Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications

Abstract

The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.

Pitfalls of using sequence databases for heterologous expression studies – a technical review

“…A post-transcriptional modification of adenosine to inosine has been reported, for example, in a number of neurotransmitter receptors and ion channels of the nervous system (Hood & Emeson, 2012). Many more J Physiol 601.9 of these modifications have been identified and these studies are an effort to understand the epitranscriptome of normal or diseased cells (for review see: Arzumanian et al, 2022). To assess changes between nucleotide sequences deriving from genomic sequences and cDNA sequences, a comparison between closely related species might reveal whether these changes are consistent or not.…”

Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop

“…13−18 Chemically modified RNA molecules can also adapt to thermal and environmental changes 19−22 or lead to various diseases, including obesity, heart failure, and cancer. 14,18,23,24 Therefore, chemical modifications in RNA may also be targeted for therapeutic intervention. 23−31 RNA chemical modifications range from methylation to more complex modifications, including glycosylation, carboxylation, geranylation, isomerization, and phosphorylation.…”

“…14,32,33 Among these, methylation is a commonly characterized RNA modification. 14,18,34 RNA nucleotides can be methylated at distinct nitrogen atoms in nucleobases (e.g., N1, N2, N6, or N8) or on the 2′ oxygen of the ribose sugar. 31 However, the N 6 -methyladenosine (m 6 A) is the most prevalent modification in eukaryotic RNA.…”

“…14 The "writer" enzymes (e.g., METTL3, METTL14) add the N 6 -methyl group primarily in the 3′ untranslated region (3′UTR) and near the splicing sites in RNA. 14,35 The mechanism of gene regulation by m 6 A was suggested to depend on reader proteins (e.g., YTHDC1) which recognize the m 6 A-modified nucleotides and alter the RNA structure. 25,31,36,37 The m 6 A modification is proposed to act as a biological switch for modulating RNA activity and function.…”

“…14,40,46 Specifically, it is crucial to probe the diverse effects of m 6 A on the local and global conformational dynamics of RNA to fully resolve the structural details of recognition of methylated RNA molecules by proteins. 14,41,46 Computational methods have been applied to characterize the structural effects of naturally occurring modifications in tRNA molecules. 47−54 These studies have suggested that a modified base could destabilize the local base pairing interactions in which the base is directly involved, leading to the formation of new interactions which can improve the overall stability of tRNA.…”