Extended Data Fig. 6. X-chromosomal transcripts harbour less m⁶A sites than autosomal transcripts in male mESC.

a. Transcripts were stratified into 12 bins (#1–12) according to their expression in male mESC (transcripts per million [TPM, log₁₀], see Methods). x-axis depicts boundaries between bins (in TPM). Bin number (#) and number of transcripts therein are given below and above each bar, respectively. Bins #3–8 that were used for quantifications of m⁶A sites per transcripts are highlighted in black. b. Quantification of m⁶A for each transcript in the different expression bins of autosomal (grey) and X-chromosomal (orange) transcripts. Boxes represent quartiles, centre lines denote medians, and whiskers extend to most extreme values within 1.5× interquartile range. c. Quantification of m⁶A sites per transcript for all mouse chromosomes. Data points indicate mean number of m⁶A sites per transcript and 95% confidence interval (left y-axis) in each expression bin (x-axis, bins as defined in a) for all chromosomes (chromosome name and total number of expressed transcripts given above). Grey bars indicate the percentage of transcripts in each expression bin (right y-axis) relative to all expressed transcripts on the chromosome. Absolute numbers of transcripts in each bin are given above the bars. Only genes with a mean TPM > 1 over all samples were considered. d. Fold change (log₂, grey dots) in mean m⁶A sites per transcripts for expression bins #3–8 (n of mean of expression bins = 6) on an individual chromosome over the mean m⁶A sites per transcripts across all chromosomes. Red dots indicate mean fold change of the six bins on the given chromosome. Boxes as in b. e. Same as d. using only m⁶A sites in a fixed window around stop codons (−50 nt to +150 nt) to exclude confounding effects of transcript length differences. Boxes as in b. f. Same as c. after randomly subsampling n = 30 genes from expression bins #3–5 to exclude potential biases from different numbers of transcripts in the expression bins for each chromosome. Shown is the distribution of mean m⁶A sites per transcript for each chromosome from 100 repeats of subsampling. Boxes as in b.

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