Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles.

ABSTRACT: Nucleosomal profiling is an effective method to determine the positioning and occupancy of nucleosomes, which is essential to understand their roles in genomic processes. However, the positional randomness across the genome and its relationship with nucleosome occupancy remains poorly understood. Here we present a computational method that segments the profile into nucleosomal domains and quantifies their randomness and relative occupancy level. Applying this method to published data, we find on average ~ 3-fold differences in the degree of positional randomness between regions typically considered "well-ordered", as well as an unexpected predominance of only two types of domains of positional randomness in yeast cells. Further, we find that occupancy levels between domains actually differ

SUBMITTER: Wang Y 

PROVIDER: S-EPMC7990035 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature