome Trust awarded to SH (106985/Z/15/Z) and a CRUK PhD studentship awarded to HP. The Proteomics work was supported by the CRUK–UCL Centre Award [C416/A25145]. The CLIP work was supported by grants from the European Research Council (ERC, 311704) and Worldwide Cancer Research (21-0255), to RGJ. We are grateful to Jernej Ule for his support with DRIP-sequencing and to Julian Zagalak and the CRICK sequencing facility for reagents, advice and assistance. We thank Stanimir Dulev for his contributions at the early stages of the project and Jiten Manji for his support with microscopy. We also thank Konstantina Skourti-Stathaki for advice about S9.6 antibody, IFs and R-loops. We are grateful to the ...