Human Histone Interaction Networks: An Old Concept, New Trends

J Mol Biol. 2021 Mar 19;433(6):166684. doi: 10.1016/j.jmb.2020.10.018. Epub 2020 Oct 22.

Abstract

To elucidate the properties of human histone interactions on the large scale, we perform a comprehensive mapping of human histone interaction networks by using data from structural, chemical cross-linking and various high-throughput studies. Histone interactomes derived from different data sources show limited overlap and complement each other. It inspires us to integrate these data into the combined histone global interaction network which includes 5308 proteins and 10,330 interactions. The analysis of topological properties of the human histone interactome reveals its scale free behavior and high modularity. Our study of histone binding interfaces uncovers a remarkably high number of residues involved in interactions between histones and non-histone proteins, 80-90% of residues in histones H3 and H4 have at least one binding partner. Two types of histone binding modes are detected: interfaces conserved in most histone variants and variant specific interfaces. Finally, different types of chromatin factors recognize histones in nucleosomes via distinct binding modes, and many of these interfaces utilize acidic patches among other sites. Interaction networks are available at https://github.com/Panchenko-Lab/Human-histone-interactome.

Keywords: histone; interaction; interactome; network; nucleosome.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Chromosomal Proteins, Non-Histone / chemistry*
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism
  • Databases, Protein
  • Histones / chemistry*
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Internet
  • Nucleic Acid Conformation
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism
  • Nucleosomes / ultrastructure*
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Protein Interaction Maps*
  • Software

Substances

  • Chromosomal Proteins, Non-Histone
  • Histones
  • Nucleosomes
  • DNA