Abstract
Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing) and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP dependent chromatin remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the “ruler” that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element in the INO80 remodeler complex. More generally, we propose that a remodeler ruler regulates the nucleosome sliding direction in response to nucleosome environment. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine defined steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.
