Long noncoding RNA complementarity and target transcripts abundance

Eukaryotic mRNA metabolism regulates its stability, localization, and translation using complementarity with counter-part RNAs. To modulate their stability, small and long noncoding RNAs can establish complementarity with their target mRNAs. Although complementarity of small interfering RNAs and microRNAs with target mRNAs has been studied thoroughly, partial complementarity of long noncoding RNAs (lncRNAs) with their target mRNAs has not been investigated clearly.

To address that research gap, researchers from the Medical University of South Carolina investigated whether the sequence complementarity of two lncRNAs, lincRNA-p21 and OIP5-AS1, influenced the quantity of target RNA expression. They predicted a positive correlation between lncRNA complementarity and target mRNA quantity. They confirmed this prediction using RNA affinity pull down, microarray, and RNA-sequencing analysis. In addition, the researchers utilized the information from this analysis to compare the quantity of target mRNAs when two lncRNAs, lincRNA-p21 and OIP5-AS1, are depleted by siRNAs. They observed that human and mouse lincRNA-p21 regulated target mRNA abundance in complementarity-dependent and independent manners. In contrast, affinity pull down of OIP5-AS1 revealed that changes in OIP5-AS1 expression influenced the amount of some OIP5-AS1 target mRNAs and miRNAs, as they predicted from our sequence complementarity assay. Altogether, the current study demonstrates that partial complementarity of lncRNAs and mRNAs (even miRNAs) assist in determining target RNA expression and quantity.

Mouse lincRNA-p21 is associated a subset of mRNA


(a) Schematic of target mRNAs containing partial complementarity with mouse lincRNA-p21. (b) Schematic of affinity pull down using MS2 aptamer for mouse lincRNA-p21 enrichment. (c) List of representative mRNAs enriched in mouse lincRNA-p21 pull down and cDNA microarray from mouse embryonic fibroblasts. (d) Existence of RNA-RNA interaction was validated by MS2 pulldown and UV crosslinking followed by qPCR analysis. *p < 0.05 (student’s t-test), compared with control condition.

Zealy RW, Fomin M, Davila S, Makowsky D, Thigpen H, McDowell CH, Cummings JC, Lee ES, Kwon SH, Min KW, Yoon JH. (2018) Long noncoding RNA complementarity and target transcripts abundance. Biochim Biophys Acta [Epub ahead of print]. [abstract]

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