Naturally existing isoforms of miR-222 have distinct functions

Deep-sequencing reveals extensive variation in the sequence of endogenously expressed microRNAs (termed 'isomiRs') in human cell lines and tissues, especially in relation to the 3' end. From the immunoprecipitation of the microRNA-binding protein Argonaute and the sequencing of associ...

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Bibliographic Details
Published in:Nucleic acids research 2017-11, Vol.45 (19), p.11371-11385
Main Authors: Yu, Feng, Pillman, Katherine A, Neilsen, Corine T, Toubia, John, Lawrence, David M, Tsykin, Anna, Gantier, Michael P, Callen, David F, Goodall, Gregory J, Bracken, Cameron P
Format: Article
Language:English
Subjects:
Apoptosis - genetics
Cell Line
Cell Line, Tumor
Cell Proliferation - genetics
Gene Expression Regulation
Humans
Immunoblotting
MCF-7 Cells
MicroRNAs - genetics
Phosphatidylinositol 3-Kinases - genetics
Phosphatidylinositol 3-Kinases - metabolism
Proto-Oncogene Proteins c-akt - genetics
Proto-Oncogene Proteins c-akt - metabolism
Reverse Transcriptase Polymerase Chain Reaction
RNA and RNA-protein complexes
RNA Isoforms - genetics
Signal Transduction - genetics
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Summary:Deep-sequencing reveals extensive variation in the sequence of endogenously expressed microRNAs (termed 'isomiRs') in human cell lines and tissues, especially in relation to the 3' end. From the immunoprecipitation of the microRNA-binding protein Argonaute and the sequencing of associated small RNAs, we observe extensive 3'-isomiR variation, including for miR-222 where the majority of endogenously expressed miR-222 is extended by 1-5 nt compared to the canonical sequence. We demonstrate this 3' heterogeneity has dramatic implications for the phenotype of miR-222 transfected cells, with longer isoforms promoting apoptosis in a size (but not 3' sequence)-dependent manner. The transfection of longer miR-222 isomiRs did not induce an interferon response, but did downregulate the expression of many components of the pro-survival PI3K-AKT pathway including PIK3R3, a regulatory subunit whose knockdown phenocopied the expression of longer 222 isoforms in terms of apoptosis and the inhibition of other PI3K-AKT genes. As this work demonstrates the capacity for 3' isomiRs to mediate differential functions, we contend more attention needs to be given to 3' variance given the prevalence of this class of isomiR.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx788