Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories.

ABSTRACT: Most studies of genome organization have focused on intra-chromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Inter-chromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework to identify sets of loci that jointly interact in trans from Hi-C data. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum

SUBMITTER: Hristov BH 

PROVIDER: S-EPMC10542540 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature