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. 2021 Aug 19;12:5043. doi: 10.1038/s41467-021-25170-w

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© The Author(s) 2021

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a–d Scatterplot showing the total mRNA abundance (log10(FPKM-total)) values of all, 5’ UTR, 3’ UTR or CDS DHX36-bound mRNAs in Ctrl vs KO; the number of up- (KO vs Ctrl ≥1.5 fold), down-(≤0.66 fold) or unchanged mRNAs are shown. e Kernel density estimates showing log2(∆FPKM-total) values of mRNAs with DHX36 binding only in 5’ UTRs, 3’ UTRs, or CDS. ∆FPKM-total: the mRNA level alteration in KO vs Ctrl. f–h Prediction of rG4 formation in the binding sites of 5’ UTR, 3’ UTR, and CDS-bound mRNAs was conducted and the number of sites possessing each subtype is shown in up- or downregulated mRNAs. i 5’ UTR region predicted folding energies of rG4 and dsRNA structures in up and downregulated mRNAs with 5’ UTR binding, n = 116 (upregulated mRNAs), 1075 (background mRNAs), 22 (downregulated mRNAs). Data represent mean values ± s.d. j The number of 3’ UTR-bound mRNAs possessing ARE sites is shown. k Predicted folding energies of dsRNAs in up- or downregulated mRNAs with 3’ UTR ARE binding, n = 9 (upregulated mRNAs), 2499 (background mRNAs), 18 (downregulated mRNAs). Data represent mean values ± s.d. l Left: Scatterplot illustrating TE (y axis) and mRNA (x axis) alterations in KO vs Ctrl with a threshold of ±0.585 (dashed line) for 7300 genes with FPKM-total values larger than 1 in either Ctrl or KO condition. Blue dots: TE-up genes with DHX36 binding; yellow dots: TE-down genes with DHX36 binding. Gray dots: the genes with no significant TE change or no DHX36 binding. Right: A total of five bound genes (yellow dots) including Ubq1n1, Nfix, Gnai2, Fzd2, and Zdhhc16 (red font) showed constant mRNA and decreased TE levels in KO vs Ctrl using a more stringent threshold (log2(ΔTE) <−1, ΔTE<0.5). Gray dots: 197 genes with significant TE decrease and constant mRNA levels but with no DHX36 binding. m DHX36 binding regions and ΔTE values are shown for the five genes in panel l and Gnai2 is highlighted. One-tailed Mann–Whitney test was used to calculate the statistical significance between folding energy values in panels i and k with P values shown in the figure.