Comparative analysis of m6A mRNA modification in de novo and established genes during yeast sporulation

Abstract

De novo genes, a subset of young and lineage-restricted genes arising from ancestrally non-genic sequences, serve as a reservoir for evolutionary innovation. Despite their potential significance, the regulatory mechanisms governing de novo genes remain largely unexplored, particularly regarding post-transcriptional modifications. While N6-methyladenosine (m6A) mRNA modification has been extensively studied in epitranscriptomics, its role and dynamics in de novo genes compared to established protein-coding genes have not been investigated. This study investigates the m6A epitranscriptome in Saccharomyces cerevisiae, examining modification landscapes, peak quantification, position, consensus motif, and temporal dynamics in a curated collection of de novo genes using high-resolution m6A-seq2 data. We analyzed the relationships between m6A modifications and gene characteristics including transcript length, expression levels, and evolutionary age during sporulation. To establish connections between differential gene expression and m6A modification patterns, we performed conjoint analyses of differential m6A modification and RNA expression profiles to elucidate the regulatory role of m6A in gene expression control. Functional annotation of key genes was conducted to provide biological context for our findings. Our results reveal that de novo genes exhibit a lower apparent per gene m6A burden than established protein coding genes, characterized by fewer modification peaks per transcript, lower peak intensities, and reduced m6A motif density. However, this difference is primarily explained by the shorter transcript lengths and lower GAC motif densities characteristic of DNGs, rather than by evolutionary age itself. Consistent with this interpretation, evolutionary age was not a significant independent predictor of m6A modification after controlling for transcript length and other variables in multivariable analysis. Notably, DNGs display parallel temporal modification patterns across sporulation stages, indicating that they are subject to the same stage-specific m6A dynamics as established genes.