Evolution of the RNA N⁶-Methyladenosine Methylome Mediated by Genomic Duplication

Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA

“…In agreement with early biochemical studies of animal, viral, and plant mRNA (Wei et al, 1976;Dimock and Stoltzfus, 1977;Schibler et al, 1977;Wei and Moss, 1977;Canaani et al, 1979;Nichols and Welder, 1981), transcriptome-wide mapping of m 6 A has identified RR [m 6 A]CH (R 5 A/G, H 5 A/C/U) as the most significantly enriched motif in m 6 A peaks of all eukaryotes analyzed to date (Dominissini et al, 2012;Meyer et al, 2012;Schwartz et al, 2013;Ke et al, 2015;Linder et al, 2015;Lence et al, 2016;Zhao et al, 2017;Li et al, 2019), including plants Wan et al, 2015;Shen et al, 2016;Duan et al, 2017;Wang et al, 2017;Anderson et al, 2018;Miao et al, 2019;Parker et al, 2019). This finding strongly supports the existence of a conserved mechanism of m 6 A deposition in eukaryotic mRNA and is in perfect agreement with the fact that the adenosine methyltransferase complex is conserved across eukaryotes but not in prokaryotes, in which m 6 A occurs in a completely different sequence context in mRNA (Box 2; Deng et al, 2015).…”

“…In addition to its presence in a defined consensus motif, m 6 A was predominantly found in the 39-UTR of mRNAs by most of the above-mentioned studies in eukaryotes, again supporting a highly conserved mechanism of adenosine methylation, while it is distributed more or less evenly along prokaryotic transcripts (Deng et al, 2015). Nonetheless, recent reports have raised the question of whether different m 6 A motifs exist in plants (Li et al, 2014c;Anderson et al, 2018;Wei et al, 2018b;Luo et al, 2019;Miao et al, 2019;Zhang et al, 2019a), a debate that is detailed in Box 2 and illustrated in Figure 1. It is our judgment that the current evidence most strongly supports predominant use of the pan-eukaryotic RR[m 6 A]CH motif.…”

“…In plants, there are now reports on mapping of three distinct covalent nucleotide modifications in the bodies of mRNA: m 6 A (Li et al, 2014c;Wan et al, 2015;Shen et al, 2016;Duan et al, 2017;Anderson et al, 2018;Miao et al, 2019;Parker et al, 2019), 5-methylcytidine (m 5 C; Cui et al, 2017;David et al, 2017;Yang et al, 2019), and pseudouridine (C; Sun et al, 2019). Other types of mRNA modifications, including C-U editing of mitochondrial and plastidial mRNAs (Shikanai, 2006), alternative 59-caps (Kiledjian, 2018;Wang et al, 2019), and untemplated addition of nucleotides to mRNA 39-ends (De Almeida et al, 2018), will not be covered here.…”

The Dynamic Kaleidoscope of RNA Biology in Plants

“…An Update contributed by Arribas-Hernández and Brodersen (2020) considers the m 6 A modification present on many plant transcripts and compares the proteins involved in targeted modification and the impact on posttranscriptional processes, by comparing knowledge from plants with that of other eukaryotes. This review is complemented by two research articles on the m 6 A epitranscriptome of maize, one considering the relevance of the modification in mRNA translation (Luo et al, 2020) and the other evaluating coevolutionary patterns of genes with m 6 A modification in the two subgenomes of maize that arose through an ancient genome duplication (Miao et al, 2020).…”

“…There is considerable room for future analyses of the functions of m 6 A, as only a small proportion of the transcriptome has a particular m 6 A modification. Adding to the intrigue are the findings of Miao et al (2020) related to gene evolution and m 6 A modification. They report that transcripts produced from the two subgenomes of maize differ, with higher m 6 A in transcripts of the singleton and duplicated genes of the subgenome that has more actively expressed genes.…”