RNA is best known for its role in protein synthesis. A section of chromosomal DNA is copied (transcribed) into a single strand of the chemically similar RNA, which migrates from the nucleus into the cytoplasm. The 4-letter RNA code is then translated into a specific protein sequence.
But RNA is not just an intermediate between DNA and protein; in fact, it quite possibly pre-dates both. The RNA World hypothesis was based on the finding that some RNA molecules have catalytic activities, similar to those of the more familiar protein-based enzymes. The hypothesis proposes that the most primitive life on earth was based on these active RNA molecules, known as ribozymes.
Echoes of this ancient world can still be seen in modern genomes, which encode ribozymes with various molecular functions that mostly involve the manipulation of RNA itself. Other classes of RNA molecule with no catalytic activity are also known to play a role in the cell, especially in the regulation of gene expression. Our understanding of the cellular functions of RNA is increasing rapidly, and may even yield new medical treatments based on RNA-mediated gene silencing.
A couple of recent papers highlight the difficulties and rewards of RNA research*. The first is a review by Christian Hammann and Eric Westhof. The paper begins with a comprehensive description of the major classes of known ribozymes and their biochemical activities. The diversity of these molecules is quite incredible, and raises many interesting questions about the evolution of catalytic RNA. However, this same diversity also causes great difficulties when trying to identify novel ribozymes.
Some classes of ribozyme do contain short stretches of conserved sequence that are amenable to whole genome searching. However, ribozyme molecules bend and fold into complex secondary structures that are much more difficult to compare and predict. Two similar sequences can fold quite differently, resulting in distinct biochemical activities. And different molecules with different structures have been found to control very similar reactions.
A more recent innovation involves high-throughput functional screening for catalytic RNA. Genomic DNA is divided into short circular sections, which are then separately transcribed into RNA. An output of short RNA molecules rather than one continuous strand would demonstrate the presence of an RNA entity capable of cleaving itself in two, a common ribozymal function.
Hammann and Westhof conclude that a combination of improved sequence searching algorithms and more functional screening assays is required to help identify novel classes of ribozymes. One approach they did not mention is sequence comparisons between different species. I may be biased by my work in the field of gene promoter evolution, but I would expect that comparing the sequences of known ribozymes in different species would yield some interesting insights into the general patterns of ribozyme conservation throughout evolution. Novel ribozymes could then conceivably be identified by screening genomes for regions of unknown function that display similar patterns of sequence conservation.
That thought leads me nicely into the second paper, by Shaun Mahony and colleagues from the University of Pittsburgh. This group used the concept of multi-species sequence comparisons to investigate the regulation of microRNAs. These short stretches of non-catalytic RNA are found throughout the genome, and help control gene expression by binding to RNA gene transcripts that have a complementary sequence. MicroRNA binding triggers a set of reactions that ultimately degrade the complementary transcript, resulting in lower levels of target gene expression.
Sequence comparisons revealed that the regions thought to control the transcription of microRNAs were better conserved throughout evolution than the regions that control expression of most actual genes. Indeed, the regulation of microRNAs appeared to be just as well conserved as that of genes involved in embryonic development. (This process must obviously be very tightly controlled, as the effects of any changes in gene expression during early development can be massively amplified in subsequent stages and wreak havoc in the embryo). MicroRNAs must therefore have some essential function, one that can not be disrupted without disastrous repercussions for the organism.
We are only beginning to understand the many functions of RNA. It is clear that the tools originally developed to analyse protein-coding genes will have only limited function when applied to the RNA world within our genome. With new tools will come new discoveries, and new reminders of how RNA continues to play its ancient role in the lives of modern organisms.
*and I'm not just talking about the notoriously unstable nature of RNA, which succumbs very easily to the mysterious enzymes known as fingerases regardless of what precautions you take and how many times you spray your gloved hands with ethanol.
Update: ERV also has something about the RNA World hypothesis today!