An integrative analysis of nucleosome occupancy and positioning using diverse sequence dependent properties

Nucleosome organization dictates eukaryotic DNA compaction and access, and plays a critical regulatory role in various eukaryotic genomic functions. It is well known that DNA sequence dependent histone octamer binding is important for nucleosome formation. However, many aspects of the phenomenon remain elusive. Here, we systematically analyze diverse sequence-dependent properties, consisting of multi-scale sequence compositional properties and twelve structural properties on the entire Saccharomyces cerevisiae genome. Based on comparative correlation analysis, the features that are highly correlated with nucleosome formation are identified and are integrated into a multilayer perceptron model for genome-wide nucleosome occupancy prediction. Furthermore, we predict nucleosome positions along genome based on the integrative profile of these properties. The results indicate the substantial effect on nucleosome formation and positioning along the entire genome.