Fig. 4

Dissection of determinants of m6A evolution in mammalian cells. a The relative frequency of DRACH motifs over a 200-nt window centered around the detected m6A peak summits in mammalian samples (blue), in comparison to randomly sampled regions across the same genes (gray). b Log2 fold changes in m6A levels between human and mouse alleles in monochromosomal hybrids (Y axis) as a function of log2 fold-changes in pseudo-parental counterparts across 2016 sites on human chromosomes 1, 2 and 3 and corresponding mouse alleles. Shown is Pearson R. c Classification of the detected m6A sites in mammals into differentially methylated sites in cis (DM-cis), trans (DM-trans), cis–trans interaction sites, or into invariable sites as in Fig. 2a. Δparental indicates the log2(human m6A scores)—log2(m6A scores at homologous locus at mice), while Δhybrid indicates the corresponding value between the two alleles in the cross-species hybrid. d-g Sequence coverage plots of m6A-seq2 IP for mice, humans, and their corresponding in the hybrids. Shown are examples of the four main regulatory determinant types of m6A sites identified in mammals: DM-cis (d), Invariable (e), cis–trans interaction (f), and DM-trans m6Asites (g). The green bars indicate the position of the detected m6A and its homologous locus on the other species, as in Fig. 2b-e. The 13-nt sequence in each of the two species/alleles are shown on the bottom, indicating the methylated adenosine (green), a motif-damaging mutation (red), or another m6A DRACH motif (green). h Boxplot displaying the difference in the predicted MFE between humans and mice in the two main groups of sites: invariable m6A sites and DM-cis sites. The prediction is made for 61 nt window around the methylated adenosine. Sites exclusive to humans are more structured in mice, and those exclusive to mice are more structured in humans. As in yeast, values are shown only for sites without motif-damaging mutation and at least one allele with a predicted solid structure (MFE < -8 kcal/mol) are displayed (n = 431)