What is an RNA? A top layer for RNA classification

Abstract

Every ribonucleic acid begins its cellular life as a transcript. If the transcript or its processing product has a function it should be regarded an RNA. Nonfunctional transcripts, by-products from processing, degradation intermediates, even those originating from (functional) RNAs, and non-functional products of transcriptional gene regulation accomplished via the act of transcription, as well as stochastic (co)transcripts could simply be addressed as transcripts (class 0). The copious functional RNAs (class I), often maturing after one or more processing steps, already are systematized into ever expanding sub-classifications ranging from micro RNAs to rRNAs. Established sub-classifications addressing a wide functional diversity remain unaffected. mRNAs (class II) are distinct from any other RNA by virtue of their potential to be translated into (poly)peptide(s) on ribosomes. We are not proposing a novel RNA classification, but wish to add a basic concept with existing terminology (transcript, RNA, and mRNA) that should serve as an additional framework for carefully delineating RNA function from an avalanche of RNA sequencing data. At the same time, this top level hierarchical model should illuminate important principles of RNA evolution and biology thus heightening our awareness that in biology boundaries and categorizations are typically fuzzy.

Keywords: Background transcription; functional RNA; fuzzy boundaries; mRNA; spurious transcripts; three superclasses.

Figure 1.

A basic classification of transcripts and RNAs including the fuzziness of boundaries. Depicted is a continuum of the 3 ribonucleic acid superclasses: the first includes stochastic transcripts, other transcripts generated during gene regulation by acts of transcription, secondary products of RNA maturation such as introns etc., and RNA turnover products (transcripts, class 0) in yellow, functional RNAs (RNAs, class I) in blue, and classic mRNAs (mRNAs, class II) in red. Hybrid zones, interphases, or transitions between the 3 classes, for example, reflecting chimeras of 2 classes or those in the process of exaptation or abandonment are shown in purple, orange, and green. This figure does not represent quantitative measures of ribonucleic acid species or their abundances.