Introducing…RNAi

Nucleic acids (DNA and RNA) underpin everything in biology.  All the information about an organism is stored in nucleic acid form; and all the actions that are taken from this information rely (directly or indirectly) on nucleic acids.  So it should be no surprise that a system has evolved that allows one individual directly to manipulate the nucleic acids of another.  But the dual simplicity and intricacy of this system are truly astounding, all the more so as new discoveries are rapidly made.

The system is RNA interference (RNAi).  It is based on two simple concepts: extreme specificity in recognising its RNA targets, and generality in the mechanisms that deal with these targets.  Though it was only discovered (somewhat unwittingly) by Napoli et al in 1990, it has since been comprehensively characterised (resulting in the 2006 Nobel Prize being awarded to Andrew Mello and Craig Fire).  While its mechanisms and functions vary between different groups and even kingdoms, the basic idea is as follows:

 

The generality of the system comes from the large proteins that do the cutting: just a few different proteins can be recruited to degrade a wide array of targets.  And the specificity is conferred by the small RNAs: because they are derived from the target itself, they will necessarily be specific to that target.

It is the fourth step in the mechanism – where RNA derived from the target guides the rest of the machinery to the correct place on the correct target messenger RNA (mRNA) – that makes the system so effective and economical.  Regardless of mutations that occur in the target’s genome, the cell will always be able to deal with it, as it will use this newly mutated sequence to guide its machinery – the target can never escape degradation simply by mutational change.

These small RNAs can be broadly classified into three types.  Small interfering RNA (siRNA) targets extracellular parasites such as viruses, and hence is integral to the immune system.  Piwi-interacting RNA (piRNA) targets intracellular parasites like transposable elements (sections of the host’s own genome which can cut themselves out, or copy their sequence, and paste this back into the host’s genome), and is thought to be expressed exclusively in the germline (reproductive cells) where these elements are most active.  And microRNA (miRNA) targets the host’s own gene transcripts, allowing it to fine-tune gene expression.

These different small RNA types mean that the RNAi pathway has a dizzying array of functions in different organisms: stem cell maintenance, chromatin formation and upkeep of fertility to name just a few, as well as the antiparasite role mentioned earlier.  They have also become a standard tool for investigations into gene function and expression: by injecting the right double-stranded RNA sequence into a cell, one can knockout a specific gene while keeping everything else constant.  By seeing what the cell can no longer do, or what it starts to do, reliable inferences can then be made as to this gene’s function.

However, recent work is calling into question the strict delineation of function between the different small RNA types.  Interactions between pathways and crossover in their functions are blurring the boundaries between siRNA, miRNA and piRNA.  Most excitingly, new work is building the case for RNAi occurring in humans: future discoveries, and applications of these discoveries, will be truly fascinating.

References

Napoli, C., Lemieux, C. and Jorgensen, R. (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans.  The Plant Cell 2: 279-289

Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E. and Mello, C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.  Nature 391: 806-811

Okamura, K. (2011) Diversity of animal small RNA pathways and their biological utility.  WIREs doi: 10.1002/wrna.113

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  1. Pingback: Arms race gains a third layer of counteradaptative complexity « Beagle and beyond

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