期刊
INTERNATIONAL JOURNAL OF CANCER
卷 147, 期 8, 页码 2210-2224出版社
WILEY
DOI: 10.1002/ijc.33132
关键词
enhancer RNA; eRNA pipeline; sORF; transcription factor
类别
资金
- National Undergraduate Training Programs for Innovation [201810304026Z, 201710304030Z]
- Postgraduate Research & Practice Innovation Program of Government of Jiangsu Province [KYCX17_1933]
- Jiangsu University Natural Science Research Project [17KJB310012]
- Distinguished Professorship Program of Government of Jiangsu Province
- National Natural Science Foundation of China [30801350, 81600386, 81641164, 31770935]
Enhancer can transcribe RNAs, however, most of them were neglected in traditional RNA-seq analysis workflow. Here, we developed a Pipeline for Enhancer Transcription (PET, ) for quantifying enhancer RNAs (eRNAs) from RNA-seq. By applying this pipeline on lung cancer samples and cell lines, we showed that the transcribed enhancers are enriched with histone marks and transcription factor motifs (JUNB, Hand1-Tcf3 and GATA4). By training a machine learning model, we demonstrate that enhancers can predict prognosis better than their nearby genes. Integrating the Hi-C, ChIP-seq and RNA-seq data, we observe that transcribed enhancers associate with cancer hallmarks or oncogenes, among which LcsMYC-1 (Lung cancer-specific MYC eRNA-1) potentially supports MYC expression. Surprisingly, a significant proportion of transcribed enhancers contain small protein-coding open reading frames (sORFs) and can be translated into microproteins. Our study provides a computational method for eRNA quantification and deepens our understandings of the DNA, RNA and protein nature of enhancers.
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