CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin

Abstract

The cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, we mapped the genetic dependencies of human cell lines defective of cohesion regulators DDX11 and ESCO2. The obtained synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identify the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravates cohesion defects in ESCO2 mutant cells, leading to mitotic cell death. PAXIP1 promotes global chromatin association of cohesin, independent of DNA replication, a function that cannot be explained by indirect effects of PAXIP1 on transcription or DNA repair. Cohesin regulation by PAXIP1 requires its binding partner PAGR1 and a conserved FDF motif in PAGR1. PAXIP1 co-localizes with cohesin on multiple genomic loci, including active gene promoters and enhancers. Possibly, this newly identified role of PAXIP1-PAGR1 in regulating cohesin occupancy on chromatin is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.

Mapping of DDX11 genetic interactions defines sister chromatid cohesion as the major dependency

“…We identified many genes involved in DNA replication, repair, and sister chromatid cohesion, supporting the key role that DDX11 plays in linking DNA repair with establishment of sister chromatid cohesion and maintenance of genome stability. Our work supports another recent study using CRISPR screens in DDX11 and ESCO2 mutant cell lines that also shows a strong dependency of DDX11-deficient cells on cohesion regulators ( van Schie et al . 2023 ).…”

“…2021 ). To find common GIs with loss of DDX11 and to corroborate the GIs found in the HAP1 CRISPR screen, we compared the top negative GIs reported by van Schie et al . (2023) with the top negative interactions found in our CRISPR screen.…”

“…b) A comparative analysis of DDX11 GIs in HAP1 and RPE1 cell lines. GIs derived in the RPE1 cell line from van Schie et al . (2023) (smaller red circle).…”

“…A recent paper reported negative GIs for a DDX11 KO in immortalized RPE1 cell lines ( van Schie et al . 2023 ).…”

“…(2023) with the top negative interactions found in our CRISPR screen. Of the 105 top negative interactions with DDX11 RPE1 ( van Schie et al . 2023 ) and the 127 top negative interactions, we found in DDX11 KO HAP1 cells, 35 were common to both screens and were highly enriched for cohesion-associated genes ( Fig.…”