Major Determinants of Nucleosome Organization

Abstract

The stereotypical nucleosome organization at the gene promoters, a nucleosome-free region (NFR) flanked by regularly spaced nucleosomes [1-5], is common among different species, e.g. yeast, fly, mouse, human. We study the major determinants of nucleosome organization in vivo, and the common principles that can explain the similarities in nucleosome distribution among different organisms. We show that in yeast, the DNA sequence alone is not able to generate either the proper NFRs, or the nucleosome phasing. Transcription, chromatin remodeling factors, and transcription factors play key roles in establishing the distribution of the nucleosomes [6-9]. We analyze the roles of remodelers Isw1, Isw2, Chd1 and RSC in chromatin organization. We find that in vivo, Isw2 and RSC are responsible for creating proper NFRs and positioning the neighboring nucleosomes at the correct locations, while Isw1 and Chd1 act on gene bodies to generate regular arrays of nucleosomes.