Post-Transcriptional Regulation of Viral RNA through Epitranscriptional Modification

Abstract

The field of mRNA modifications has been steadily growing in recent years as technologies have improved and the importance of these residues became clear. However, a subfield has also arisen, specifically focused on how these modifications affect viral RNA, with the possibility that viruses can also be used as a model to best determine the role that these modifications play on cellular mRNAs. First, virologists focused on the most abundant internal mRNA modification, m⁶A, mapping this modification and elucidating its effects on the RNA of a wide range of RNA and DNA viruses. Next, less common RNA modifications including m⁵C, Nm and ac⁴C were investigated and also found to be present on viral RNA. It now appears that viral RNA is littered with a multitude of RNA modifications. In biological systems that are under constant evolutionary pressure to out compete both the host as well as newly arising viral mutants, it poses an interesting question about what evolutionary benefit these modifications provide as it seems evident, at least to this author, that these modifications have been selected for. In this review, I discuss how RNA modifications are identified on viral RNA and the roles that have now been uncovered for these modifications in regard to viral replication. Finally, I propose some interesting avenues of research that may shed further light on the exact role that these modifications play in viral replication.

Keywords: 5-methylcytosine; HIV-1; N6-methyladenosine; RNA; epitranscriptomic; mapping; modification; pseudouridine; virus.

Figure 1

Schematic of the four main methods of mapping RNA modifications. Antibody mapping and protein clip mapping are straightforward techniques involving capture of modified RNA fragments by antibodies before elution and next-generation sequencing, which yields footprints of 20–100 nt. Biochemical mapping generally involves either chemical labelling of a modified residue to block reverse transcription, or a mutant reverse transcriptase that spontaneously stops upon encountering a modified residue. Again, these products undergo next-generation sequencing, but the resultant footprint of these methods is 1 nt. Finally, Nanopore mapping uses a new technique of nucleotide detection by calculating electrical current as the RNA passes through a pore. Each nucleotide alters the electrical current differently, with minor fluctuations also detectable when modified nucleotides are present. This method also results in a 1 nt footprint and is capable of sequencing native RNA.