title: Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues.
abstract: Enhancers play a crucial role in gene regulation but the participation of enhancer transcripts (i.e. enhancer RNA, eRNAs) in regulatory systems remains unclear. We provide a computational analysis on eRNAs using genome-wide data across 12 mouse tissues. The expression of genes targeted by transcribing enhancer is positively correlated with eRNA expression and significantly higher than expression of genes targeted by non-transcribing enhancers. This result implies eRNA transcription indicates a state of enhancer that further increases gene expression. This state of enhancer is tissue-specific, as the same enhancer differentially transcribes eRNAs across tissues. Therefore, the presence of eRNAs describes a tissue-specific state of enhancer that is generally associated with higher expressed target genes, surmising as to whether eRNAs have gene activation potential. We further found a large number of eRNAs contain regions in which sequences and secondary structures are similar to microRNAs. Interestingly, an increasing number of recent studies hypothesize that microRNAs may switch from their general repressive role to an activating role when targeting promoter sequences. Collectively, our results provide speculation that eRNAs may be associated with the selective activation of enhancer target genes.
authors.affiliation: Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.
authors.forename: Jen-Hao
authors.initials: JH
authors.lastname: Cheng
authors.affiliation: Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.
authors.forename: David Zhi-Chao
authors.initials: DZ
authors.lastname: Pan
authors.affiliation: Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.
authors.forename: Zing Tsung-Yeh
authors.initials: ZT
authors.lastname: Tsai
authors.affiliation: Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.
authors.forename: Huai-Kuang
authors.initials: HK
authors.lastname: Tsai
mesh_terms: D000818:Animals; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012313:RNA / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D012313:RNA