Abstract
The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m6A) 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 m6A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F1 hybrids. Generally, the transcriptome-wide pattern of m6A methylation tends to be conserved between accessions. Approximately 74% of m6A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m6A methylation is maintained after hybridization. We found a significant association between differential expression and differential m6A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m6A 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 m6A 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 m6A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation.
Highlights
Heterosis refers to the increased performance of hybrid offspring relative to their parents in many traits, such as growth rate and biomass (Birchler et al, 2003, 2010; Hochholdinger and Hoecker, 2007; Chen, 2010; Birchler, 2015)
We found that the normalized reads from m6A-RNA input and immunoprecipitation (RIP) of all samples are enriched in the 3’ UTR of the transcripts (Figure 1A), which is similar to the results of previous research (Luo et al, 2014; Wan et al, 2015)
To further study global patterns of m6A in Col-0, Landsberg erecta (Ler) and their hybrids, we identified m6A peaks using a transcriptomic peak caller, METPeak (Cui et al, 2016)
Summary
The reprogramming and corresponding effect of mRNA m6A methylation on hybrids remain highly unknown. We demonstrated the pattern of conserved inheritance of m6A methylation from parents to hybrids and the potential impact on heterosis formation, uncovering mRNA m6A methylation as a new layer of regulatory mechanisms in the formation of hybrid vigor
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