Fig. 9: m⁶A modification is a global and dynamic process across the whole transcriptome.

a The histogram (top) and cumulative distribution function (bottom) of the number of m⁶A-modified sites within a gene detected in the HEK293T (blue) and HeLa (orange) transcriptomes. Dashed lines and the corresponding numbers indicate 50^th and 90^th percentiles for each cell line, and gray lines indicate 50^th and 90^th percentiles of the expressed genes. b Top 10 genes harboring the largest number of m⁶A sites and their respective number of m⁶A sites detected in the HEK293T (left) and HeLa (right) transcriptomes. c Examples of the differentially modified genes between the HEK293T and HeLa transcriptomes. Modification stoichiometries of detected m⁶A sites are shown as bars (left y-axis), and log₁₀(sequencing depth) is shown as area plots (right y-axis). Those sites with a sequencing depth of < 20 in either transcriptome were not included in the plots. d The relative fraction of DRACH and non-DRACH contexts among the static and differential m⁶A sites. Static and differential sites are those sites modified in both and only in one of the transcriptomes, respectively. The relative fraction of the non-DRACH sites is indicated (left). Examples of genes containing differentially modified non-DRACH sites are shown (right). Otherwise, as in (c). e The relative fraction of static and differential m⁶A sites among the m⁶A sites detected within weakly (with < 5 m⁶A sites), moderately (with 5–10 m⁶A sites), and heavily (with > 10 m⁶A sites) modified genes. The relative fractions of the static and differential m⁶A sites are indicated (middle). Examples of genes only containing the static sites (left) and containing the differential sites (right) are shown. Otherwise, as in (c).