Yeast CAF-1 assembles histone (H3-H4)2 tetramers prior to DNA deposition

• Published in: Nucleic acids research Vol. 40; no. 20; pp. 10139 - 10149
• Main Authors: Winkler, Duane D, Zhou, Hui, Dar, Mohd A, Zhang, Zhiguo, Luger, Karolin
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.11.2012
• Subjects: Acetylation; Animals; Chromatin Assembly Factor-1 - metabolism; DNA - metabolism; Fungal Proteins - metabolism; Gene Regulation, Chromatin and Epigenetics; Histones - genetics; Histones - metabolism; Protein Binding; Protein Multimerization; Sequence Deletion; Thermodynamics; Xenopus laevis; Yeasts - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gks812

Following acetylation, newly synthesized H3-H4 is directly transferred from the histone chaperone anti-silencing factor 1 (Asf1) to chromatin assembly factor 1 (CAF-1), another histone chaperone that is critical for the deposition of H3-H4 onto replicating DNA. However, it is unknown how CAF-1 binds and delivers H3-H4 to the DNA. Here, we show that CAF-1 binds recombinant H3-H4 with 10- to 20-fold higher affinity than H2A-H2B in vitro, and H3K56Ac increases the binding affinity of CAF-1 toward H3-H4 2-fold. These results provide a quantitative thermodynamic explanation for the specific H3-H4 histone chaperone activity of CAF-1. Surprisingly, H3-H4 exists as a dimer rather than as a canonical tetramer at mid-to-low nanomolar concentrations. A single CAF-1 molecule binds a cross-linked (H3-H4)2 tetramer, or two H3-H4 dimers that contain mutations at the (H3-H4)2 tetramerization interface. These results suggest that CAF-1 binds to two H3-H4 dimers in a manner that promotes formation of a (H3-H4)2 tetramer. Consistent with this idea, we confirm that CAF-1 synchronously binds two H3-H4 dimers derived from two different histone genes in vivo. Together, the data illustrate a clear mechanism for CAF-1-associated H3-H4 chaperone activity in the context of de novo nucleosome (re)assembly following DNA replication.