Structure of the variant histone H3.3–H4 heterodimer in complex with its chaperone DAXX

Abstract

Mammalian H3.3 is a variant of the canonical histone H3.1 essential for genome reprogramming in the fertilized eggs and maintenance of chromatin structure in neuronal cells. An H3.3-specific histone chaperone, DAXX, directs the deposition of H3.3 onto pericentric and telomeric heterochromatin. H3.3 differs from H3.1 by only five amino acids, yet DAXX can distinguish the two with high precision. By a combination of structural, biochemical and cell-based targeting analyses, here we show that Ala87 and Gly90 are the principal determinants of H3.3 specificity. DAXX uses a shallow hydrophobic pocket to accommodate the small, hydrophobic Ala87 of H3.3, whereas a polar binding environment in DAXX prefers Gly90 in H3.3 over the hydrophobic Met90 in H3.1. An H3.3-H4 heterodimer is bound by the histone-binding domain of DAXX, which makes extensive contacts with both H3.3 and H4.

Integrated molecular mechanism directing nucleosome reorganization by human FACT

“…In the chromatin-based transcription, the superhelical torsion locally disrupts DNA-histone contacts within the nucleosome (Sheinin et al 2013). In addition, the previous structural reports indicate competitive relationships between the nucleosomal DNA and several histone chaperones, including FACT, during the association with internal histones (Hu et al 2011;Winkler et al 2011;Elsässer et al 2012;Liu et al 2012;Chen et al 2015;Huang et al 2015;Kemble et al 2015;Richet et al 2015). Thus, we assumed that the interaction of hFACT with nucleosomes would involve local detachments of the nucleosomal DNA from histones (Winkler et al 2011;Hsieh et al 2013;Kemble et al 2015).…”

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

“…In vivo , the assembly process is catalyzed by histone chaperones, a diverse class of proteins that is involved in histone turnover including transport, transfer, and storage (De Koning et al , 2007). Structural studies of histone chaperones bound to cognate histones have revealed that histone chaperones frequently protect hydrophobic histone interfaces that become solvent‐exposed outside of the context of the nucleosome or neutralize excess positive charge by providing an acidic binding pocket to directly compete with non‐specific electrostatic histone–DNA interactions (English et al , 2006; Zhou et al , 2008, 2011; Cho & Harrison, 2011; Hu et al , 2011; Elsasser et al , 2012; Liu et al , 2012; Hondele et al , 2013; Obri et al , 2014; Huang et al , 2015). However, how chaperones mediate the final deposition onto DNA to assemble nucleosomes remains poorly understood (Loyola & Almouzni, 2004; De Koning et al , 2007; Elsasser & D'Arcy, 2012).…”

Structural transitions of centromeric chromatin regulate the cell cycle-dependent recruitment of CENP-N

“…To monitor the interaction between CENP-A and CENP-N, we used a cell-based approach using the LacO/I targeting system in A03_1 cells (Supplemental Fig. S1A; Liu et al 2012). Initially, to test whether the LacI-CENP-A or LacI-H3 is incorporated into chromatin in our system, the retention ratio of LacI dots was analyzed following IPTG treatment.…”

“…LacO/I targeting assays were performed as previously described with some modifications (Liu et al 2012). In brief, plasmids were transfected into cells with LipoD293 (SignaGen) according to the manufacturer's instructions.…”