The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future

Abstract

Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.

Figure 1

Previously detected RNA covalent modification profiles on plant mRNAs. Representation of gene structure showing typical locations of detected modifications (upper panel), and graphical representation of transcriptome coverage plots (lower panels) from previous experiments depicting the relative positional enrichments of the m⁵C, m¹A, and m⁶A mRNA modifications in plant systems. Relative peak height/intensity are graphical interpretations from cited sources and do not represent actual data points.

Figure 2

Detecting post-transcriptional mRNA modifications in plants. Key steps in a few of the approaches for investigating covalent nucleotide modifications in plant mRNAs include NAD⁺ capping (NAD⁺), m¹A, m⁵C, pseudouridine (Ψ), and m⁶A. These approaches include the click chemistry-based NAD⁺ -seq, the antibody-based immunocapture approaches for numerous modifications (Me-RIP-seq), the chemical-based probing of pseudouridine (Pseudo-seq), and the demethylase-mediated pulldown of m⁶A sites (m⁶A-SEAL-seq). Continual developments in nanopore-seq offer the potential to simultaneously detect numerous mRNA modifications with a single experimental approach. It is notable that this sequencing technology is already being used in studies of various RNA modifications as noted throughout the text herein.