Friday, January 17, 2014

Elephant sharks and the power of the genome

Recently an article was published in Nature News called Why Sharks have no bones. Now as you know, I'm a plant biologist who studies soybean. So what is my interest in sharks? My first love has always been marine biology, in fact my master's degree is in marine biology/biochemistry where I studied marine algae. Anything ocean is going to pique my interest. That was enough to make me click the link, and then I saw this:
Norbert Wu/Minden Pictures/Getty Images
That is an elephant shark.. something I was not even aware existed! It looks like a vacuum cleaner! I personally think it is one of the coolest sharks I have ever seen! They sequenced the genome of this shark, the first shark to ever have its genome fully sequenced. That, in of itself, is an accomplishment. It amazes me how quickly genomes can be churned out. Modern DNA sequences are incredible, they can do hundreds of thousands of nucleotides in mere hours! It used to take us weeks to accomplish less than a day's worth of sequencing.

After sequencing they went and compared protein families found in this shark with that found in bony fish and lampreys (which are jawless fish) to try and see what proteins might be missing that could explain why sharks and rays do not have calcified bones but only cartilage. They used genomic and transcript levels, which is DNA and RNA respectfully, to examine what genes were present, as well as being produced, in this fish. Some might be wondering how they can be comparing protein families when they measured DNA and RNA. DNA stores all the information of every protein the shark is capable of making, but RNA will show only those genes which the shark is actually using. And since RNA is the blueprint from which proteins are synthesized, and we know how to read these blue prints, it is easy to take an RNA sequence and relate it to known protein sequences. This technique let them distinguish between genes that are simply not present (not found in the DNA) or are not being expressed (in DNA but no RNA) in the shark. It answers the question of are they capable of calcifying bones but those genes are not activated for whatever reason, or are they incapable of turning cartilage to bone.

When the compared the information they found in the shark with the known bony fish genetic information, they found that sharks do have some of the protein families known to regulate the transformation of cartilage into bone but are missing one specific family (secretory calcium-binding phosphoprotein (SCPP). To confirm that this, the researches turned those genes off in Zebrafish (a bony fish) and found that their ability to turn cartilage into bone was significantly diminished.

So why is this cool? For starters any time someone publishes a new genome I think that is cool. The fact that all of the complex differences in biology are controlled by a simple set of 4 nucleotide "letters" is incredible. The ability to sequence and compare genomes will let us pinpoint the function of more genes across species. Who knows what information we can find! It's like a huge biological scavenger hunt! This study is a step above simple genome, they were able to find a family of genes that are lacking in this shark yet present in bony fish. They took the step beyond just comparing their database with the other ones already on the internet and knocked those genes out of a bony fish to see the effect. Studies like this are my favorite, combining the power of bioinformatics and wet lab physiology experiments. So powerful!

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