Fig. 1

Comparisons of m⁶A between pseudogenes and their cognate protein-coding genes in GM12878 cell line. a Box plot comparing the m⁶A levels among different biotypes. b Box plot comparing the m⁶A levels between pseudogenes and their cognate protein-coding genes for processed pseudogenes and unprocessed pseudogenes respectively. c Scatter plot comparing the m⁶A levels between pseudogenes and their cognate protein-coding genes for processed pseudogenes and unprocessed pseudogenes respectively. d Stacked bar plot comparing the percent of pseudogenes and their cognate protein-coding genes with or without m⁶A peaks. The frequencies were displayed in the corresponding boxes. e UCSC genome browser tracks of m⁶A-seq and m⁶A-LAIC-seq data showing representative examples of pseudogenes and their cognate protein-coding genes. Read-coverage tracks of input, m⁶A-negative, and m⁶A-positive fractions of m⁶A-LAIC-seq shown along with overlay tracks of m⁶A-seq (red for RIP and cyan for input; predicted m⁶A sites in m⁶A peaks are indicated by arrows). Read coverage (y-axis) of m⁶A negative and m⁶A positive are normalized as previously described [28] to reflects the calculated m⁶A levels (i.e., equal signals in m⁶A positive (eluate) versus m⁶A negative (supernatant) indicate m⁶A levels of 50%), while input and m⁶A-seq tracks are shown for optimal viewing