Identification of cell states using super-enhancer RNA

BMC Genomics

卷:22

Research

Yueh-Hua Tu¹  Hsueh-Fen Juan²  Hsuan-Cheng Huang³ 

[1] Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, 106, Taipei, Taiwan;Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, 115, Taipei, Taiwan;Institute of Biomedical Informatics, National Yang-Ming University, 112, Taipei, Taiwan;

[2] Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, 106, Taipei, Taiwan;Department of Life Science, Center for Computational and Systems Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, 106, Taipei, Taiwan;

[3] Institute of Biomedical Informatics, National Yang-Ming University, 112, Taipei, Taiwan;Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong Street, 112, Taipei, Taiwan;

关键词: Super enhancer;    Enhancer RNA;    Super-enhancer RNA;    Cell state;    FANTOM5;   

DOI  :  10.1186/s12864-021-08092-1

 received in 2021-10-14, accepted in 2021-10-15,  发布年份 2021

来源: Springer

【 摘 要 】

BackgroundA new class of regulatory elements called super-enhancers, comprised of multiple neighboring enhancers, have recently been reported to be the key transcriptional drivers of cellular, developmental, and disease states.ResultsHere, we defined super-enhancer RNAs as highly expressed enhancer RNAs that are transcribed from a cluster of localized genomic regions. Using the cap analysis of gene expression sequencing data from FANTOM5, we systematically explored the enhancer and messenger RNA landscapes in hundreds of different cell types in response to various environments. Applying non-negative matrix factorization (NMF) to super-enhancer RNA profiles, we found that different cell types were well classified. In addition, through the NMF of individual time-course profiles from a single cell-type, super-enhancer RNAs were clustered into several states with progressive patterns. We further investigated the enriched biological functions of the proximal genes involved in each pattern, and found that they were associated with the corresponding developmental process.ConclusionsThe proposed super-enhancer RNAs can act as a good alternative, without the complicated measurement of histone modifications, for identifying important regulatory elements of cell type specification and identifying dynamic cell states.

【 授权许可】

CC BY   
© The Author(s) 2021

【 图 表 】

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