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This Genome's Got Back

September 13, 2012

Eva Gusnowski

How much junk is in your genome’s trunk? Is it draggin’ a wagon? Or maybe that baby’s just got back. Sir Mix-A-Lot may have had the right idea, and was actually way ahead of scientists these days.

On a fateful day in 2003, sequencing of the human genome was completed. Well, there’s some speculation that the typical middle-aged Caucasian male genome was sequenced **cough** Craig Venter **cough**. Nonetheless, the sequencing of the human genome was a remarkable feat, and we were more than ready to discover how superior we were to everything else in the world.

And then the shit hit the reality fan.

The human genome consists of 23 pairs of chromosomes (22 pairs of autosomes and 1 pair of sex chromosomes), and about 3 billion base pairs. Once thought to consist of well over 100 000 genes (because, well, humans are just so gosh darned complicated), the human genome was found to consist of only 20 000 – 25 000 protein coding genes. Surprise! Contrast this with C. elegans, a wee little 1 mm long nematode that lacks bones and eyes, which has a set of over 19 000 genes. It turned out that what made us so much more complex than other little beasties wasn’t simply a higher number of genes.

With the overall lack of identified protein coding genes, our genomes have always been considered to be full of “junk”; that is, non-coding DNA that is found between coding sequences for genes. Conservatively, it was estimated that the junk in our trunks comprised 98% of the human genome. For quite some time following the sequencing analysis, this was thought to be true: we weren’t complex and we weren’t streamlined. So what were we?

 



The discovery of functional RNA sequences in humans (after their discovery in model organisms) began to turn this concept around. RNA-coding genes have been found throughout the genome and begin to recycle some of our genome’s trash. Recently published evidence in both Nature, Genome Research and Genome Biology in early September has now taken the human genome past the bottle depot and down to the high-tech recycling facility.

New analyses with ENCODE, the Encyclopedia of DNA Elements, have assigned at least some sort of function to approximately 80% of the genome, whether this is the production of RNA/proteins, RNA, enhancer, promoter and repressor sequences. And guess what? They’re only half done with the current project.

 



But why do we care?

From my perspective, coming from both a genetics and a medical student point of view, its easy to mistake mutations in protein-coding genes that cause disease states as the only major impact that the genome has on health. Essentially, this means that we focus our sequencing efforts in disease states on only 2% of the genome. However there are many, many, MANY conditions that appear to have a hereditary link, and yet lack any known mutations; but maybe we’re just looking in the wrong places. If more people can appreciate the utility of looking in sections of the genome that used to be considered only “junk” for links to disease states, maybe we’ll be able to predict disease states at a more appreciable level. That’s not to say that this won’t be difficult or that it won’t require more research on techniques and analyses. But the human genome is our genome for a reason, and I’m glad that we’re now learning to appreciate its absolute complexity.

One genome’s junk is one scientist’s treasure!

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