Research projects

Our lab is using live animal (Drosophila and zebrafish), genome-scale approaches to understand biological processes. The lab has two main areas of focus. The first involves the nuclear hormone receptor family of ligand activated transcription factors, which control metabolism, growth, behavior, sexual dimorphism, immunity and aging. The second focuses on the process of RNA transport within cells and how this affects cellular architecture and function.


Nuclear hormone receptors:

Hormones are chemicals that circulate within the body and trigger specific responses in target tissues. Steroids, such as the estrogens used to treat or postpone menopause and the muscle building steroids taken by some athletes, are a well known example of these. These particular hormones penetrate cells and elicit responses by binding to a family of proteins called nuclear hormone receptors (NHRs). NHRs control many of the metabolic pathways in our body as well as related processes such as memory, behaviour and aging. Consequently, a large number of human diseases – for example diabetes, obesity and Alzheimers – are caused, or enhanced, by NHR malfunctions. Fortunately, the ability of these proteins to respond to small molecules that move efficiently within the body makes them ideal drug targets. In fact, a disproportionate percentage of the most successful and important pharmaceuticals target specific NHRs. This is despite the fact that hormone partners have yet to be identified for more than half of NHRs. We have devised new methods to identify the unknown hormone partners in live animals. These methods allow us to screen for compounds that may only work in specific cells or tissues. We can also screen for compounds that do not cross-react with other NHRs, act in the wrong tissues or cause detrimental side effects. These are common problems in drug discovery that usually only come to light during subsequent clinical trials. These studies began with initial studies on the orphan nuclear receptor FTZ-F1 (Guichet et al, 1996; Schwartz et al, 2001). We have since published results (Reiniking et al, 2005) showing that the Drosophila receptor E75 uses heme as a constitutive ligand, which in turn allows it to respond to the signaling gas Nitric oxide. In the animal, this allows it to coordinate metabolism with timed processes such as circadian rhythm and metamorphosis. More recently, we have found that the human orthologues of E75, called Rev-erb alpha and beta, also bind heme and respond to Nitric oxide.

Close-up of Rev-erb beta ligand binding pocket structure with heme  bound coordinately


Subcellular trafficking of RNA :

Until recently, it was thought that the shape and polarity of a cell is controlled by the directed movements of proteins to the sites where they are needed. However, we have shown recently that much of subcellular protein distribution and subsequent activity is controlled by the trafficking of messenger RNAs prior to their conversion into protein. This was first shown with mRNA that encodes a secreted signaling molecule – Drosophila Wg/Wnt Simmonds et al (2001). We showed that localization of wg mRNA is required for the proper localization, processing, secretion and function of the highly conserved and important protein.

 

Then, to see how prevalent and important the process of mRNA localization is overall, we embarked on a genome scale project to determine the localization of all mRNAs encoded in the Drosophila genome. First, we developed a highly sensitive, spatially accurate and high-throughput method for localizing mRNAs in whole embryos in high throughput. Thus far, we have completed analysis of approximately 1/4 of the fly genome. The results are surprising, with over 70% of mRNAs exhibiting subcellular localization, and with a large variety of never seen before patterns. These initial results are described in Lecuyer et al, 2007 (editor's pick top paper of the year, Nature). A searchable database with images and descriptions of each mRNA pattern is provided at Fly-fish.  

 

                                         

 

Compilation of images showing examples of localization patterns. Click for larger view