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Open AccessArticle

The Impact of Population Variation in the Analysis of microRNA Target Sites

School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
Author to whom correspondence should be addressed.
Current address: Faculty of Life Sciences & Medicine, King’s College London, London SE1 9RT, UK.
Non-Coding RNA 2019, 5(2), 42;
Received: 22 March 2019 / Revised: 11 June 2019 / Accepted: 20 June 2019 / Published: 22 June 2019
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
The impact of population variation in the analysis of regulatory interactions is an underdeveloped area. MicroRNA target recognition occurs via pairwise complementarity. Consequently, a number of computational prediction tools have been developed to identify potential target sites that can be further validated experimentally. However, as microRNA target predictions are done mostly considering a reference genome sequence, target sites showing variation among populations are neglected. Here, we studied the variation at microRNA target sites in human populations and quantified their impact in microRNA target prediction. We found that African populations carry a significant number of potential microRNA target sites that are not detectable in the current human reference genome sequence. Some of these targets are conserved in primates and only lost in Out-of-Africa populations. Indeed, we identified experimentally validated microRNA/transcript interactions that are not detected in standard microRNA target prediction programs, yet they have segregating target alleles abundant in non-European populations. In conclusion, we show that ignoring population diversity may leave out regulatory elements essential to understand disease and gene expression, particularly neglecting populations of African origin. View Full-Text
Keywords: miRNAs; human populations; gene regulation; microRNA target prediction; evolution miRNAs; human populations; gene regulation; microRNA target prediction; evolution
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Helmy, M.; Hatlen, A.; Marco, A. The Impact of Population Variation in the Analysis of microRNA Target Sites. Non-Coding RNA 2019, 5, 42.

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