Abstract
The discovery of mechanisms that alter genetic information via RNA editing or introducing covalent RNA modifications points towards a complexity in gene expression that challenges long-standing concepts. Understanding the biology of RNA modifications represents one of the next frontiers in molecular biology. To this date, over 130 different RNA modifications have been identified, and improved mass spectrometry approaches are still adding to this list. However, only recently has it been possible to map selected RNA modifications at single-nucleotide resolution, which has created a number of exciting hypotheses about the biological function of RNA modifications, culminating in the proposition of the ‘epitranscriptome’. Here, we review some of the technological advances in this rapidly developing field, identify the conceptual challenges and discuss approaches that are needed to rigorously test the biological function of specific RNA modifications.
Highlights
Gene expression is a multi-layered process that starts with controlling access to particular sequence information encoded in DNA, followed by copying this information to RNA molecules, which branch off into transferring their sequence information into polypeptides, or which function as non-coding RNAs
No single rRNA modification was found to be essential for ribosome function under standard conditions [14,15]. In support of this notion, ribosomal assembly can be achieved using in vitro-transcribed 23S rRNA [16], which even allows for peptidyl transfer [17], and in vitrotranscribed tRNAs lacking all modifications are functional in reconstituted protein translation assays [18]
While C appeared to cluster in mRNA coding sequences [28], m5C was mapped at 50 and 30 untranslated regions (UTRs) in mRNAs of a highly unstable cancer cell line [29], at translation start sites in mouse embryonic stem cells and whole brain tissues [30], and to coding sequences in different mouse tissues [31] and in Arabidopsis [32]
Summary
Gene expression is a multi-layered process that starts with controlling access to particular sequence information encoded in DNA, followed by copying this information to RNA molecules, which branch off into transferring their sequence information into polypeptides (as coding RNAs, cRNAs), or which function as non-coding RNAs (ncRNAs). (NGS) as well as mass spectrometry, an ‘explosion’ of activity in RNA modification research has started a feverish race aiming to comprehensively map specific RNA editing and modification patterns transcriptome-wide and in various tissues and cell types. These are exciting times, for RNA biologists, and for structural and systems biologists. While quantitatively more is known about the position of particular RNA modification sites, obtaining functional insight is lagging behind Despite these shortcomings, already the mapping of inosine, m6A, C, m5C or m1A, especially to low-abundance RNAs (i.e. cRNAs and long ncRNAs), has given rise to testable hypotheses and has opened new avenues for exploration. Because of the recent introduction of terms such as ‘RNA epigenetics’ and ‘epitranscriptomics’ into the field, we aim to critically discuss their definition, especially in the light of an invoked similarity to the complexities observed for epigenetic gene regulation systems
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