Biogenesis and function of microRNAs

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The RNA silencing system comprises various classes of small RNAs. MicroRNAs (miRNAs) are nucleolytically processed from short hairpin-containing transcripts encoded in the genome. They reduce the expression of cognate messenger RNAs via an increased mRNA turnover and/or translational repression. In contrast, short interfering RNAs (siRNAs) derive from a dsRNA precursor that is generated e.g. by a replicating RNA virus. They lead to the cleavage of perfectly complementary RNAs and thus a sequence-specific response against the virus. Indeed, flies carrying mutations in the gene r2d2, the homolog of loqs acting in the siRNA pathway, are highly susceptible to infections with RNA viruses. A third class of small RNAs, called endo-siRNAs, was discovered by deep sequencing of the small RNA repertoire. Like siRNAs, they derive from dsRNA and are loaded in Ago2; but for endo-siRNAs, the dsRNA precursor is of genomic origin rather than from an exogenous source. Some endo-siRNAs originate from long hairpin forming transcripts, but most of them correspond to transposons that have invaded the genome. Silencing of these elements is essential in the germ line, where the related piRNAs serve as defense system, but must also occur in somatic cells to avoid damage in the genome caused by transposition events.  
We use the fruit fly Drosophila melanogaster as a model system to study the biogenesis of small RNAs with a combination of genetic and biochemical tools. It is still an open question how the cell recognizes transposons, then initiates repression. Is this simply a matter of specific chromatin environments into which the transposon eventually integrates? Or is there a mechanism that detects unwanted proliferation of a transposon-sequence? We also want to find out how the various precursor molecules can be distinguished by the processing complexes. Furthermore, we have developed tools to identify the target mRNAs of a given miRNA experimentally using a pulse-labeling strategy that allows us to measure changes in mRNA decay rates genome-wide. We are now applying this technique in combination with other biochemical and genetic approaches to define the biological relevance of individual miRNAs.