Structure of a human ASF1a–HIRA complex and insights into specificity of histone chaperone complex assembly

Abstract

Human HIRA, ASF1a, ASF1b and CAF-1 are evolutionally conserved histone chaperones that form multiple functionally distinct chromatin assembly complexes, with roles linked to diverse nuclear process, such as DNA replication and formation of heterochromatin in senescent cells. We report the crystal structure of an ASF1a/HIRA heterodimer and a biochemical dissection of ASF1a's mutually exclusive interactions with HIRA and the p60 subunit of CAF-1. The HIRA B-domain forms an antiparallel β-hairpin that binds perpendicular to the strands of the β-sandwich of ASF1a, via β-sheet, salt-bridge and van der Waals contacts. The N-and C-terminal regions of ASF1a and ASF1b determine the different affinities of these two proteins for HIRA, by contacting regions outside the HIRA B-domain. CAF-1 p60 also employs B-domain-like motifs for binding to ASF1a, thereby competing with HIRA. Together, these studies begin to define the molecular determinants of assembly of functionally diverse macromolecular histone chaperone complexes. KeywordsHistone Deposition; Chromatin Regulation; Histone Chaperones; ASF1; HIRA; CAF-1The basic repeating unit of eukaryotic chromatin is the core nucleosome. Each core nucleosome consists of a histone (H3/H4) 2 heterotetramer, two histone (H2A/H2B) heterodimers and about 147 base pairs of DNA. During chromatin assembly, histone chaperones donate histones to DNA 1 . In human cells, the deposition of the histone H3/H4 complex involves four histone chaperones, Chromatin Assembly Factor 1 (CAF-1), HIstone Regulatory Homolog A (HIRA), and two Anti-Silencing Factor paralogs (ASF1a and ASF1b).CAF-1, an evolutionarily conserved heterotrimeric chaperone comprised of p150, p60 and p48 subunits, mediates DNA synthesis-coupled chromatin assembly in S-phase 1,2 . CAF-1 is also 4 Correspondence should be addressed to R.M. or P.D. A., Ronen Marmorstein, Tel: (215) FAX: (215) marmor@wistar.org, Peter D. Adams, Tel: (215) FAX: (215) 728 3616, Peter.Adams@fccc.edu. 5 Y.T. and M.V.P contributed equally to this work.The coordinates of the ASF1a/HIRA complex structure has been deposited with the Protein Data Bank (PDB) with access code 2I32. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. AUTHOR CONTRIBUTIONSY.T. and M.V.P. designed and carried out experiments reported in the manuscript, and prepared manuscript figures and text; K.Z., M.G., A.C. and R.D. carried out preliminary studies that led to experiments reported in the manuscript; P.D.A and R.M. designed and supervised experiments and prepared manuscript text. All authors read and approved the submitted manuscript. NIH Public Access Author ManuscriptNat Struct Mol Biol. Author manuscript; available in PMC 2010 September 6. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript required for chromatin assembly coupled to DNA repair 3-8 , formation of specialized chromatin structures, such as transcriptionally silent chromatin at telomeres, rDNA yeast mating loci, and plant gene loci 3,...

Myogenic transcriptional activation of MyoD mediated by replication-independent histone deposition

“…Interestingly, the expression fate of two isotypes of Asf1 diverged during differentiation such that Asf1a persisted, similar to HIRA, while Asf1b decreased, similar to CAF1, consistent with their pairwise interaction (Fig. 1B) (1,27). Consistent with the expression pattern of HIRA, two mouse H3.3 genes, H3.3a and H3.3b, were continuously expressed as previously reported in chicken myogenesis (28), whereas canonical H3s (H3.1s and H3.2s) and other variant histones, macroH2A, H2A.X, H2A.Z, and CENP-A, were down-regulated after withdrawal from the cell cycle ( Fig.…”

Remodeling of chromatin structure in senescent cells and its potential impact on tumor suppression and aging

“…Regardless of the species, the Asf1 protein forms an elongated immunoglobulin-like β-sandwich fold, with three α-helices in the loops between the β-strands. Together, these studies indicate that HIRA and the histone H3/H4 heterodimer bind to distinct faces of the Asf1 polypeptide (126). HIRA binds to a shallow hydrophobic groove on ASF1a, perpendicular to the strands of the β-sandwich, and is anchored at one end of the groove by a cluster of salt bridge interactions.…”

“…Recently, several groups have described molecular structures of Asf1 proteins, either as free proteins or bound to histones, HIRA or fragments of either (32,39,84,126). Regardless of the species, the Asf1 protein forms an elongated immunoglobulin-like β-sandwich fold, with three α-helices in the loops between the β-strands.…”

ANTI-SILENCING FUNCTION1 Proteins Are Involved in Ultraviolet-Induced DNA Damage Repair and Are Cell Cycle Regulated by E2F Transcription Factors in Arabidopsis

“…In yeast and animals, ASF1 proteins play important roles in chromatin-related processes, such as transcription and DNA replication and repair. They participate both in the replication-dependent and the replication-independent chromatin assembly pathways, as ASF1 copurifies with the replication-specific histone H3.1 and with the transcription-specific HIS-TONE H3.3 and HIRA, respectively (Tyler et al, 1999;Myung et al, 2003;Adkins et al, 2004;Prado et al, 2004;Ramey et al, 2004;Tagami et al, 2004;Franco et al, 2005;Zhang et al, 2005;Tang et al, 2006). In Arabidopsis, there are two genes encoding ASF1 homologs, AtASF1A and AtASF1B (At1g66740 and At5g38110, respectively; Zhu et al, 2011).…”