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. 2023 May 18;30(8):1207–1215. doi: 10.1038/s41594-023-00997-7

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© The Author(s) 2023, corrected publication 2023

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, GGACH motifs (normalized to region length) in different transcript regions of autosomal (gray) and X-chromosomal transcripts (orange) in mouse (P value = 1.38 × 10^–29 (CDS, n = 16,631 annotations), P value = 1.06 × 10^–40 (3′ UTR, n = 16,484 annotations) and 0.2707 (5′ UTR, n = 16,490 annotations), two-tailed Wilcoxon rank-sum test). b, Methylation levels of GGACH motifs are slightly reduced on X-chromosomal transcripts. Fraction of m⁶A sites per chromosome with methylation in miCLIP2 data from male mESCs. Boxes represent quartiles, center lines denote medians, and whiskers extend to most extreme values within 1.5 × interquartile range. c, Location of mouse X-chromosomal orthologs in human, opossum (Monodelphis domestica), and chicken. d, Percentage of orthologs of X-chromosomal or autosomal genes in mouse that are located on autosomes or sex chromosomes in human, opossum, and chicken. e, GGACH motifs in transcripts (exons) from mouse genes and corresponding orthologs in chicken, opossum, and human (n = 6,520). Orthologs to mouse X-chromosomal and autosomal genes are indicated in orange and gray, respectively (two-tailed Wilcoxon rank-sum test, *P value < 0.05, **P value < 0.01, ***P value < 0.001, P value = 1.2 × 10^–18 (mouse), 2.7 × 10^–6 (human), 0.001227 (opossum), 0.8602 (chicken)). Boxes are as in a. f, Effects of m⁶A depletion on expression of autosomal and X-chromosomal transcripts in XX and X0 clones of female mESCs (P value = 1.64 × 10^–12 and 3.5 × 10^–11, respectively, two-tailed Wilcoxon rank-sum test, Extended Data Fig. 9a–c). Median fold changes (log₂) of transcripts from autosomes (n = 19, gray) and the X chromosome (n = 1, orange), estimated by RNA-seq after m⁶A depletion (STM2457, 9 h). Boxes are as in a. g, X:A expression ratios are significantly reduced upon m⁶A depletion (P value = 4.12 × 10^–15 (mESC), P value = 2.06 × 10^–11 (female mESC XX), P value = 1.08 × 10^–10 (female mESC X0). P values are as in Figure 2b, multiple testing correction). h, Median fold change (log₂) of m⁶A sites per transcript on each chromosome relative to all chromosomes (P = 0.0018, autosomal (gray) versus X-chromosomal (orange) transcripts, two-tailed Wald test in generalized linear mixed model for negative binomial data).

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