Transcriptome-Wide Analysis of RNA m⁶A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m(6)A) methylation is the most abundant type of post-transcriptional modification for mRNAs, but the pattern of inheritance from parents to hybrids and potential impact on heterosis are largely unknown. We constructed transcriptome-wide mRNA m(6)A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F-1 hybrids. Generally, the transcriptome-wide pattern of m(6)A methylation tends to be conserved between accessions. Approximately 74% of m(6)A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m(6)A methylation is maintained after hybridization. We found a significant association between differential expression and differential m(6)A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m(6)A level between Col-0 and Ler is clearly different but tended to disappear at the allelic sites in the hybrids. Interestingly, many enriched biological functions of genes with differential m(6)A modification between parents and hybrids are also conserved, including many heterosis-related genes involved in biosynthetic processes of starch. Collectively, our study revealed the overall pattern of inheritance of mRNA m(6)A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation.