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. 2020 Jul 30;21:187. doi: 10.1186/s13059-020-02098-w

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Population differences in miRNA expression. a Example of a miRNA (miR-4482-3p) differentially expressed between populations. Expression of miR-4482-3p is shown separately for African- (AFB) and European- (EUB) ancestry individuals. b IsomiRs of miR-146a-3p are differentially expressed between populations. For each population and isomiR, isomiR ratios are shown in the R848 condition where the difference is the strongest. All isomiRs with < 1 RPM on average, are pooled and annotated as other. c Amplitude of population differences in expression of miRNAs and protein-coding genes, at basal state and upon stimulation. d Sharing of pop-DE-miRs and pop-DE-isomiRs across conditions. For the 244 pop-DE-miRs and 188 pop-DE-isomiRs, number of conditions where we observed a difference between populations. e Expression of miR-155-5p is differential between African- and European-ancestry individuals, specifically in TLR-stimulated conditions. For simplicity, only Pam₃CSK₄ condition is shown. f–h Signatures of positive selection targeting the miR-QTL hotspot rs12881760. f Genomic context of the miR-QTL hotspot, displaying protein coding genes (yellow), RNA genes (cyan), snoRNAs (purple), and miRNAs (red) in a 1 Mb-window around the locus. Red lines link the miR-QTL to its target miRNAs, the name of which are indicated above. g Impact of the rs12881760 variant on a CTCF motif, and worldwide frequency of the motif-disrupting C allele. h Signatures of positive selection at the rs12881760 locus. |iHS| are displayed for all SNPs with MAF > 5% in Europeans, and dots are colored according to the sign of the iHS statistic (red, positive; blue, negative). The black line indicates the percentage of outliers (|iHS| > 2.5) on a sliding window of 100 consecutive SNPs with a MAF > 5% (right axis). Recombination rate is overlaid in light blue and normalized to the maximum recombination rate in the region (peak, 152 cM/Mb)