Molecular genetics; RNA and RNA-protein interactions; developmental biology
Our work lies at the interface between developmental biology, molecular genetics and biochemistry. How are mRNAs controlled? How is that control used to regulate development, cell growth and memory? We combine in vivo approaches and test tube assays, and use a range of organisms — yeast, worms, flies, and frog embryos. In parallel, we develop genetic strategies that exploit functional genomics to reveal the circuitry of mRNA regulation. We focus on several interconnected problems.
Understanding how mRNAs are regulated
It is not enough to make an mRNA: you have to know how and when to use it. mRNAs are controlled at many levels — they can be turned on or off, be destroyed or stabilized, and can be moved within the cell. These controls are critical in biology — in development, viral replication and human pathologies, for example. Our work aims at identifying the molecular mechanisms that execute these controls. The powerful molecular genetics of the yeast, S. cerevisiae, is invaluable for this purpose, and has led to the identification of key players in the process.
Focusing on a regulatory hot spot
The region of the mRNA between the termination codon and the poly(A) tail — the 3’ untranslated region (3’UTR) — often governs when, where and how much protein an mRNA produces. A key first step in figuring out how 3’UTRs work is identifying the regulators they bind to. Using methods we developed, we identified and cloned 3’UTR regulators in both C. elegans and yeast. At the same time, we have identified mRNA targets for regulators we already knew. The challenges now are to understand how these mRNA-protein complexes, located in the 3’UTR, regulate an mRNA’s expression, how they are integrated, and how they evolve.
Development and the brain
To understand how mRNA controls work during development, we generally focus on the first few hours of an animal’s life, and exploit the molecular genetics of C. elegans and Xenopus. Key mRNA regulators control many key decisions in the germ line and in stem cells. We now want to know how these regulators are coordinated to do the right thing at the right time.
Learning and memory appear to rely on the activation and repression of specific mRNAs. Changes in translation at synapses are critical for establishing neuronal circuits. Many of the regulatory proteins used are the same as those used in early development. We want to understand how these mRNA control events work in the brain. We use genetics and biochemistry for this purpose.
Complete genome sequences open the door to understanding the functions of the entire protein complement of an organism. But they only open the door: to make use of the information, you have to develop ways to see the connections among the genes, among the RNAs and the proteins, and to understand how both of them function in the cell.
RNA protein complexes
We use a variety of methods, ranging from biochemistry to molecular genetics and structural analysis, to dissect specific RNA-protein interactions. We focus on a web of interacting regulatory proteins found throughout the animal and plant kingdoms. We dissect RNA-protein and protein-protein interactions that underlie biological regulation, aiming to get a detailed molecular understanding of the complexes involved.