Stefan Ameres, PhD

Lab Website

 

Mechanism and Biology of RNA Silencing

 

The implementation of distinct gene expression profiles is essential for organismal development, physiological responses to external stimuli and pathogens, and defines a primary cause for disease. My lab is fascinated by the molecular events that control these processes at the post-transcriptional level by focusing on two major areas:

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Small RNA silencing. Small silencing RNAs regulate gene expression in nearly all eukaryotes and have enormous biotechnological and therapeutic potential. Among these, microRNAs belong to the larges family of trans-acting gene regulatory molecules in multicellular organisms. In flies and mammals, they control more than half of the protein-coding transcriptome, and act as key regulators of organismal development, physiology, and disease. We are interested in molecular mechanisms that govern small RNA silencing pathways in flies and mammals. Our focus lies on processes that regulate the production of small RNAs, their assembly into functional ribonucleoprotein complexes, and the disassembly thereof in response to synthetic and natural triggers. Our goal is to unravel mechanistic principles of small RNA-mediated gene regulation, a phenomenon that impacts virtually every aspect of metazoan biology.

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The Epitranscriptome. For RNA to fulfil its essential function within the cellular environment, numerous chemical modifications have evolved to sculpt its physical and functional interactions. Although more than hundred types of RNA modifications have built the descriptive foundation of what is referred to as the epitranscriptome, their mode of action remains largely unknown. We are studying the function of chemical RNA modifications, at the intersection of small RNA silencing pathways and general RNA metabolism. Our focus lies on the post-transcriptional addition of nucleotides to the 3´ end of RNA (i.e. tailing) by the only rudimentary characterized enzyme family of terminal nucleotidyltransferases in order to dissect the regulation of microRNA biogenesis and function; and the role of small RNA ribose methylation in order to gain insights into the antiviral immune response through the RNAi pathway in flies. The emerging concepts will inevitable impact our view on more general functions of post-transcriptional modifications in RNA metabolism. And we are applying our mechanistic insights to the development of novel epitranscriptomics approaches to probe post-transcriptional gene regulatory networks at the transcriptome-wide level.

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Drosophila melanogaster provides a unique combination of in vitro biochemical methods, cell culture experiments, and in vivo genetics to dissect the mechanisms and biological implications of RNA silencing. We are combining the strength of this model organism with the power of modern deep-sequencing technology and bioinformatics. The hypotheses that emerge from our fly studies are directly tested in human cell extracts and in cultured mammalian cell lines in order to determine the conservation and divergence of key principles in small RNA-mediated gene regulation and RNA metabolism in flies and mammals.  

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Overall, our goal is to determine fundamental biological mechanisms of post-transcriptional gene regulation through pathways with enormous biological, biomedical, and technological impact.