N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner

Leilei Zhou,Guozheng Qin,Xiaojing Li,Renkun Tang,Shiping Tian,Bingbing Li

doi:10.1186/s13059-021-02385-0

Abstract

BackgroundEpigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, which has been shown to regulate ripening of the tomato, a typical climacteric fruit, is functionally conserved for ripening control among different types of fruits.ResultsHere we show that m6A methylation displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m6A modification in coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m6A around the stop codons and within the 3′ untranslated regions is generally negatively correlated with the abundance of associated mRNAs. We identified thousands of transcripts with m6A hypermethylation in the CDS regions, including those of NCED5, ABAR, and AREB1 in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrate that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m6A modification promotes mRNA stability of NCED5 and AREB1, while facilitating translation of ABAR.ConclusionOur findings uncover that m6A methylation regulates ripening of the non-climacteric strawberry fruit by targeting the ABA pathway, which is distinct from that in the climacteric tomato fruit.

Highlights

As the most prevalent chemical modification in eukaryotic messenger RNAs, N6-methyladenosine (m6A) has been demonstrated to functionally modulate multiple biological processes through interfering mRNA metabolism [1,2,3,4]
Results m6A methylation is a common feature of mRNAs in strawberry fruit To investigate whether m6A methylation participates in modulating ripening of nonclimacteric fruits, we performed m6A-seq [37] to characterize m6A methylomes on diploid woodland strawberry (Fragaria vesca) at three developmental stages, i.e. S6 (the growth stage 6, approximately 15 days post-anthesis (DPA)), ripening stage 1 (RS1), and ripening stage 3 (RS3) (Fig. 1a) [38]
In the m6A-seq analysis, we found that transcripts of key genes in abscisic acid (ABA) biosynthesis and signaling pathway, including 9-cis-epoxycarotenoid dioxygenase 5 (NCED5) [38], putative ABA receptor (ABAR) [34], and ABA-responsive element-binding protein 1 (AREB1) [46], exhibit hypermethylation in the coding sequence (CDS) region at the initiation stage of strawberry fruit ripening (Fig. 4b, c)

Summary

Results

M6A methylation is a common feature of mRNAs in strawberry fruit To investigate whether m6A methylation participates in modulating ripening of nonclimacteric fruits, we performed m6A-seq [37] to characterize m6A methylomes on diploid woodland strawberry (Fragaria vesca) at three developmental stages, i.e. S6 (the growth stage 6, approximately 15 days post-anthesis (DPA)), RS1 (the ripening stage 1, 21 DPA), and RS3 (the ripening stage 3, 27 DPA) (Fig. 1a) [38]. To assess the potential correlation between m6A modification and mRNA abundance in strawberry fruit, we compared the list of transcripts harboring altered m6A methylation with the differentially expressed genes (fold change ≥ 1.5 and P value < 0.05) obtained from our parallel RNA-seq analyses In the m6A-seq analysis, we found that transcripts of key genes in ABA biosynthesis and signaling pathway, including 9-cis-epoxycarotenoid dioxygenase 5 (NCED5) [38], putative ABA receptor (ABAR) [34], and ABA-responsive element-binding protein 1 (AREB1) [46], exhibit hypermethylation in the CDS region at the initiation stage of strawberry fruit ripening (from S6 to RS1) (Fig. 4b, c).

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