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Series GSE26803 Query DataSets for GSE26803
Status Public on Jun 15, 2011
Title Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (KD)
Organism Homo sapiens
Experiment type Other
Summary Modification of microRNA sequences by the 3' addition of nucleotides to generate so-called “isomiRs” adds to the complexity of miRNA function, with recent reports showing that 3' modifications can influence miRNA stability and efficiency of target repression. Here we show that the 3' modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation, and are seen across tissue types, disease states, and developmental stages. To quantitatively profile 3' nucleotide additions, we developed and validated a novel assay based on NanoString Technologies' nCounter platform. For certain miRNAs, the frequency of modification was altered by processes such as cell differentiation, indicating that 3' modification is a biologically regulated process. To investigate the mechanism of 3' nucleotide additions, we used RNA interference to screen a panel of eight candidate miRNA nucleotidyl transferases for 3' miRNA modification activity in human cells. Multiple enzymes, including PAPD1, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3' nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes–PAPD1, ZCCHC6 and TUT1–have not previously been known to modify miRNAs. Collectively, our results indicate that 3' modification observed in next generation small RNA sequencing data is a biologically relevant process, and identify enzymatic mechanisms that may lead to new approaches for modulating miRNA activity in vivo.
 
Overall design Total RNA was isolated from HCT-116 cells 48 hours post transfection with siRNAs targeting a panel of nucleotidyl transferases, and profiled with a version of the NanoString nCounter miRNA expression assay adapted to discriminate miRNA 3' variants. Four biological replicates of cells treated with the negative control siRNA directed against Cyclophilin B were profiled. Two biological replicates of cells treated individually with siRNAs targeting each of eight nucleotidyl transferases were profiled.
 
Contributor(s) Wyman SK
Citation(s) 21813625, 23874977
Submission date Jan 21, 2011
Last update date Sep 16, 2019
Contact name Muneesh Tewari
E-mail(s) mtewari@fhcrc.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Tewari
Street address 1100 Fairview Ave, N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL11642 NanoString nCounter miRNA expression platform
Samples (60)
GSM659308 HCT-116 siCyclophilin B replicate 1 variant 1 assay
GSM659309 HCT-116 siCyclophilin B replicate 1 variant 2 assay
GSM659310 HCT-116 siCyclophilin B replicate 1 canonical assay
This SubSeries is part of SuperSeries:
GSE26970 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity
Relations
BioProject PRJNA142025

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE26803_KD_raw_counts.txt.gz 9.0 Kb (ftp)(http) TXT
GSE26803_RAW.tar 420.0 Kb (http)(custom) TAR (of RCC)
Processed data included within Sample table
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