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. 2019 Dec 16;10:5713. doi: 10.1038/s41467-019-13360-6

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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. 4 — a 5′-UTR minimum free energy and length of the mRNAs translationally upregulated and top 180 downregulated in persister cells. b GC content of the mRNAs translationally upregulated and top 180 downregulated in persister cells. TE: translation efficiency. c The distribution of m⁶A peaks for mRNA upregulated (red) and downregulated (blue) at the translational level in persister cells. The whole population of mRNAs was plotted in green as a control. d Heavy polysome-bound mRNAs were extracted and purified for m⁶A dot plot assay, m⁶A LC/MS-MS assay and m⁶A RNA immunoprecipitation followed by RNA sequencing (m⁶A-seq) in persister vs. parental cells. e Liquid chromatography–mass spectrometry (LC/MS-MS) nucleoside modification analysis. Total RNAs were purified by poly(A) enrichment and were subjected to digestion. Triplicate samples were then subjected to LC/MS-MS quantification. Each type of RNA methylation was first normalized to non-methylated nucleotide base (A or G) and polysome RNA methylation was then normalized to total RNA methylation (input). m⁶A: 6-methyladenosine; m⁶A_m: N⁶,2’-O-dimethyladenosine; A_m: 2’-O-methyladenosine; m¹A: 1-methyladenosine; m⁷G: 7-methylguanosine; A: adenosine; G: guanosine (n = 3, unpaired t-test, ns: nonsignificant). f Metagene profiles of enrichment of m⁶A modifications across mRNAs corresponding to translationally upregulated transcripts and the top 180 translationally downregulated transcripts in parental and persister cells. Top panel, metagene profiles of m⁶A modifications of total lysate from parental or persister cells; bottom panel: metagene profiles of m⁶A modifications of heavy polysome fractions from parental or persister cells. CDS, coding sequence. g RT-qPCR quantification of m⁶A enrichment in polysome-bound CREBBP mRNA and HPRT mRNA at indicated time points (n = 3, **p-value < 0.01, unpaired t-test). The raw data of e and g are available in Source Data.