Acute BAF perturbation causes immediate changes in chromatin accessibility

Nat Genet. 2021 Mar;53(3):269-278. doi: 10.1038/s41588-021-00777-3. Epub 2021 Feb 8.

Abstract

Cancer-associated, loss-of-function mutations in genes encoding subunits of the BRG1/BRM-associated factor (BAF) chromatin-remodeling complexes1-8 often cause drastic chromatin accessibility changes, especially in important regulatory regions9-19. 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, abrogating the formation or activity of BAF complexes9,20-24. 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 subunits25,26, 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Animals
  • Cell Line
  • Chromatin / genetics*
  • Chromatin / metabolism
  • DNA Helicases / genetics
  • DNA Helicases / metabolism*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Drosophila / cytology
  • Enhancer Elements, Genetic
  • Gene Knockout Techniques
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Multiprotein Complexes / genetics*
  • Multiprotein Complexes / metabolism
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*

Substances

  • ARID1A protein, human
  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • Multiprotein Complexes
  • Nuclear Proteins
  • SMARCA2 protein, human
  • SMARCC1 protein, human
  • SMARCC2 protein, human
  • Transcription Factors
  • SMARCA4 protein, human
  • DNA Helicases