Abstract The cohesin complex topologically encircles chromosomes and mediates sister chromatid cohesion to ensure accurate chromosome segregation upon cell division. Cohesin also participates in DNA repair and gene transcription. The Nipped-B – Mau2 protein complex loads cohesin onto chromosomes and the Pds5 - Wapl complex removes cohesin. Pds5 is also essential for sister chromatid cohesion, indicating that it has functions beyond cohesin removal. The Brca2 DNA repair protein interacts with Pds5, but the roles of this complex beyond DNA repair are unknown. Here we show that Brca2 opposes Pds5 function in sister chromatid cohesion by assaying precocious sister chromatid separation in metaphase spreads of cultured cells depleted for these proteins. By genome-wide chromatin immunoprecipitation we find that Pds5 facilitates SA cohesin subunit association with DNA replication origins and that Brca2 inhibits SA binding, mirroring their effects on sister chromatid cohesion. Cohesin binding is maximal at replication origins and extends outward to occupy active genes and regulatory sequences. Pds5 and Wapl, but not Brca2, limit the distance that cohesin extends from origins, thereby determining which active genes, enhancers and silencers bind cohesin. Using RNA-seq we find that Brca2, Pds5 and Wapl influence the expression of most genes sensitive to Nipped-B and cohesin, largely in the same direction. These findings demonstrate that Brca2 regulates sister chromatid cohesion and gene expression in addition to its canonical role in DNA repair and expand the known functions of accessory proteins in cohesin’s diverse functions. Author summary The cohesin protein complex has multiple functions in eukaryotic cells. It ensures that when a cell divides, the two daughter cells receive the correct number of chromosomes. It does this by holding together the sister chromatids that are formed when chromosomes are duplicated by DNA replication. Cohesin also helps repair damaged DNA, and to regulate genes important for growth and development. Even minor deficiencies in some proteins that regulate cohesin cause significant human birth defects. Here we investigated in Drosophila cells how three proteins, Pds5, Wapl and Brca2, determine where cohesin binds to chromosomes, control cohesin’s ability to hold sister chromatids together, and participate in gene expression. We find that Pds5 and Wapl work together, likely during DNA replication, to determine which genes bind cohesin by controlling how far cohesin spreads out along chromosomes. Pds5 is required for cohesin to hold sister chromatids together, and Brca2 counteracts this function. In contrast to the opposing roles in sister chromatid cohesion, Pds5 and Brca2 work together to facilitate control of gene expression by cohesin. Brca2 plays a critical role in DNA repair, and these studies expand the known roles for Brca2 by showing that it also regulates sister chromatid cohesion and gene expression. BRCA2 mutations in humans increase susceptibility to breast and ovarian cancer, and these findings raise the possibility that changes in chromosome segregation or gene expression might contribute to the increased cancer risk associated with these mutations.
