Deciphering hierarchical organization of topologically associated domains through change-point testing.

ABSTRACT:

Background

The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them.

Results

We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p

SUBMITTER: Xing H 

PROVIDER: S-EPMC8037919 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature