Your Genome’s a Mess

"What a piece of work is man! How noble in reason! How infinite in faculty! In form and moving how express and admirable! In action how like an angel! In apprehension how like a god! The beauty of the world, the paragon of animals!"  Hamlet, (Act II, Sc. II).
Throughout my time as a scientist, I’ve always been curious about genetics and evolution, and our recent capacity to accurately and rapidly sequence whole genomes is shedding all sorts of new light on life and how different organisms go about it.
Certainly, it stands to reason that our big brains (Beverly Hills Chuhuahua being #1 at the box-office and the current financial climate notwithstanding) reflect on a macro-level our excellence at the genomic level.  If “survival of the fittest” rules, then our genome should rock, right?

Wrong. It turns out that only about 5% of our genome is what’s required to make us, well, us.  The rest?  More or less crap.  As a species, we’ve incorporated lots of genetic flotsam into our 3.4 billion base-pair genome – the majority of it consists of repetitive stretches of DNA called LINEs and SINEs (Long – and Short – INterspersed Elements) – which are the debris of DNA copying machinery mistakes.  It is the equivalent of storing all your junkmail into a giant spare room.

Well, maybe all species are like that?  Nope.  Some species do better – much better.  Microorganisms have incredibly lean genomes.  Among vertebrates, the winner for efficiency (dare I say the most Intelligent Design?) is the puffer fish.  The puffer fish has just as many functional genes as you or me (~30,000), but its total genome is about 1/8th the size of ours.  The reason for this efficiency: the puffer fish has developed a way to keep the spare room of his genome clean. Go fugu!

Does that help the puffer fish in any meaningful way? (And conversely, does our accumulated crap hurt us?)  Not that we can tell, and it seems like the nucleus can carry a bunch of extra baggage and not really care.  But to me, it’s sort of a humbling lesson – that at a very fundamental level, we’re not remarkably special.  Many genomes are much larger (wheat’s genome is five times the size of ours) and many are better organized.
More than 500 years ago, Copernicus taught us that we weren’t the center of the astrophysical universe.  Turns out, we’re not center of the biological one, either. 

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15 thoughts on “Your Genome’s a Mess

  1. Excellent post! I never thought about how much of our genome is actually useful vs. transcription errors. Glad to hear that we've got a giant room of junk that nobody ever goes in and yet doesn't impact us in any way – it seems my genome is mirroring the reality of my home relatively well.

  2. Thanks Ross — ironically it's a lot like a lab-bench too. If you have 3-feet of space, you fill it. If you have 10-feet of space, you fill that too and wonder how you ever got along before with just 3.

  3. The thing that's really cool is that there are going to be enough versions of the human genome in the near future that you'll be able to look across a group of individuals and see what parts are the same and what parts have variability — that's been possible at the genetic-locus level, but never at the individual nucleotide level before.

  4. And that's why I panic when they point out the new desk I might be moving to, and it's about 2/3 the size of my current one. I'm not sure how I'm going to get all my crap that's sitting out back into a smaller footprint.

  5. Wow, that's got to be one of the best blog posts ever. Thanks for the lesson o' the day! Perfect amount of information for me to digest given my short attention span while at work. :-)

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