Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1.

Paul Victor Sauer,Christophe Velours,Daniel Panne,Elisabetta Boeri-Erba,Geneviève Almouzni,Norbert Mücke,Jennifer Timm,Jörg Langowski,Danni Liu,Françoise Ochsenbein,David Sitbon

doi:10.7554/elife.23474

Abstract

How the very first step in nucleosome assembly, deposition of histone H3-H4 as tetramers or dimers on DNA, is accomplished remains largely unclear. Here, we report that yeast chromatin assembly factor 1 (CAF1), a conserved histone chaperone complex that deposits H3-H4 during DNA replication, binds a single H3-H4 heterodimer in solution. We identify a new DNA-binding domain in the large Cac1 subunit of CAF1, which is required for high-affinity DNA binding by the CAF1 three-subunit complex, and which is distinct from the previously described C-terminal winged-helix domain. CAF1 binds preferentially to DNA molecules longer than 40 bp, and two CAF1-H3-H4 complexes concertedly associate with DNA molecules of this size, resulting in deposition of H3-H4 tetramers. While DNA binding is not essential for H3-H4 tetrasome deposition in vitro, it is required for efficient DNA synthesis-coupled nucleosome assembly. Mutant histones with impaired H3-H4 tetramerization interactions fail to release from CAF1, indicating that DNA deposition of H3-H4 tetramers by CAF1 requires a hierarchical cooperation between DNA binding, H3-H4 deposition and histone tetramerization.

Highlights

Nucleosomes in eukaryotic cells enable packaging of the DNA within the cell nucleus and provide an important layer in genome regulation
In agreement with recent negative stain electron microscopy data (Kim et al, 2016), we found that yeast CAF1 (yCAF1) forms an elongated heterotrimer containing a single copy of each subunit and that H3-H4 binds in a central position
As the isolated Cac1 subunit is able to interact with H3H4 (Liu et al, 2016), our data are in agreement with the model that Cac1 contributes substantially to H3-H4 binding while Cac2 and Cac3 provide accessory interactions

Summary

Introduction

Nucleosomes in eukaryotic cells enable packaging of the DNA within the cell nucleus and provide an important layer in genome regulation. They are composed of an octameric core of histones, around which 147 bp of DNA are wrapped (Luger et al, 1997). The majority of nucleosomes in chromatin contain two copies of each of the four major histones H2A, H2B, H3 and H4 that are assembled in a step-wise manner (Smith and Stillman, 1991). Nucleosome assembly is promoted via the action of histone chaperones, (De Koning et al, 2007; Gurard-Levin et al, 2014).

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