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Genomics. 2014 Aug;104(2):70-8. doi: 10.1016/j.ygeno.2014.07.003. Epub 2014 Jul 23.

Integrating epigenetic marks for identification of transcriptionally active miRNAs.

Author information

1
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
2
Department of Neurology, The Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150086, China.
3
Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China; Key Laboratory of Medical Genetics, Harbin Medical University, Heilongjiang Higher Education Institutions, Harbin 150081, China.
4
Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China; Key Laboratory of Medical Genetics, Harbin Medical University, Heilongjiang Higher Education Institutions, Harbin 150081, China. Electronic address: JY8085@yahoo.com.cn.
5
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. Electronic address: lixia@hrbmu.edu.cn.

Abstract

MicroRNAs have been identified as important regulators involved in biological processes and human diseases. We proposed a computational approach to systematic identification of active promoters of miRNAs by active models using epigenetic characteristics at active promoters of protein-coding genes together with a genomic context-based filtering step in nine human cell types, which were validated to exhibit greater conservation, more overlap with CAGE-identified TSSs, more conserved TFBSs and higher transcription factor binding signal intensities. Furthermore, expression analysis showed discordance between transcriptional activation of miRNAs and expression of their precursor and mature forms, indicating that precursor and mature miRNA expression is insufficient to account for transcriptional activation of miRNAs. Compared to other methods, our approach identified higher percentages of active miRNAs with CAGE-detected TSS activity and primary transcript expression, further supporting the validity of our approach, which will be valuable to understand the biological roles of miRNAs in specific cell contexts.

KEYWORDS:

Epigenetic; Promoter; Transcriptionally active; miRNA

PMID:
25063529
DOI:
10.1016/j.ygeno.2014.07.003
[Indexed for MEDLINE]
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