The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres

Nature. 2010 Sep 16;467(7313):347-51. doi: 10.1038/nature09323. Epub 2010 Aug 25.

Abstract

Centromeres are specified epigenetically, and the histone H3 variant CENP-A is assembled into the chromatin of all active centromeres. Divergence from H3 raises the possibility that CENP-A generates unique chromatin features to mark physically centromere location. Here we report the crystal structure of a subnucleosomal heterotetramer, human (CENP-A-H4)(2), that reveals three distinguishing properties encoded by the residues that comprise the CENP-A targeting domain (CATD; ref. 2): (1) a CENP-A-CENP-A interface that is substantially rotated relative to the H3-H3 interface; (2) a protruding loop L1 of the opposite charge as that on H3; and (3) strong hydrophobic contacts that rigidify the CENP-A-H4 interface. Residues involved in the CENP-A-CENP-A rotation are required for efficient incorporation into centromeric chromatin, indicating specificity for an unconventional nucleosome shape. DNA topological analysis indicates that CENP-A-containing nucleosomes are octameric with conventional left-handed DNA wrapping, in contrast to other recent proposals. Our results indicate that CENP-A marks centromere location by restructuring the nucleosome from within its folded histone core.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Autoantigens / chemistry*
  • Autoantigens / metabolism*
  • Binding Sites
  • Centromere / chemistry*
  • Centromere / metabolism*
  • Centromere Protein A
  • Chromatin Assembly and Disassembly
  • Chromosomal Proteins, Non-Histone / chemistry*
  • Chromosomal Proteins, Non-Histone / metabolism*
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / metabolism
  • Deuterium Exchange Measurement
  • Epistasis, Genetic
  • Histones / chemistry*
  • Histones / metabolism*
  • Humans
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism
  • Protein Multimerization
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Rotation
  • Scattering, Small Angle
  • Structure-Activity Relationship
  • Substrate Specificity

Substances

  • Autoantigens
  • CENPA protein, human
  • Centromere Protein A
  • Chromosomal Proteins, Non-Histone
  • Histones
  • Nucleosomes
  • DNA

Associated data

  • PDB/3NQJ
  • PDB/3NQU