CCIP: predicting CTCF-mediated chromatin loops with transitivity.

ABSTRACT:

Motivation

CTCF-mediated chromatin loops underlie the formation of topological associating domains and serve as the structural basis for transcriptional regulation. However, the formation mechanism of these loops remains unclear, and the genome-wide mapping of these loops is costly and difficult. Motivated by the recent studies on the formation mechanism of CTCF-mediated loops, we studied the possibility of making use of transitivity-related information of interacting CTCF anchors to predict CTCF loops computationally. In this context, transitivity arises when two CTCF anchors interact with the same third anchor by the loop extrusion mechanism and bring themselves close to each other spatially to form an indirect loop.

Results

To determine whether transitivity is informative

SUBMITTER: Wang W 

PROVIDER: S-EPMC8665748 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature