Enhancer architecture

There were a few really interesting talks on enhancer architecture in the gene expression session this morning. Here’s a quick summary of the work, and why I think it’s really cool.

Enhancers, otherwise known as cis-regulatory modules (CRMs), are sequences outside of core promoter regions, which affect gene expression. They can be extremely complex, with a large number of interacting modules working together to facilitate dynamic changes in gene expression. A lot of work has been done on characterising individual enhancers (for a collection of experimentally validated enhancers known for Drosophila, check out REDfly), but we are only just beginning to understand how they interact and work together. Uncovering the design constraints and the action of interacting enhancers is a cornerstone of our efforts to understand genome regulation, which makes this a really interesting topic of research.

The first talk, by Jelena Erceg (working in the Furlong lab in EMBL, Heidelberg) used the enhancers for pMad and Tinman, known from in vivo experiments. From these, she constructed a series of synthetic enhancers attached to a reporter gene, with the aim of finding out the effects of enhancer distance and orientation on their effects on gene expression. It is perhaps unsurprising that both of these do have an impact on the regulatory effects of the enhancer. However, what was interesting is that the effects varied from tissue to tissue – in the visceral mesoderm, the enhancer appeared to be very robust, and only changed effect in response to large changes in spacing. In the cardiac mesoderm, on the other hand, small changes in the layout of the enhancer sites had a large effect on the reporter gene expression, showing that the enhancer is much less robust in this tissue. Getting to the root of these differences sounds like a really interesting problem.

The second talk, by Tara Martin (from the DePace lab at Harvard Medical School), uses the same methods to address a slightly different question. She starts off with two different models of enhancer action. One is an ‘enhanceosome’ – an enhancer where the entirety of it acts as one entity, with the positioning of the elements being important, and the other is a ‘billboard model’ – where the enhancer is composed of a large number of independent modules, with the effects on gene expression being additive. She then used synthetic promoter regions attached to a reporter to test which of these models is plausible – additions of extra modules should not have an effect on an enhanceosome, while they would have an effect on a billboard model enhancer. Her conclusions were very interesting – there were small, independent modules present, but those were composed of a number of enhancer site units. It appeared that the presence or absence of enhancer sites conveyed tissue specificity, while the number of enhancer sites in the module conveyed the strength of the regulation effect.

The reason I love these studies, is that they draw on previous in vivo research, and then use a structured synthetic biology approach to try and unveil regulatory design principles. As well as giving really interesting results, the carefully constructed experiments that systematically test interactions and effects are, well, pretty. They have that lovely traditional appeal of “carving nature at its joints” – just what science should be like!