Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

ABSTRACT: Discriminating the gene target of a distal regulatory element from other nearby transcribed genes is a challenging problem with the potential to illuminate the causal underpinnings of complex diseases. We present TargetFinder, a computational method that reconstructs regulatory landscapes from diverse features along the genome. The resulting models accurately predict individual enhancer-promoter interactions across multiple cell lines with a false discovery rate up to 15 times smaller than that obtained using the closest gene. By evaluating the genomic features driving this accuracy, we uncover interactions between structural proteins, transcription factors, epigenetic modifications, and transcription that together distinguish interacting from non-interacting enhancer-promoter pairs. Most

SUBMITTER: Whalen S 

PROVIDER: S-EPMC4910881 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature