Knockout of miR-221 and miR-222 reveals common and specific targets for paralogous miRNAs

Abstract

MicroRNAs (miRNAs) regulate the expression of mRNA through sequence-specific binding of the 3 0 untranslated region (UTR). The seed sequence of miRNAs is the key determinant for target site recognition. Paralogous miRNAs, which share the same seed sequences but differ in their 3 0 regions, are known to regulate largely overlapping groups of mRNAs. However, no study has analyzed functional differences between paralogous miRNAs with proper experimental methods. In this study, we compared the targets of paralogous miRNAs, miR-221 and miR-222. Using a nuclease-mediated genome engineering technique, we established knockout cell lines for these miRNAs, and precisely analyzed differences in target regulation. We found that miR-221 and miR-222 suppress the previously identified targets, CDKN1B and CDKN1C, differentially. Whereas both miRNAs suppressed CDKN1B, only miR-221 suppressed CDKN1C. From transcriptome analyses, we found that several different target mRNAs were regulated by each of miR-221 and miR-222 independently, although a large number of mRNAs responded commonly to miR-221 and miR-222. This is the first study to compare the mRNA regulations by paralogous miRNAs and illustrate that paralogous miRNAs with the same seed sequence also have difference in target regulation.

miR‐221‐3p inhibits oxidized low‐density lipoprotein induced oxidative stress and apoptosis via targeting a disintegrin and metalloprotease‐22

“…The expression of ADAM22 detected by qRT-PCR in macrophages after ADAM22 siRNA transfection. [39][40][41] This finding highly agrees with our results in this study, because cancer cells generally escape programmed cell death, causing accumulated DNA damage and abolished apoptosis. C, Quantification of the oil red intensity in (B), ***P represents a significant difference compared with the ox-LDL.…”

“…C, Quantification of the oil red intensity in (B), ***P represents a significant difference compared with the ox-LDL. 21,[44][45][46][47] A recent study conducted by Jeong et al 40 has suggested common and exclusive targets for miR-221 and miR-222 using nuclease-mediated knockout cell line. *P < 0.05 vs the ox-LDL.…”

Identification of microRNA that represses IRS-1 expression in liver

“…Furthermore, it has been reported that these two miRNAs have similar functions and expression patterns [ 29 , 30 ]. However, miRNAs with the same seed sequences do not always regulate the same target genes [ 31 ]. Further examination is needed to demonstrate the role of miR-221 in future experiments.…”

MiR-146a wild-type 3’ sequence identity is dispensable for proper innate immune function in vivo

“…A functional role for 3' pairing has also recently been corroborated in vitro in mammalian cells and in vivo in C. elegans (Broughton et al 2016;Jeong et al 2017;Zhang et al 2015). The collective implication of these studies is that the 3' region of a given miRNA may confer an important but as-yet-undefined role in determining the target spectrum (and thus function) of the miRNA.…”