De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.

ABSTRACT: Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We pr

SUBMITTER: Chen Y 

PROVIDER: S-EPMC4914103 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature