Analysis of functional linkages between nucleosome dynamics and trans-regulatory factors

摘要

Intergenic regions are far from stable owing to the trans-regulatory factors that regulate chromatin structure. Nucleosome organization at promoter has been shown to exhibit distinct patterns corresponding to gene expression levels. In regulatory processes, such trans-factors as post-translational modifications (PTMs) and transcriptional regulators are presumably related to the establishment of such nucleosome dynamics. However, their concrete relationships, especially in gene regulation, remain elusive. We, therefore, sought to understand the functional linkages among these factors (8 PTMs and 15 transcriptional regulators) and nucleosome dynamics in S.cerevisiae by deriving a Bayesian network (BN)-based model representing their interactions. Our recovered network shows consistency with reports in literature as well as gives some new insights, such as the linkages of H3 methylation, transcriptional regulators and nucleosome dynamics in pre-initiation complex (PIC) assembly/disassembly, gene repression, and postinitia-tion regulation. The results also hint that nucleosome organization at promoter is intentionally volatile in various regulatory pathways and that trans-factors take part in regulating nucleosome dynamics.