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TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.
- Source :
-
RNA biology [RNA Biol] 2017 Feb; Vol. 14 (2), pp. 259-274. Date of Electronic Publication: 2016 Dec 16. - Publication Year :
- 2017
-
Abstract
- MicroRNAs are small non-coding RNAs acting as posttranscriptional repressors of gene expression. Identifying mRNA targets of a given miRNA remains an outstanding challenge in the field. We have developed a new experimental approach, TargetLink, that applied locked nucleic acid (LNA) as the affinity probe to enrich target genes of a specific microRNA in intact cells. TargetLink also consists a rigorous and systematic data analysis pipeline to identify target genes by comparing LNA-enriched sequences between experimental and control samples. Using miR-21 as a test microRNA, we identified 12 target genes of miR-21 in a human colorectal cancer cell by this approach. The majority of the identified targets interacted with miR-21 via imperfect seed pairing. Target validation confirmed that miR-21 repressed the expression of the identified targets. The cellular abundance of the identified miR-21 target transcripts varied over a wide range, with some targets expressed at a rather low level, confirming that both abundant and rare transcripts are susceptible to regulation by microRNAs, and that TargetLink is an efficient approach for identifying the target set of a specific microRNA in intact cells. C20orf111, one of the novel targets identified by TargetLink, was found to reside in the nuclear speckle and to be reliably repressed by miR-21 through the interaction at its coding sequence.
Details
- Language :
- English
- ISSN :
- 1555-8584
- Volume :
- 14
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- RNA biology
- Publication Type :
- Academic Journal
- Accession number :
- 27982722
- Full Text :
- https://doi.org/10.1080/15476286.2016.1270006