期刊
GENOME RESEARCH
卷 21, 期 9, 页码 1450-1461出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.118059.110
关键词
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资金
- Chromosome Metabolism Training Grant [5 T32 CA09657-16]
- Rosetta Inpharmatics Fellowship in Molecular Profiling
- American Cancer Society/Canary Foundation
- National Institute of General Medical Sciences [T32 GM07270]
- Jaconnette L. Tietze Young Scientist Award
- Prostate Cancer Foundation Creativity Award
- National Institutes of Health [DK-085714]
- Damon Runyon-Rachleff Innovation Award
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 MTPAP, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3' nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes-MTPAP, 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.
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