Thermosensitive Nucleosome Editing Reveals the Role of DNA Sequence in Targeted Histone Variant Deposition

Abstract

Summary: In preparation for transcription, the chromatin remodeler SWR installs homotypic ZZ nucleosomes at promoters by replacing the two nucleosomal H2A with H2A.Z in a stepwise manner. Nucleosome-free regions (NFRs) help recruit SWR to promoters; this is thought to position SWR asymmetrically on one side of the +1 nucleosome. How SWR accesses the opposite side of +1 to generate a ZZ nucleosome remains unclear. Using biochemical assays that monitor the sub-nucleosomal position of nascent H2A.Z, we find that NFR-recruited SWR switches sides to insert H2A.Z into asymmetrically positioned nucleosomes; however, at decreasing temperatures, H2A.Z insertion becomes progressively biased for one side. We find that a 16-bp element containing G/C runs (>3 consecutive G or C nucleotides) is sufficient to promote H2A.Z insertion. Because H2A.Z-rich +1 nucleosomes in yeast have more G/C runs, we propose that nucleosome editing is a thermosensitive process that can be hard coded by the genome. : The SWR remodeler edits promoter-proximal +1 nucleosomes by sequentially replacing the two copies of histone H2A with H2A.Z. Sun et al. show that temperature and DNA sequence strongly influence on which side of the nucleosome SWR inserts H2A.Z first, thereby affecting the remodeling outcome. Keywords: SWR1, H2A.Z, NFR, yeast, nucleosome, temperature, histone exchange, chromatin remodeling