Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.

ABSTRACT: Adapting a well-established formalism in polymer physics, we develop a minimalist approach to infer three-dimensional folding of chromatin from Hi-C data. The three-dimensional chromosome structures generated from our heterogeneous loop model (HLM) are used to visualize chromosome organizations that can substantiate the measurements from fluorescence in situ hybridization, chromatin interaction analysis by paired-end tag sequencing, and RNA-seq signals. We demonstrate the utility of the HLM with several case studies. Specifically, the HLM-generated chromosome structures, which reproduce the spatial distribution of topologically associated domains from fluorescence in situ hybridization measurement, show the phase segregation between two types of topologically associated domains explicitly.

SUBMITTER: Liu L 

PROVIDER: S-EPMC6697451 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature