Predicting CTCF-mediated chromatin loops using CTCF-MP.

ABSTRACT:

Motivation

The three dimensional organization of chromosomes within the cell nucleus is highly regulated. It is known that CCCTC-binding factor (CTCF) is an important architectural protein to mediate long-range chromatin loops. Recent studies have shown that the majority of CTCF binding motif pairs at chromatin loop anchor regions are in convergent orientation. However, it remains unknown whether the genomic context at the sequence level can determine if a convergent CTCF motif pair is able to form a chromatin loop.

Results

In this article, we directly ask whether and what sequence-based features (other than the motif itself) may be important to establish CTCF-mediated chromatin loops. We found that motif conservation measured by 'branch-of-origin' that accounts for motif tu

SUBMITTER: Zhang R 

PROVIDER: S-EPMC6022626 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature