Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

摘要

Motivation: Understanding the mechanisms that govern nucleosome positioning over genomes in vivo is essential for unraveling the role of chromatin organization in transcriptional regulation. Until now, models for predicting genome-wide nucleosome occupancy have assumed that the DNA associations of neighboring nucleosomes on the genome are independent. We-present a new modelthat relaxes this independence assumption by Modeling interactions between adjacent nucleosomes. Results: We show 'that 'modeling interactions between adjacent nucleosomes improves genome-wide nucleosome occupancy predictions in an in vitro system that includes only nucleosomes and purified DNA, where the resulting model has a preference for short spacings (linkers) of less than 20 bp in length between neighboring nucleosomes. Since nucleosome occupancy' in vitro 'depends only on properties-intrinsic to nucleosomes, these results suggest that the interactions we find are intrinsic to nucleosomes and do not depend on other factors, such as transcription factors and chromatin remodelers. We also- show that modeling these intrinsic interactions significantly improves genome-wide predictions of nucleosome occupancy in vivo.