Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data.

ABSTRACT: Conformation capture technologies measure frequencies of interactions between chromatin regions. However, understanding gene-regulation require knowledge of detailed spatial structures of heterogeneous chromatin in cells. Here we describe the nC-SAC (n-Constrained-Self Avoiding Chromatin) method that transforms experimental interaction frequencies into 3D ensembles of chromatin chains. nC-SAC first distinguishes specific from non-specific interaction frequencies, then generates 3D chromatin ensembles using identified specific interactions as spatial constraints. Application to α-globin locus shows that these constraints (∼20%) drive the formation of ∼99% all experimentally captured interactions, in which ∼30% additional to the imposed constraints is found to be specific. Many novel specifi

SUBMITTER: Gursoy G 

PROVIDER: S-EPMC5714131 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature