Thursday, August 4, 2011

Not Quite Gattaca: Part 2 - The Reason

In my last post, I discussed some of the major technological breakthroughs in the last few years that have enabled DNA sequencing to become faster and cheaper. But the next question is why?

Well, the cliché answer is the pursuit of knowledge. By gathering DNA and RNA sequence from many organisms, and also understanding variation between a population of organisms scientists learn more about the world around us, and of course, what makes people different, and the genetic code in both health and disease.

I mentioned RNA or as it’s known in its full form - ribonucleic acid. In the simplest of terms, RNA functions as the messenger between DNA and protein, it's even known as messenger RNA or mRNA for short. DNA consists of two major parts – introns and exons. Exons are encoded into proteins which build our cells and regulate everything from cell metabolism to cell death. However RNA can influence DNA by intereacting with it, and the overall behaviour of the central dogma of molecular biology (Figure 1) is far more complex than turning DNA into a product. Add to this the effect of the environment on the genetic code, and the system is one of massive complexity.

Figure 1. The central dogma of molecular biology, now understood to be less than straightforward.

Not long ago it was thought the genetic code would read much like a book, however this is rapidly being overturned as researchers began pulling apart the human genome. Whilst the draft of the human genome was published in 2000, the 6 billion base pairs sequenced is the tip of the iceberg. Understanding the obvious outcome of genetic mutations in disease, as well as the more complex traits arising from that interaction of environment has proven to be anything other than straightforward.

But cheaper, large scale DNA technology doesn’t end with human genetics. The study of plants and animals has been revolutionised through new technology. This not only includes the living animals, but also extinct animals. In 2008, the woolly mammoth genome was published – the first extinct animal to have its genome decoded. This was possible due to new sequencing technology, which as well as being able to generate sequence for millions of bases of DNA per run, but also is far more sensitive. This sensitivity is ideal for sequencing the small, degraded fragments of ancient DNA, and the large coverage enables endogenous sequence to be sequenced against the high background often seen in ancient DNA samples. Since the first Neanderthal DNA sequences, we’ve seen the entire Neanderthal genome published, DNA from cave bears, extinct equine species and even the giant moas of New Zealand. And it’s not just extinct animals that of interest; understanding population dynamics of currently extant populations is important. From understanding previous human migrations, to the effects of climate change on different animal populations, to domestication events on plants and animals large scale DNA sequencing has allowed for an improved understanding of evolution, the impact of human interaction on animal and plant species and the impact of large climatic events on ecosystems.

New sequencing technology has opened many doors – from medical genetics to conservation to evolutionary biology. It’s a great time to be a biologist, and all this new technology is giving us improved methods to understanding the basis of life - the genetic code. And as it has been realised, the genetic code isn’t a straight forward page turner, it’s more like a choose your own adventure book – not to be read from front to back, but rather backwards, forwards and under the influence of the environment around it. Thus all these tools have come at an ideal time for we are firmly in the era of the genome in all its wonderful and varied complexity.

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