A DRACH Observed/Expected Metric Reveals the Evolutionary Landscape of Epitranscriptomic Regulation Across Bilateria

ABSTRACT

N ⁶ ‐methyladenosine (m ⁶ A) RNA modification is a dynamic post‐transcriptional regulatory mechanism that rapidly modulates gene expression by influencing RNA stability, export, splicing, translation, and decay. In bilaterians, m ⁶ A is predominantly deposited at the DRACH consensus motif, which comprises 18 sequence variants. Although the presence of a DRACH motif does not indicate whether a transcript is currently, or has ever been, methylated, it reflects its potential for m ⁶ A‐mediated regulation. Here, we introduce a new metric, DRACH observed/expected (DRACH o/e), to quantify the relative enrichment of DRACH motifs independently of sequence composition. We applied this approach to characterize the abundance, distribution, and genomic organization of DRACH motifs in the Pacific oyster Magallana gigas , a representative lophotrochozoan species in which m ⁶ A regulation remains poorly characterized. These analyses were extended to eight additional species spanning major bilaterian lineages and exhibiting contrasting ecological traits. Comparative analysis revealed strong conservation of the m ⁶ A regulatory machinery together with conserved and lineage‐specific patterns of DRACH motif distribution and functional enrichment. This work introduces a robust framework for estimating the potential for transcript m ⁶ A methylation while overcoming the inherent variability of epitranscriptomes, thereby paving the way to explore comparative analyses of its potential phylogenetic and/or ecological drivers.