Acute BAF perturbation causes immediate changes in chromatin accessibility

Loss-of-function mutations in genes coding for subunits of the large, multifarious BRG1/BRM associated factor (BAF) chromatin remodeling complexes are frequently causative for cancer or developmental diseases. Cells lacking the most frequently mutated subunits, like the ATPase SMARCA4, typically exhibit drastic chromatin accessibility changes, especially of important regulatory regions. However, so far it remains unknown how these changes are established over time, and whether they are causative for intra-complex synthetic lethalities abrogating the formation or activity of BAF complexes. Here, we utilize the dTAG system to induce acute degradation of BAF subunits in wildtype and BAF mutant backgrounds and analyze the resulting chromatin accessibility changes with high kinetic resolution. We observe that chromatin alterations are established faster than the duration of one cell cycle and 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. Overall design: ATAC-seq, RNA-seq, PRO-seq experiments were performed in duplicates, ChIP-seq once. All experiments contain respective control samples. ChIP antibody details: H3K27ac (Abcam, catalog# ab4729, lot# 3211741-1), ARID1A (Abcam, catalog# ab182560, lot# GR269670-9), IgG (Cell Signaling, catalog# CS 2729S, lot# 9), BRD4 (Abcam, catalog# ab128874, lot# GR3251918-7).