Phyloseminar: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

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Next up on phyloseminar:

Mike Lin speaks Tuesday, April 26th at 12pm PST on “Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes”

The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes—especially at synonymous sites. We developed a method to systematically locate short regions within known ORFs that show conspicuously low estimated rates of synonymous substitution, based on phylogenetic codon rate models and likelihood ratio tests.

We applied this method to genome alignments of 29 placental mammals, resulting in more than 10,000 “synonymous constraint elements” (SCEs) with resolution down to nine-codon windows. These are found within more than a quarter of all human protein-coding genes and contain ~2% of their synonymous sites. We collected numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. We also ruled out certain alternative explanations such as codon usage bias and neutral rate variation.

Our initial results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape. Furthermore, anticipating the future availability of additional mammalian and vertebrate genomes, we are currently developing Bayesian codon modeling methods to measure synonymous rates at even higher resolutions, perhaps eventually allowing the detection of individual regulator binding sites embedded in protein-coding ORFs.

Japan 04:00 (04:00 AM) on Wednesday, April 27
New Zealand 07:00 (07:00 AM) on Wednesday, April 27
West Coast USA 12:00 (12:00 PM) on Tuesday, April 26
East Coast USA 15:00 (03:00 PM) on Tuesday, April 26
England 20:00 (08:00 PM) on Tuesday, April 26
France 21:00 (09:00 PM) on Tuesday, April 26

6 Comments

Very cool!

Incidentally, although the term “degeneracy” has been the accepted term for decades, in retrospect, “redundancy” of the genetic code might have been a clearer synonym.

Also, I was going to go out today and buy a bunch of Ed Hardy bikinis, Gucci sunglassess, and Coach necklaces, but now I’m so offended by the spam that I changed my mind!!!!!

Way to go, mingego, costing your clients sales.

At least they have the decency to read the post before spamming these days.

[This comment, which was for some reason held for moderation, refers to a new wave of spammers who actually read the post and appear to comment on it, though at least one got it exactly wrong. The spam comments have already been deleted.]

Of course it needs to be pointed out that this result is exactly what one would expect if eukaryotic genomes are the product of billions of years of random mutation and natural selection. Now we have ten thousand more examples of chance events and cooptions that have shaped the genetic landscape. This is evidence that can be instantly be used to fight creationism whenever it rears its ugly head.

Once again, all the creationists can do is wave their hands in the air and claim that they “predicted” this all along and that this is exactly what an intelligent designer would do. One wonders why, if this were indeed the case, they were not the ones doing the research and publishing the results? I guess it’s just another case of: “I do so love science, you do it”.

harold said:

Incidentally, although the term “degeneracy” has been the accepted term for decades, in retrospect, “redundancy” of the genetic code might have been a clearer synonym.

Also, I was going to go out today and buy a bunch of Ed Hardy bikinis, Gucci sunglassess, and Coach necklaces, but now I’m so offended by the spam that I changed my mind!!!!!

Way to go, mingego, costing your clients sales.

Well this just proves that if the genetic code was designed, it was designed by a degenerate.

I see the teabaggers got some money to send out more spam.

About this Entry

This page contains a single entry by Reed A. Cartwright published on April 20, 2011 5:45 PM.

This Week in Intelligent Design - 20/04/11 was the previous entry in this blog.

The conceptual alchemy of ID, transmuting baseless assertions into scientific predictions is the next entry in this blog.

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