Acute BAF perturbation causes immediate changes in chromatin accessibility

Cancer-associated loss-of-function mutations in genes coding for subunits of the BRG1/BRM associated factor (BAF) chromatin remodeling complexes(1–8) often cause drastic chromatin accessibility changes, especially in important regulatory regions(9–19). However, it remains unknown how these changes are established over time (e.g. immediate consequences or long-term adaptations), and whether they are causative for intra-complex synthetic lethalities abrogating the formation or activity of BAF complexes(9,20–24). Here, we use the dTAG system to induce acute degradation of BAF subunits and show that chromatin alterations are established faster than the duration of one cell cycle. Using a pharmacological inhibitor and a chemical degrader of the BAF complex ATPase subunits(25,26), we show that maintaining genome accessibility requires constant ATP-dependent remodeling. Completely abolishing BAF complex function by acute degradation of a synthetic lethal subunit in a paralog-deficient background results in a near-complete loss of chromatin accessibility at BAF-controlled sites, especially at super-enhancers, providing a mechanism for intra-complex synthetic lethalities.