RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 that is required for tomato fruit ripening

For exploring whether mRNA m6A modification participates in the regulation of tomato fruit ripening, we performed m6A-seq in three tomato fruit samples, including wild-type (WT) at 39 days post-anthesis (DPA) and 42 DPA, and Cnr mutant at 42 DPA, with three biological replicates. mRNA methylome analysis reveals that m6A methylation is a prevalent modification in mRNA of tomato fruit and the m6A sites are predominantly enriched in the stop codon and 3’ untranslated region, where m6A deposition has been proved to negatively correlate with gene expression. Hundreds of ripening-induced and ripening-repressed genes, including the SlDML2, were found to harbour changed m6A levels during fruit ripening or in the Cnr mutant, implicating the involvement of m6A modification in the regulation of fruit ripening. mRNA m6A methylation profiles in tomato fruits of 39 DPA and 42 DPA wild-type and 42 DPA Cnr mutant were generated by m6A-seq, in triplicate, using Illumina Hiseq X.

为探究mRNA m⁶A修饰是否参与番茄果实成熟的调控，我们对3组番茄果实样本开展了m⁶A测序（m6A-seq），样本包括开花后39天（days post-anthesis, 39 DPA）、42天（42 DPA）的野生型（WT）样本，以及42 DPA的Cnr突变体样本，每组均设置3次生物学重复。mRNA甲基化组分析显示，m⁶A甲基化修饰在番茄果实mRNA中广泛存在，且m⁶A位点主要富集于终止密码子与3’非翻译区（3’ untranslated region, 3’UTR），该区域的m⁶A沉积已被证实与基因表达呈负相关。本研究发现，包括SlDML2在内的数百个成熟诱导基因与成熟抑制基因，在果实成熟过程中或Cnr突变体背景下存在m⁶A水平的显著变化，提示m⁶A修饰参与了番茄果实成熟的调控过程。本研究通过Illumina Hiseq X测序平台，对39 DPA野生型、42 DPA野生型及42 DPA Cnr突变体的番茄果实开展了3次生物学重复的m⁶A测序，构建了对应的番茄果实mRNA m⁶A甲基化图谱。