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. 2019 Nov 25;10:5332. doi: 10.1038/s41467-019-13317-9

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© The Author(s) 2019

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. 2 — Characterize the role of CDS m⁶A in translation efficiency. a Aggregation plots show the mean ribosome densities along mRNA regions aligned to the RRAC motif with (pink line) or without (blue line) m⁶A modification. Right panels show the mean ribosome densities along mRNA regions aligned to GAA or GAC codons with (pink line) or without (blue line) m⁶A modification. A minus position value indicates upstream of m⁶A sites, whereas a positive value indicates downstream of m⁶A sites. The m⁶A site in RRAC motif or codons is highlighted by red. b The fold change of translation efficiency upon METTL3 knockdown is plotted as accumulative fractions (Wilcox test, P = 1.9 × 10⁻⁸) for mRNAs bearing CDS methylation (m⁶A+) or not (m⁶A−). Both groups have similar levels of basal TE. c Aggregation plots show the mean ribosome densities along mRNA regions aligned to the RRAC motif with (top panel) or without (bottom panel) m⁶A modification. Plots from cells with or without METTL3 knockdown are color coded. The m⁶A site in RRAC motif is highlighted by red. d From the same data sets as c, the fold change of ribosome accumulation upstream of the motif in response to METTL3 knockdown is calculated for transcripts with or without m⁶A modification (Wilcox test, P < 0.001). For the boxplot in d and e, the median value in each group is indicated by a center line, the box shows the upper and lower quantiles, whiskers shows the 1.5× interquartile range, and the outliers are indicated by points. e A histogram shows the distribution of changes of regional ribosome density in response to METTL3 knockdown. A sliding window of 30 nt in length with a step of 3 nt are used to calculate the local ribosome density. Regions with <1/3-fold (Dec, blue) and >3-fold (Inc., red) changes are highlighted by color coding. The right box plot shows the predicted minimum folding free energy (MFE) for regions with <1/3-fold (Dec) and >3-fold (Inc.) changes (Wilcox test, P < 2.2 × 10⁻¹⁶). Source data are provided as a Source Data file.