Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks.

ABSTRACT: Cellular identity relies on cell-type-specific gene expression controlled at the transcriptional level by cis-regulatory elements (CREs). CREs are unevenly distributed across the genome, giving rise to individual CREs and clusters of CREs (COREs). Technical and biological features hinder CORE identification. We addressed these issues by developing an unsupervised machine learning approach termed clustering of genomic regions analysis method (CREAM). CREAM automates CORE detection from chromatin accessibility profiles that are enriched in CREs strongly bound by master transcription regulators, proximal to highly expressed and essential genes, and discriminating cell identity. Although COREs share similarities with super-enhancers, we highlight differences in terms of the genomic dist

SUBMITTER: Madani Tonekaboni SA 

PROVIDER: S-EPMC6771399 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature