Acute BAF perturbation causes immediate changes in chromatin accessibility
- 28 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Genetics
- Vol. 53 (3), 269-+
- https://doi.org/10.1038/s41588-021-00777-3
Abstract
Cancer-associated, loss-of-function mutations in genes encoding 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 (for example, immediate consequences or long-term adaptations), and whether they are causative for intracomplex synthetic lethalities, abro-gating the formation or activity of BAF complexes(9,20-24). In the present study, 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 an almost complete loss of chromatin accessibility at BAF-controlled sites, especially also at superenhancers, providing a mechanism for intracomplex synthetic lethalities.Keywords
This publication has 66 references indexed in Scilit:
- Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancyNature Genetics, 2013
- The Spectrum of SWI/SNF Mutations, Ubiquitous in Human CancersPLOS ONE, 2013
- clusterProfiler: an R Package for Comparing Biological Themes Among Gene ClustersOMICS: A Journal of Integrative Biology, 2012
- ATP-dependent chromatin remodeling: genetics, genomics and mechanismsCell Research, 2011
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics, 2010
- Universal sample preparation method for proteome analysisNature Methods, 2009
- Cluster-Buster: finding dense clusters of motifs in DNA sequencesNucleic Acids Research, 2003
- Diversity and specialization of mammalian SWI/SNF complexes.Genes & Development, 1996
- Persistent Site-Specific Remodeling of a Nucleosome Array by Transient Action of the SWI/SNF ComplexScience, 1996