Thursday, May 20, 2010

"The hottest molbio topics" Series : The Allure of Regulatory RNAs

Our poll “The hottest molbio topics: the next few years” is now over and I have invited notorious bloggers (and experts in the fields in question) to discuss and contextualize the results for our readers, in a way to present them in a more attractive way [See Which will be the hottest topic in molecular biology in a few years? The results].

First is David García, a graduate student at MIT working in David Bartel’s Lab. He’s been studying miRNAs for three years now and blogs over at You'd Prefer An Argonaute.

So, why did people vote for Regulatory RNAs? Here’s David’s take on the subject:

The Allure of Regulatory RNAs

The upward bound of popularity of regulatory RNAs has seemed limitless. Continually they are found to be involved in diverse biological processes at a rate of discovery that for the moment is perpetually increasing. They’re here to stay--they are not a fad. (While the peak in frequency of their appearance in high impact journals may have passed, their total publication rate continues to rise.) I think you can put the field of regulatory RNAs alongside transcription, splicing, and translation—not yet in terms of size, of course, but in the sense that they’re giving rise to new projects, labs, and institutes focused on their mode of gene regulation. The field shows no signs of deflating anytime soon.

In this piece, I’ll offer thoughts on why I think regulatory RNAs are so popular. It won’t be a review of the literature—this would be futile given numerous excellent reviews already out there (see below for a sampling). If you wish to gleam more info from the blogosphere about regulatory RNAs, I recommend you hop on over to the blog that I run, You’d Prefer An Argonaute, which leans heavily towards discussion of small RNA biology.

To begin let’s define “regulatory RNAs.” They’re RNA molecules that regulate something, often gene expression, but other things too like transposable elements or protection from viruses. The term “regulatory RNAs” is often used synonymously with small RNAs, such as miRNAs, siRNAs, piRNAs, and CRISPR RNAs. Larger non-coding RNAs, such as linc RNAs, also bear consideration, although their functions aren’t well understood at the moment. Since much more is known about the pathways in which small RNAs participate, I’m limiting my focus to them in this piece, and will use the terms interchangeably. There are numerous classes of small RNAs. Some can be expressed in many cell types, like miRNAs, while others such as piRNAs are tissue specific.

Following are the principal reasons for why I think regulatory RNAs are so popular today: they’re “new”; they’re widespread in nature; they’re involved in diverse biological pathways; studying them benefits the general use of RNAi in the lab, a technique that itself has revolutionized laboratory biological science; they’re relatively easy to study; their study has emerged alongside novel high-throughput methods; and finally there’s an intrinsic attraction to studying RNA because of the many biological processes it innervates. I’ll continue simply by expanding these points. But in a nutshell, the combination of these factors has made regulatory RNAs super-popular.

Despite regulatory RNAs being a relatively fresh discovery, they’re found throughout nature. It’s not often that a new mode of gene regulation, present across domains, is uncovered. They’re in bacteria, archaea, and eukaryotes, this last domain that, after closest study, has brought to light numerous classes and pathways in which regulatory RNAs participate. It’s hard to imagine how their presence escaped us until so recently.

Implicit with the ubiquitousness of regulatory RNAs in life is their importance. Knocking out central components of their pathways in whole animals results in severe phenotypes. The phenotypes resulting from knockout of individual regulatory RNAs has depended on the organism/cell type, and the targets of the RNAs. Misregulation of regulatory RNAs has also been implicated in human disease, and some biomedical researchers now seek them as diagnostic tools or targets for intervention. They serve as important components of many pathways, including developmental timing, protection from foreign elements, regulation of transcriptional regulators, patterning of tissues, suppression of repetitive elements, and others. There are just too many to fully list here.

The discovery of small regulatory RNA pathways has also offered a huge bonus to all researchers: RNAi. RNA interference as an experimental tool is now mainstream in the lab. In the post-genome era it has offered the simple promise to knockdown any gene one desires. Even so, the straightforwardness of RNAi can still benefit from improvements, and therefore the study of endogenous small RNA pathways continues to yield greater gains in our ability to silence genes for research purposes.

Regulatory RNAs can be studied with relatively uncomplicated methods. Anyone with even a rudimentary understanding of RNA biochemistry, gene cloning, and basic computer skills can begin to investigate whether small RNAs may be relevant to whatever biological process they’re interested in—no specific expertise is required. This isn’t to say, however, that it’s any easier to make firm, interesting and new conclusions from studying small RNAs (although the literature has suffered on occasion, by lowering the bar for what constitutes a solid study in the small RNA field, yielding to its vogue).

Modern high-throughput sequencing technologies, sometimes coupled with biochemical manipulations, have also spurred regulatory RNAs. Being composed of RNA that targets other RNA, small RNAs and their targets are ideal subjects for new sequencing technologies. Big, expensive toys that yield mountains of data, represent the dreams of many scientists, and in the case of small RNAs, companies like 454 and Illumina are developing sequencing technologies that satisfy these geeky needs while also generating highly useful results. Newly emerging applications of next-generation sequencing technologies, like the HITS-CLIP and PAR-CLIP methods, are going to be very useful in resolving which portions of the transcriptome are bound by certain RNA-binding proteins under specific conditions. The researchers who have developed these protocols have shown off small RNA targets as ideal guinea pigs for these applications. Sometimes it can be hard to tell whether the biological questions drive the technology or the other way around.

My final reason for their popularity is that regulatory RNAs offer researchers another reason to study the greatest biomolecule: RNA. Ribonucleic acid is central to gene expression and regulation, and protein production; it can be an enzyme; it can encode a genome; and RNA or an RNA-like molecule most likely preceded the emergence of life on earth. RNA is the king of multitaskers in molecular biology. Who wouldn’t want to study it?

-David Garcia

Want to know more about regulatory RNAs? Here's an incomplete but nonetheless useful list of reviews about endogenous regulatory RNAs:

RNA interference
Hannon, GJ
Nature. 2002 Jul 11;418(6894):244-51.

MicroRNAs: genomics, biogenesis, mechanism, and function
Bartel, D.P.
Cell 116:281-297, 2004.

Post-transcriptional small RNA pathways in plants: mechanisms and regulations
Hervé Vaucheret
Genes & Dev. 2006. 20: 759-771.

The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race
Aravin AA, Hannon GJ, Brennecke J.
Science. 2007 Nov 2;318(5851):761-4.

MicroRNAs: Target recognition and regulatory functions
Bartel, D.P.
Cell 136:215-233, 2009.

Small RNAs as guardians of the genome
Malone CD, Hannon GJ
Cell. 2009 Feb 20;136(4):656-68.

CRISPR/Cas, the Immune System of Bacteria and Archaea
Philippe Horvath and Rodolphe Barrangou
Science Vol. 327. no. 5962, pp. 167 – 170, 2010

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