Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome.

ABSTRACT: Chromatin three-dimensional (3D) structure plays critical roles in gene expression regulation by influencing locus interactions and accessibility of chromatin regions. Here we propose a Markov process model to derive a chromosomal equilibrium distribution of randomly-moving molecules as a functional consequence of spatially organized genome 3D structures. The model calculates steady-state distributions (SSD) from Hi-C data as quantitative measures of each chromatin region's dynamic accessibility for transcription factors and histone modification enzymes. Different from other Hi-C derived features such as compartment A/B and interaction hubs, or traditional methods measuring chromatin accessibility such as DNase-seq and FAIRE-seq, SSD considers both chromatin-chromatin and protein-chromatin

SUBMITTER: Wang Y 

PROVIDER: S-EPMC5449544 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature