Knockout of miR-221 and miR-222 reveals overlapping and specific function between paralogous miRNAs

MicroRNAs (miRNAs) regulate the expression of mRNAs through sequence-specific binding into their 3' untranslated region (UTR). The seed sequence of miRNAs is the key determinant to recognize the target sites. The paralogous miRNAs, which share the same seed sequences but differ in their 3' parts, are known to regulate largely overlapping group of miRNAs. However, there is still no study which analyzes the functional difference among paralogous miRNAs. In this study, we compared the function between paralogous miRNAs, miR-221 and miR-222. By employing nuclease-mediated genome engineering technique, we established the knockout cell lines for these miRNAs, and analyzed their difference in target regulation precisely. We found that miR-221 and miR-222 suppress the previously identified targets, CDKN1B and CDKN1C, differentially. From the transcriptome analyses, we also found that large number of different transcripts with independent functions respond exclusively only to each of miR-221 and miR-222, respectively. Therefore, the miRNAs with common seed sequences can exert dissimilar function by regulating different groups of target mRNAs. This study illustrates that more researches are required to establish the rules of target site recognition by miRNAs. Overall design: The mRNAs from each of four different cell lines (WT, 221KO, 222KO, DKO) were applied for RNA-seq.

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Jeong G, Lim YH, Kim NJ, Wee G, Kim YK