Accessible Research: Fast Times at DuplicatedGene High

Part of my goal with this accessible research is to introduce you, dear readers, to some topics you might otherwise overlook because they seem uninteresting, irrelevant, or just unaccessible. Many apologies to the scientists' whose research I paraphrase if you come across my blog and think I've over-simplified, or somehow mis-represented your results. That is certainly not my intention - and I welcome your comments!

Also, may thanks for putting up with my very lame, and sometimes obscure, sense of humor. :) Today's title was chosen because the I thought the tagline for Fast Times at Ridgemont High fit well:

Fast Cars, Fast Girls, Fast Carrots...Fast Carrots?

Today we'll look at a paper in GBE, which you can all freely access here.

Noncoding Sequences Near Duplicated Genes Evolve Rapidly

Dennis Kostka^*,1, Matthew W. Hahn² and Katherine S. Pollard^1,3,4
Genome Biology and Evolution Vol. 2:518; doi:10.1093/gbe/evq037

Okay, okay, I admit it, we're not looking at cars, girls or carrots. Instead, the researchers here studied noncoding sequences, duplicated genes and rates of evolution.

Noncoding sequences are DNA sequences that do not code for a protein. Most of what is discussed in the mainstream media is coding sequence. Generally, when a gene is discussed, we are actually referring to the protein it produces; this protein is made from the coding sequence of the gene.

So why do we care about how noncoding sequence evolves? The noncoding sequences can be very useful because they can contain signals that tell the protein how to fold, tell the gene when and where to be expressed, and how much should be produced. For example, in typing this, I'm pretty glad that signals were given to make sure that cells in my heart differentiated properly into the right kind of muscle tissue to be able to pump blood through my body, while the cells in the back of my eyeballs developed light-receptors, instead of the other way around. There are still so many factors both genetic and environmental) that determine how tissues differentiate, and what genes are expressed when, but one way to get a handle on this is to look at how the noncoding sequence evolves.

In particular, these researchers looked at the noncoding sequence around genes that have duplicated - that is, there are two copies of these genes in our genome.

If both are retained, it is likely that one, or both copies evolved a new function (See Hughes, 2005 in PNAS for a short review). The new function could have come from changes in the coding sequence (changing the protein itself, and therefore what it does), or could have come from changes in the noncoding region (potentially changing the timing, location or abundance of the protein produced).

Here it is good to mention that many genes have more than just one function, and may be expressed in many tissues, performing different functions based on the tissues in which they are expressed. So, it is expected that changes in the noncoding region may have a large impact on the gene. These changes may be responsible for many of the differences observed between species.

Indeed, these Kostka, Hahn and Pollard (2010) found that the noncoding regions around duplicate genes (duplicated only in humans & chimpanzees after their divergence from macaque) evolve faster than the noncoding regions around single-copy genes (that are single copy in human and macaque). Both this study, and a similar one by Park and Makova (2009), show that noncoding sequences around duplicate genes evolve quite rapidly, complementing work by Chung et al., (2006), which found that the coding sequence of duplicate genes also evolves rapidly.

The current study goes further to look at the functions of the genes nearby the noncoding sequence and finds that many of them are expressed during pregnancy and the formation of the placenta.

So, while my little bun in the oven kicks to remind me she's working hard on developing, I now know the sequence likely involved in regulating the formation of her protective placenta has evolved pretty rapidly over the past few million years, and, although it still needs to be tested, hopefully it is due to selection on beneficial mutations (stay safe in there little one!).