The DNA-encoded nucleosome organization of a eukaryotic genome

TLDR

Nucleosome organization, governed by chromatin remodelers, DNA‑binding proteins, and DNA sequence preferences, is essential for gene regulation but its relative contributions in vivo are difficult to disentangle. The study aims to quantify the influence of nucleosome DNA sequence preferences on genome‑wide nucleosome positioning. This was achieved by measuring nucleosome occupancy on purified yeast genomic DNA assembled in vitro and by performing a micrococcal nuclease–independent affinity assay on ~40,000 150‑bp oligonucleotides. The resulting intrinsic‑sequence‑based map closely matches in vivo nucleosome patterns, shows depletion at transcription factor sites and gene boundaries, and a computational model derived from the data predicts in vivo occupancy in *C.

Abstract

Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for approximately 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.