As I write this, many of my colleagues are in Vienna, gathering for the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB).
I’m not going to attend ISMB this year, unfortunately—a confluence of new job and busy schedule. Next year, ISMB will be closer to home in Toronto. I’m looking forward to it, because it will also give me a good reason to stop by and visit a scientist I know, Professor Laurence (Larry) Moran up at U of Toronto.
Dr. Moran is interested in many things, including the molecular-level effects of evolutionary processes. If you read the Usenet newsgroup talk.origins you’ll find some very good posts by Larry on many topics, including neutral selection. His website linked above has other interesting sites he’s authored, I recommend them. He also blogs at Sandwalk: strolling with a skeptical biochemist
Over the past few years, I’ve had some interesting discussions (sometimes heated) online with Larry on neutral selection, biological “noise”, and alternative splicing. For example, in the past discussions Larry’s viewpoint was that the majority of alternative splicing was noise with some functional exceptions. My viewpoint at the time, back in 2003 or so, was that there was a definite use for alternative splicing with specific examples, and we discussed the possibility that many of the alternative forms were in fact nonfunctional noise that yet provided a selectable background of protein forms for evolution.
Until recently, I had been working at a biopharma company that was interested in alternative splice products…like many other biopharmas at the time. The idea was that the discovery of an alternative splice product would be a chance to get some intellectual property rights on a protein and its use. I had seen countless examples of such alternative splicing products when combing through EST databases. Some genes had a plethora of alternatively spliced forms. In fact, we published a paper on the complexity of a particular GPCR family, the LGR receptors, in Molecular Human Reproduction in which we found several alternatively spliced variants of the receptor that seemed to have expressed protein products that had a functional activity in vivo.
There is other evidence for the complexity and functionality of splice variants, see for example this excellent open access review, Benjamin J. Blencowe Cell, Vol 126, 37-47, 14 July 2006 . The review is complex and detailed and I can only suggest you read it if you’re interested, as I can’t hope to do it justice here. One of its subsections gives a discussion of the global consequence of alternative splicing. Acknowledging the stochastic nature of splicing, and that many transcripts may in fact have no apparent biological function, the author proposes a new level of regulatory complexity: an alternative splicing “network” which may further regulate cellular proceses by providing different isoforms in different contexts—essentially, for specific interaction coordination in different tissues. He writes, “An emerging model is that these subsets of genes may comprise “layers” of gene networks that coordinate specific cellular functions.”
At ISMB/ECCE this year will be several talks specifically discussing alternative splicing, both in evolutionary terms (primates), in humans (ENCODE), and in specific cases of certain proteins.
One such presentation will be by Michael Tress, who was the first author of many on a PNAS paper detailing analysis of manually annotated splice variants in the GENCODE project (Tress et. al, The implications of alternative splicing in the ENCODE protein complement. PNAS 2007 Mar 27;104(13):5495-5500 ) where the authors examined a small segment of the human compliment of alternative splicing: about 2600 annotated transcripts for 487 distinct loci, with an average of 2.53 transcripts per locus. Supporting the papers mentioned in the Blencowe review, the Tress publication finds that in the loci they examined, that ”…these functional alternative isoforms appear to be the exception rather than the rule.” They also conclude that many isoforms may be deleterious based on detailed structural analysis of the protein products, but they note “If alternative transcripts in low numbers do not adversely affect the organism, the selection pressure against exon loss or substitution will be reduced, and the new variants will be tolerated, making large evolutionary changes possible.”
So, where is work on alternative splicing going to lead in the future? Blencowe’s review mentioned that there is a significant number of human SNPs that may cause disease phenotypes by affecting splicing. These diseases may result in aberrant splicing in the affected gene, causing loss of a transcript by nonsense-mediated RNA decay (NMD) or causing loss of a protein domain or protein interaction region, thereby disrupting the operating characteristics of the protein. There will likely be future work in discovering these SNPs and variations leading to alternative splicing. Additionally (also in Blencowe) there will likely be further work in examining patterns of alternative splicing between species, between tissues, and between specific developmental and biochemical contexts.
There is a lot of room for new research on alternative splicing. I recently attended a Gordon conference on Bioinformatics which I cannot discuss in detail as many results were not yet published. However, I can mention that I saw some good talks by Boston labs on alternative splicing: “Cooperative, Compensatory and Context Effects in Pre-mRNA Splicing” by Chris Burge at MIT , and “Polymorphic Splicing in Humans” by Hunter Fraser at the Broad Institute.
So, when I return to Toronto for ISMB 2008 , I plan on having a good visit with Larry, and discussing how he was right in that most of alternative splicing is probably noise. A conversation in his lab in Toronto a few years ago was on the right track: it appears most of sampled human alternative splicing may be selectable noise as there are functional splice variants among that noise that might allow interaction networks to fine-tune their behavior in subnetworks of functionality.
Stochastic processes that rule such effects as non-homologous recombination, alternative splicing or non-specific molecular interactions may be tolerated as they generate a selectable background for occasional evolutionary leaps. In the cases where suboptimal splice products may become dominant in a system for a gene with an essential role, a higher population of nonfunctional variants may lead to sub-optimized networks, which in humans yield phenotypes of disease.