A systematic study of motif pairs that may facilitate enhancer–promoter interactions

Journal of Integrative Bioinformatics

Li Xiaoman¹  Wang Saidi²  Hu Haiyan² 

[1] Burnett school of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, 32816, USA;Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA;

关键词: enhancer–promoter interactions;    enhancers;    motif pairs;    promoters;    transcription factors;   

DOI  :  10.1515/jib-2021-0038

来源: DOAJ

【 摘 要 】

Pairs of interacting transcription factors (TFs) have previously been shown to bind to enhancers and promoters and contribute to their physical interactions. However, to date, we have limited knowledge about such TF pairs. To fill this void, we systematically studied the co-occurrence of TF-binding motifs in interacting enhancer–promoter (EP) pairs in seven human cell lines. We discovered 423 motif pairs that significantly co-occur in enhancers and promoters of interacting EP pairs. We demonstrated that these motif pairs are biologically meaningful and significantly enriched with motif pairs of known interacting TF pairs. We also showed that the identified motif pairs facilitated the discovery of the interacting EP pairs. The developed pipeline, EPmotifPair, together with the predicted motifs and motif pairs, is available at https://doi.org/10.6084/m9.figshare.14192000. Our study provides a comprehensive list of motif pairs that may contribute to EP physical interactions, which facilitate generating meaningful hypotheses for experimental validation.

【 授权许可】

Unknown