Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data.

ABSTRACT: Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene-gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique. A novel parameterized objective function was designed for modeling chromosome structures, which was optimized by a gradient descent method to generate chromosomal structural models that could satisfy as many intra-chromosomal contacts as

SUBMITTER: Trieu T 

PROVIDER: S-EPMC3985632 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature