A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants.

ABSTRACT: The principles that govern the organization of genomes, which are needed for an understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known. Recently, single-cell imaging techniques have been developed to determine the 3D coordinates of genomic loci in vivo. Here, we introduce a computational method (Distance Matrix to Ensemble of Structures, DIMES), based on the maximum entropy principle, with experimental pairwise distances between loci as constraints, to generate a unique ensemble of 3D chromatin structures. Using the ensemble of structures, we quantitatively account for the distribution of pairwise distances, three-body co-localization, and higher-order interactions. The DIMES method can be appli

SUBMITTER: Shi G 

PROVIDER: S-EPMC9974990 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature