The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027.

Abstract

Bromodomain and extraterminal motif (BET) proteins are pharmacologic targets for the treatment of diverse diseases, yet the roles of individual BET family members remain unclear. We find that BRD2, but not BRD4, co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites whereas BRD2 is dispensable for CTCF occupancy. Disruption of a CTCF/BRD2-occupied element positioned between two unrelated genes enables regulatory influence to spread from one gene to another, suggesting that CTCF and BRD2 form a transcriptional boundary. Accordingly, single-molecule mRNA fluorescence in situ hybridization (FISH) reveals that, upon site-specific CTCF disruption or BRD2 depletion, expression of the two genes becomes increasingly correlated. HiC shows that BRD2 depletion weakens boundaries co-occupied by CTCF and BRD2, but not those that lack BRD2. These findings indicate that BRD2 supports boundary activity, and they raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function.

Keywords: BET proteins; BRD2; CTCF; chromatin architecture; transcription.

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor
  • CRISPR-Cas Systems
  • Cell Line
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Chromatin Assembly and Disassembly*
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism*
  • Embryonic Stem Cells / metabolism*
  • Enhancer Elements, Genetic*
  • GATA1 Transcription Factor / genetics
  • GATA1 Transcription Factor / metabolism
  • Gene Editing / methods
  • In Situ Hybridization, Fluorescence
  • Membrane Transport Proteins / genetics
  • Membrane Transport Proteins / metabolism
  • Mice
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Protein Binding
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Receptors, Estrogen / genetics
  • Receptors, Estrogen / metabolism
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Single Molecule Imaging / methods
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic*
  • Transfection

Substances

  • Brd2 protein, mouse
  • Brd3 protein, mouse
  • Brd4 protein, mouse
  • CCCTC-Binding Factor
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Ctcf protein, mouse
  • GATA1 Transcription Factor
  • Membrane Transport Proteins
  • Nuclear Proteins
  • RNA, Messenger
  • Receptors, Estrogen
  • Recombinant Fusion Proteins
  • Repressor Proteins
  • Transcription Factors
  • mitoferrin protein, mouse