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Today I attended Axel Visel‘s talk about his work in identifying enhancers specific to humans at the Primate Biology Group. It was a really awesome talk, and that’s because I’m really interested in differential gene regulation and expression…. especially when it focuses on human evolution. The differences in gene expression and regulation has been one of the big mechanisms that has made humans become humans. Axel pointed out that enhancers are one of the elements that aid differential gene expression and regulation. I’ll define enhancers really soon, but before I do, I gotta tell you what I plan to share with you.

For anyone else interested in this sort of research, I’ll give a quick run down on Axel et al.’s methodology and some of his results. I’ll also share with you a database he and his group have created for all to use, because it is really useful and I hope it inspires future scientists to make their data publicly available. It is a growing trend and all the cool kids on the block are doing it. I’ve already found some impactful use of this database in comparing and contrasting conservation of enhancers to several genes I’ve had my eye on. Also to clarify, Axel Visel is a post-doc researcher associated with Len Pennacchio and Eddy Rubin‘s labs, much of the work Axel presented was done in light of collaborations between individuals in these labs.

Onto defining enhancers. If you haven’t had a formal introduction on the transcription of genes, let me first tell you that genes aren’t magically turned on and off. A whole slew of cellular machines function in turning on and off genes. Many of these machines are proteins called transcription factors, that bind in areas directly upstream from a gene (called promoters) and act as recruiters to other proteins, like polymerase, that being transcribing the DNA into an RNA molecule. If a specific transcription factor is not bound to its target, then the whole complex will not be formed and the gene will not be expressed.

Somewhere in this big bundle of transcription elements are enhancers. I imagine enhancers as little landing strips. That’s basically all they are, they are sequences of DNA that trans-acting factors bind too. Unlike transcription factors, who are directly involved in the transcription complex, trans-acting factors, or activator proteins are indirectly involved in the transcription complex. The presence of a activator protein bound to an enhancer sequence amplifies expression.

So where are enhancers located? Enhancers don’t need to be upstream of a gene. They can be anywhere really. They can be downstream of a gene, in the middle of an intron of another adjacent gene, and they can be located many megabases away. Their position isn’t really important at all, because they act on transcription complex indirectly through the bends and folds we see in long stretches DNA. That’s beside the point. The point is enhancers are located in areas of the genome that are not coded. This is critical to understand how Alex Visel and crew compared and contrasted enhancers.

Axel Visel hypothesized that there must be a set of enhancers specific to humans. All species actually should have a set of enhancers specific to them. By comparing and contrasting sequence conservation in non-coding (highly variable) regions of the genome, Axel was about to identify many locations where sequences were conserved between mice, rats, and human. This was all done computationally. Even with a very stringent p-value, he found a number of sequences that didn’t have as much variation when compared to other non-coding regions. These areas became putative enhancers, which ultraconserved regions of non-coding DNA.

To test out if these enhancers were really enhancers, he and his team inserted these sequences into reporter gene constructs. The concept they tested was if these enhancers were really helping express a gene, then they should express a reporter gene. They then took a whole number of these constructs and inserted them into mice embryos and allowed the embryos to develop. After a certain developmental stage, the developing mice were photographed. The reporter gene was lacZ, a gene that ultimately makes a blue coloration when expressed. Sure enough, Axel was able to show us that some of the putative enhancers identified through sequence comparison really acted as enhancers when the screened in a developing mouse.

Now that he was able to show that with computational tools we can identify enhancers and confirm if they are really enhancers through the transgenic assay, he shifted his attention to finding out if any enhancers have been specific to humans. To do this, Axel couldn’t compare between highly diverged species. Rather, he compared non-coding sequences of humans, chimpanzees, and macaques. That way any enhancers that were specific to humans would be singled out in light of conservation in the primate lineage. Again, was able to find a number of putative enhancers that were wildly different in humans compared to other primates, where they are more conserved. Most of these different enhancers are associated with neuronal adhesion genes, which is a remarkable thing to identify because human’s have larger brains compared to any other primate.

Axel was able to show us a number of other enhancers that act on developmental genes, which were actually found by Jim Noonan and Shyam Prabhakar (of “Accelerated Evolution of Conserved Noncoding Sequences in Humans” fame). Overall he presented a way which one can identify enhancers in vertebrates, and how one can compare and constrast the relative effectiveness of the enhancer in gene expression. If you’re curious about this, please check out Axel Visel’s database, the Enhancer Browser. You can put any gene you’re interested in and see if Axel and crew have compared the conservation of the enhancer in different vertebrates. I found it really easy to use and already am considering in doing a little project out of the data served up on their website.I really recommend you use this site if you are studying differential gene expression between vertebrates. I also really recommend you check out this database even if you’re not studying differential gene expression. Axel and the team that made this resource have done a remarkable thing that I’m seeing more and more — putting up their data for others to look at and use. We’re generating far more data than we could ever use individually, so why not share it? Others could find answers to pressing questions they weren’t able to answer.

Last but definately not least, please check out Axel’s paper on this topic. It is very recent, came out about two months ago in Nature Genetics. I’ve included the citation right below.

    Visel, A., Prabhakar, S., Akiyama, J.A., Shoukry, M., Lewis, K.D., Holt, A., Plajzer-Frick, I., Afzal, V., Rubin, E.M., Pennacchio, L.A. (2008). Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nature Genetics, 40(2), 158-160. DOI: 10.1038/ng.2007.55