The Small RNA World – a brief introduction

The first reflex when coming across the title of this blog is, most likely, that it is a blog that mentions microRNAs and small RNAs. Up until now, I suppose that I’ve been a disappointment, as the scientific focus has been on the subject matter of my lab – polyadenylation. But this changes with this essay, an overview of the field of small RNAs. My goal with this overview is to lay a foundation to which I can refer in other contexts. As always, enjoy (and feel free to ask questions or correct any mistakes you find).

To start out, it helps to clarify just what is meant by “small RNA”. In this essay, “small RNA” means RNAs of between 21 and 26 bases (or nts) long. By way of comparison, transfer RNAs may range from 75-100 nts, small nuclear RNAs (components of the splicesome and other RNA processing complexes) from 100-250 nts, ribosomal RNAs from 1500-3000 nts, and messenger RNAs from a few hundred to many thousands of nts. Small RNAs are thus truly “small”; in addition, they are rather homogeneous in size, compared with other classes of RNA in the cell. This homogeneity reflects their biogenesis, something that will be discussed later.

Small RNAs thus defined have been implicated in all manner of process, from cancer, development, responses to environment, and epigenetic phenomena associated with various aspects of genome function. They are also proving to be extremely useful tools for biological and biomedical research.

Small RNAs come in two “flavors” – microRNAs (or miRNAs) and small interfering RNAs (or siRNAs). miRNAs and siRNAs are distinguished by the nature of their biogenesis. All small RNAs are derived from precursor RNAs that are considerably larger than the mature small RNA, through characteristic RNA processing events. miRNAs are processed from a single-stranded RNA precursor that can assume a distinctive secondary structure; this structure is typified by a stem-loop that is punctuated along the stem by a few unpaired bases (or bulges). In contrast, siRNAs are processed from perfectly-base paired RNA precursors; these precursors may be double-stranded, or single-stranded RNAs that have perfect inverted repeats within them. (The latter would include so-called short hairpin or shRNAs, designed and used in the lab to elicit a gene silencing response.) This contrast in biosynthetic pathway reflects differences in the origins of the precursor RNAs, something that factors into the various functions of small RNAs.

Added to this duality is the fact that small differences in size – as little as one nt – have important functional significance.  This is because small RNAs of different size are produced by different enzymes, and they are incorporated into different complexes of enzymes that in turn do different things.

How do small RNAs work?  This is the money question because it helps us to ask (and answer) questions about the many processes into which small RNAs insert themselves.  Small RNAs work by base-pairing with target RNAs (or, in some cases, DNA) within the cell. However, they don’t work “naked”; rather, they are parts of complexes that bring other functionalities to gene silencing. Thus, this base-pairing occurs while both small RNA and target are associated with RNA binding subunits of larger complexes.  In this sense, small RNAs are similar to guide RNAs or particular snoRNAs; they bring a suite of enzymes to a target RNA by base-pairing interactions. The fate of the target is determined by the nature of the enzymes associated with the small RNA, and may include degradation, translational repression, translational activation, or DNA methylation (to name a few).

It’s no accident that I have omitted mention of the names of the “players” involved in small RNA biogenesis. These details are saved for future essays; in this one, the goal is to allow readers to become conversant with the small RNA itself, and the underlying and deceptively simple means by which these molecules act in the cell. This mechanism, restated, is this – small RNAs act by base pairing to bring enzymes to their nucleic acid targets, and it is the action of these enzymes that decides the fate of the targeted RNA or DNA.