Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1

Abstract

Eukaryotic chromatin is a highly dynamic structure with essential roles in virtually all DNA-dependent cellular processes. Nucleosomes are a barrier to DNA access, and during DNA replication, they are disassembled ahead of the replication machinery (the replisome) and reassembled following its passage. The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3–H4 directly onto newly synthesized DNA. Therefore, CAF-1 is important for the establishment and propagation of chromatin structure. The molecular mechanism by which CAF-1 mediates H3–H4 deposition has remained unclear. However, recent studies have revealed new insights into the architecture and stoichiometry of the trimeric CAF-1 complex and how it interacts with and deposits H3–H4 onto substrate DNA. The CAF-1 trimer binds to a single H3–H4 dimer, which induces a conformational rearrangement in CAF-1 promoting its interaction with substrate DNA. Two CAF-1•H3–H4 complexes co-associate on nucleosome-free DNA depositing (H3–H4)2 tetramers in the first step of nucleosome assembly. Here, we review the progress made in our understanding of CAF-1 structure, mechanism of action, and how CAF-1 contributes to chromatin dynamics during DNA replication.

Key histone chaperones have distinct roles in replisome progression and genomic stability

“…2D). These results highlight the importance of Cac1 for replisome and G2/M progression and are in good agreement with a previous study showing that Cac1 is essential for the Caf1 protein complex assembly and H3/H4 binding [13,26].Previous studies have revealed the contribution of the Caf1 subunits for H3/H4 assembly and nucleosome deposition under DNA stress conditions [30][31][32]. To further investigate the effect of cac2-or cac3-deletion on DNA replication under these conditions, we incubated the Caf1 mutant strains with 20 mM HU and measured their replication times as described above.…”

“…Histone chaperones are essential for the process of DNA replication-coupled (RC) nucleosome deposition by facilitating correct histone assembly, post-translational modifications and localization during DNA replication [5][6][7][8].Newly synthesized histones are assembled into nucleosomes by several histone chaperones including Asf1, Rtt109, Rtt106, Caf1 and the FACT complex that act in a sequential and coordinated manner to facilitate nucleosome deposition during DNA replication [5,[9][10][11]. In budding yeast, Asf1 binds newly synthesized H3-H4 histones and promotes H3K56 acetylation by Rtt109 [12].Acetylation of H3K56 enhances H3-H4 binding to Caf1 and Rtt106 that deposit (H3/H4) 2 tetramers directly onto the DNA [13][14][15]. Previous studies have shown that single-or double-mutations of histone chaperone genes including Caf1 subunits, RTT106, ASF1 or RTT109 can lead to severe replication stress, checkpoint activation, increased recombination and sensitivity to DNA damaging agents [14,16,17].…”

“…However, the effect of histone chaperone mutations on the rate of replisome progression is much less understood. While studies in human cells have shown that mutations in genes essential for the synthesis of histones significantly slowdown replisome progression [18], studies in yeast show that mutations in histone chaperones can have little effect on S-phase progression [14,17,[19][20][21].One of the most important and extensively studied histone chaperone complex for RC nucleosome deposition both in vitro and in cells is the Caf1 complex [13]. Caf1 is composed of three subunits, Cac1, Cac2 and Cac3, which are highly conserved from yeast to human [22].…”

PCNA ubiquitination protects stalled replication forks from DNA2-mediated degradation by regulating Okazaki fragment maturation and chromatin assembly

“…Concomitant with DNA replication, PCNA also controls chromatinization of the newly synthesized DNA by recruiting the chromatin assembly factor CAF-1 and other histone chaperone complexes (Alabert et al, 2017;Sauer et al, 2018). In general, these interactions are mediated by a conserved motif termed PCNA-interacting peptide (PIP)box present on most PCNA binding partners (Choe and Moldovan, 2017;Mailand et al, 2013).…”

JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability

“…tNASP, Hsp90, Hsc70, and histone H4 elute in these fractions. Another complex composed of sNASP, HAT1, H3 and H4 elutes with a molecular weight of about 100 kDa (fractions [30][31][32]. Remarkably, in siJMJD1B derived cytosolic extracts, the complex composed of tNASP, Hsp90, Hsc70, histones H3 and H4 is shifted to a heavier molecular size fraction, comprising fractions 22-24, of about 600 kDa (Fig.…”