Return to search

Systematic comparison of gene regulatory datasets using experimentally validated enhancers

Promoter-enhancer interactions are essential for gene regulating, Capture Hi-C is a chromosome conformation capture method to map promoter-enhancer interactions at high resolution. We have Capture Hi-C data forGM12878 cells, immortalized primary B lymphocytes, in three replicates. Although Capture Hi-C maps enhancer elements together with the promoters they regulate, the overlap between enhancer datasets produced by other methods such as ChIP-seq and Capture Hi-C is lower than expected. In order to understand the reasons for lower overlap, we investigated the enhancer potential of replicated and non-replicated Capture Hi-C interactors, as well as enhancer overlapping and non-overlapping Capture Hi-C interactors. We performed a systematic comparison between our interactor and experimental regulatory and transcriptomic datasets to determine the extent of enhancer mapping. The results show replicated interactors have higher enhancer potential than non-replicated ones. However, there is evidence that interactors not overlapping with experimental validated regulatory datasets can also potentially be true enhancers.

Identiferoai:union.ndltd.org:UPSALLA1/oai:DiVA.org:kth-281957
Date January 2020
CreatorsDong, Xue
PublisherKTH, Skolan för kemi, bioteknologi och hälsa (CBH)
Source SetsDiVA Archive at Upsalla University
LanguageEnglish
Detected LanguageEnglish
TypeStudent thesis, info:eu-repo/semantics/bachelorThesis, text
Formatapplication/pdf
Rightsinfo:eu-repo/semantics/openAccess
RelationTRITA-CBH-GRU ; 2020:256

Page generated in 0.0015 seconds