The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism (synthetic viability screen)

Cohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids from S-phase until mitosis. The acetylation of cohesin's SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the 3D genome. ESCO1 restricts the length of chromatin loops and architectural stripes, while HDAC8 rather promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. Using a genome-wide haploid genetic screen we reveal that acetylation rather controls cohesin's interaction with PDS5A to restrict chromatin loop length. Our data supports a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding. Overall design: Genes required for viability in ?HDAC8 cells were profiled as previously described in detail (Blomen et al., 2015). ?HDAC8 HAP1 cells were mutagenized using a gene-trap retrovirus which was produced in HEK293T cells and concentrated either by ultracentrifugation as described previously (Blomen et al., 2015), or employing centrifugal ultrafiltration devices. Here, retrovirus-containing medium was harvested on two consecutive days, filtered (0.45 um) and concentrated using Amicon Ultra-15 Centrifugal Filter Units with 100K MWCO (Merck-Millipore). The virus concentrates from both harvests were combined, supplemented with 8 ug/mL protamine sulfate (Sigma) and used to infect ~40 million HAP1 cells. 4 control datasets have been previously published (Blomen et al., 2015; NCBI SRA accession no. SRP058962)