An epigenetic 'extreme makeover': the methylation of flaviviral RNA (and beyond)

Abstract

Beyond their high clinical relevance worldwide, flaviviruses (comprising dengue and Zika viruses) are of particular interest to understand the spatiotemporal control of RNA metabolism. Indeed, their positive single-stranded viral RNA genome (vRNA) undergoes in the cytoplasm replication, translation and encapsidation, three steps of the flavivirus life cycle that are coordinated through a fine-tuned equilibrium. Over the last years, RNA methylation has emerged as a powerful mechanism to regulate messenger RNA metabolism at the posttranscriptional level. Not surprisingly, flaviviruses exploit RNA epigenetic strategies to control crucial steps of their replication cycle as well as to evade sensing by the innate immune system. This review summarizes the current knowledge about vRNA methylation events and their impacts on flavivirus replication and pathogenesis. We also address the important challenges that the field of epitranscriptomics faces in reliably and accurately identifying RNA methylation sites, which should be considered in future studies on viral RNA modifications.

Keywords: 2ʹ-O-methylation; Flavivirus; N6-methyladenosine; RNA methylation; RNA modification; West Nile virus; Zika virus; cap; dengue virus; viral RNA.

Figure 1.

The fates of methylated and non-methylated vRNA species during flavivirus life cycle

Figure 2.

Schematic representation of (A) the flavivirus cap1 structure, (B) N⁶-methyladenosine (m⁶A) and (C) 5-methylcytosine (m⁵C)

Figure 3.

Examples of ZIKV and DENV structural elements with m⁶A consensus motifs. (A) Two contiguous m⁶A-containing regions in the NS5 coding sequence of ZIKV MR766 genome (yellow and light pink circles) were identified in the reported secondary structure [14,21,121,123]. The nucleosides in predicted DRACH and MGACK m⁶A consensus motifs are circled in red and black, respectively. The RNA strand making intramolecular long-range interaction with prM coding region is indicated in grey. (B, C) Two different methylated regions of DENV2 NGC strain (yellow circles) were mapped within two independent reported structures in the NS3 coding sequence of the closely related strain DENV2 S16803 [14,21,121,123]. The nucleosides in predicted DRACH m⁶A consensus motifs are circled in red. In B, the DRACH motif is located in a 14 nucleotide-long stem flanked by unstructured regions whose SHAPE reactivity (indicated in grey) changed if vRNA was gently extracted from virions