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BMC Genomics. 2016 Nov 11;17(1):908.

Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells.

Jeong G1,2, Lim YH1,2, Kim YK3,4.

Author information

1
Department of Biochemistry, Chonnam National University Medical School, Gwangju, Korea.
2
Center for Creative Biomedical Scientists, Chonnam National University Medical School, Gwangju, Korea.
3
Department of Biochemistry, Chonnam National University Medical School, Gwangju, Korea. ykk@jnu.ac.kr.
4
Center for Creative Biomedical Scientists, Chonnam National University Medical School, Gwangju, Korea. ykk@jnu.ac.kr.

Abstract

BACKGROUND:

The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs.

RESULTS:

In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5' end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns.

CONCLUSIONS:

The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs.

KEYWORDS:

DROSHA; Knockout; MicroRNA; Promoter; Transcription start site

PMID:
27835943
PMCID:
PMC5106785
DOI:
10.1186/s12864-016-3252-7
[Indexed for MEDLINE]
Free PMC Article

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