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

Abstract

Centromeres are specified epigenetically, and the histone H3 variant, CENP-A, is assembled into the chromatin of all active centromeres1. Divergence from H3 raises the possibility that CENP-A generates unique chromatin features to physically mark centromere location. The crystal structure of the sub-nucleosomal heterotetramer reported here reveals three distinguishing properties encoded by the residues that comprise the CENP-A Targeting Domain (CATD2): (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 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 suggesting specificity for an unconventional nucleosome shape. DNA topological analysis indicates that CENP-A-containing nucleosomes are nonetheless octameric with conventional left-handed DNA wrapping, in contrast to other recent proposals3-6. Our results indicate rather that CENP-A marks centromere location by restructuring the nucleosome from within its folded histone core.

Structure of a CENP-A–histone H4 heterodimer in complex with chaperone HJURP

“…1A). The structure of the CENP-A and histone H4 heterodimer, as expected, is similar to the ones in the CENP-A-H4 tetramer (Sekulic et al 2010). Helix aA of HJURP packs against the central helix (a2) of the histone fold of CENP-A in an anti-parallel manner, with the hydrophobic side of the amphipathic aA facing CENP-A (Fig.…”

“…The crystal structure of the CENP-A-H4 tetramer shows that two CENP-A-H4 heterodimers dimerize through amino acids located on helix a3 and the C-terminal portion of a2, mainly via hydrophobic interactions (Sekulic et al 2010). Structural superposition shows that the CENP-A-H4 heterodimer superimposes with the ones from the tetrameric structure with a 0.96 Å root-mean-squared deviation (RMSD) of Ca positions.…”

“…The precise model of CENP-A-containing nucleosomes is still a matter of debate (Henikoff and Furuyama 2010;Black and Cleveland 2011). A closely relevant point here is whether a centromeric nucleosome contains a CENP-A-H4 heterodimer or heterotetramer (Dimitriadis et al 2010;Sekulic et al 2010). The structural result cannot distinguish whether a CENP-A nucleosome is octameric or a hemisome.…”

Histone H3-variant Cse4-induced positive DNA supercoiling in the yeast plasmid has implications for a plasmid origin of a chromosome centromere

“…These findings also speak to the current debate on whether CenH3-containing nucleosomes engender the normal left-handed, or the opposite right-handed DNA writhe (21)(22)(23). The in vivo topology of STB revealed in the present investigation and that of CEN deduced from an earlier study (21) are consistent with the right-handed writhe.…”

“…However, it is not certain that the reversed DNA topology applies universally to CenH3-containing nucleosomes. The crystal structure of the subnucleosomal human (CENPA-H4) 2 tetramer suggests that physical features, rather than DNA topology, provide the signature of a centromeric nucleosome (23). These features include differences between CENPA-CENPA and H3-H3 interfaces, as well as those between CENPA-H4 and H3-H4 interfaces.…”