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Series GSE77989 Query DataSets for GSE77989
Status Public on Mar 17, 2016
Title Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Exportin 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells while we detected a few DROSHA-independent miRNAs including three previously unidentified noncanonical miRNAs (miR-7706, miR-3615, and miR-1254). In contrast to DROSHA knockout, many canonical miRNAs were still detected without DICER albeit at markedly reduced levels. In the absence of DICER, pre-miRNAs are loaded directly onto AGO and trimmed at the 3′ end, yielding miRNAs from the 5′ strand (5p miRNAs). Interestingly, in XPO5 knockout cells, most miRNAs are affected only modestly, suggesting that XPO5 is necessary but not critical for miRNA maturation. Our study demonstrates an essential role of DROSHA and an important contribution of DICER in the canonical miRNA pathway, and reveals that the function of XPO5 can be complemented by alternative mechanisms. Thus, this study allows us to understand differential contributions of key biogenesis factors, and provides with valuable resources for miRNA research.
Overall design Two independent sequencing experiments (set 1 and set 2, respectively) were performed using 9 samples.
Contributor(s) Kim Y, Kim N
Citation(s) 26976605
Submission date Feb 17, 2016
Last update date May 15, 2019
Contact name Young-Kook Kim
Organization name Chonnam National University Medical School
Department Department of Biochemistry
Street address 264, Seoyang-ro
City Hwasun, Jeollanam-do
ZIP/Postal code 58128
Country South Korea
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (9)
GSM2064270 Parental cells (set 1) replicate 1
GSM2064271 Parental cells (set 1) replicate 2
GSM2064272 DROSHA KO #40 (set 1) replicate 1
BioProject PRJNA312310
SRA SRP070429

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Supplementary file Size Download File type/resource
GSE77989_RAW.tar 40.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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