Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

J Mol Biol. 2021 Oct 15;433(21):167224. doi: 10.1016/j.jmb.2021.167224. Epub 2021 Sep 8.

Abstract

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.

Keywords: DNA binding; autoinhibition; disordered loop; nuclear magnetic resonance; retinoblastoma-binding protein 1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Chromatin / chemistry*
  • Chromatin / metabolism
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism
  • Gene Expression
  • Histones / chemistry*
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Protein Isoforms / chemistry
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Retinoblastoma-Binding Protein 1 / chemistry*
  • Retinoblastoma-Binding Protein 1 / genetics
  • Retinoblastoma-Binding Protein 1 / metabolism
  • Retinoblastoma-Binding Protein 2 / chemistry
  • Retinoblastoma-Binding Protein 2 / genetics
  • Retinoblastoma-Binding Protein 2 / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Thermodynamics

Substances

  • ARID4A protein, human
  • Chromatin
  • Histones
  • Protein Isoforms
  • Recombinant Proteins
  • Retinoblastoma-Binding Protein 1
  • DNA
  • KDM5A protein, human
  • Retinoblastoma-Binding Protein 2