Fig. 1

Establishment of S. cerevisiae—S. paradoxus hybrid as a model to study m6A regulation. a schematic representation of hybrids as a system to dissect cis and trans evolution of m6A regulation. Any differences in m6A levels across the two alleles in the hybrid are defined as changes in cis. Differences between the methylation patterns across the parental strains that are not maintained across the two alleles in the hybrid are considered trans effects. b Kinetics of meiotic progression across the parental and hybrid strains used in this study. DNA DAPI staining depicts the nuclear division at different time points (x-axis) after incubation of cells in a sporulation medium (SPO). n = 200. c The relative frequency of DRAC motif along a 200 nt window centered around the m6A enrichment peak summit positions (blue), in comparison to randomly sampled regions across the same genes (gray). The median distance of the identified sites from a consensus site is 1 nt, compared to 14 nt for randomly sampled ones. d-e Sequence logo of the methylation consensus sequence based on 975 m6A sites detected in S.cer alleles (e) or 767 m6A sites identified in S.par alleles. We filtered for m6A peak summits that were within 2 nt from DRAC site. f Clustered pairwise correlation matrix of m6A peak intensities across the different backgrounds. g m6A sample index scores for the parental strains and the two alleles of the hybrid strain in the WT and ime4-deletion strains. The m6A enrichment score is calculated as the normalized sum enrichment of m6A-IP versus input reads across all of the detected m6A sites identified in any of the backgrounds. Each background was measured in three biological replicates, each biological replicate is displayed as a point