Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci.

ABSTRACT: BACKGROUND:Chromatin 3D conformation plays important roles in regulating gene or protein functions. High-throughout chromosome conformation capture (3C)-based technologies, such as Hi-C, have been exploited to acquire the contact frequencies among genomic loci at genome-scale. Various computational tools have been proposed to recover the underlying chromatin 3D structures from in situ Hi-C contact map data. As connected residuals in a polymer, neighboring genomic loci have intrinsic mutual dependencies in building a 3D conformation. However, current methods seldom take this feature into account. RESULTS:We present a method called ShNeigh, which combines the classical MDS technique with local dependence of neighboring loci modeled by a Gaussian formula, to infer the best 3D structure from n

SUBMITTER: Li FZ 

PROVIDER: S-EPMC7329537 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature