Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m6A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m6A modification has become feasible. A study suggested that m6A modification is crucial for posttranscriptional regulation related to Cd2+-induced malignant transformation, but the association between m6A modification in plants and Cd tolerance has not been reported. We investigated the m6A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m6A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m6A peaks in cv. 9311 and 2,065 differential m6A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m6A peaks indicated that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The “arginine”, “proline metabolism”, “glycerolipid”, and “protein processing in endoplasmic reticulum” metabolism pathways were significantly enriched in genes with differentially modified m6A peaks in cv. NIP. Unlike that in Arabidopsis, the m6A-modified nucleotide position on mRNAs (m6A peak) distribution in rice exhibited a preference towards both the stop codon and 3′ untranslated regions (3′ UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m6A modification in RNA in plants.
Highlights
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes
KEGG pathway analysis of the genes with differentially modified m6A peaks indicated that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd
The functions of m6A on RNA are determined by the dynamic interplay between a conserved set of proteins called writers, erasers and readers (Meyer and Jaffrey 2017). methyltransferase-like 3(METTL3) is the first m6A methyltransferase to be identified in mammals and is highly conserved in plants and mammals (Yao et al 2019). methyltransferase-like 14(METTL14) is the second most active m6A methyltransferase enzyme in humans to catalyse m6A RNA methylation and is highly homologous to METT L3
Summary
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. Unlike that in Arabidopsis, the m6A-modified nucleotide position on mRNAs (m6A peak) distribution in rice exhibited a preference towards both the stop codon and 3′ untranslated regions (3′ UTRs) These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m6A modification in RNA in plants. Introduction m6A is one of the most important internal modifications present in the mRNAs of many eukaryotic species, including yeast, plants (Wei et al 2018), flies (Lence et al 2016), and mammals (Yang et al 2018; De et al 2019) In mammals, this modification is dynamic and plays important roles in the regulation of mRNA metabolism and processing (Duan et al 2017), including alternative splicing, exportation, stability, translation, and microRNA maturation (Yang et al 2018; Shen et al 2016). The complexity of rice Cd transport and accumulation indicates the need to understand what is responsible for the Cd accumulation divergence between indica and japonica rice subspecies
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