Research Report 2010 - MDC

Structure of the GroupGroup LeaderDr. Markus LandthalerTechnical AssistantsJulia KretschmerMarkus LandthalerScientistsAlexander BaltzLea GregersenKerstin BaethgeRNA Biology and Post-transcriptionalregulationOur main interest is the understanding of post-transcriptional regulatory networkscontrolling gene expression in humans. In cells RNA stably associates with RNA-bindingproteins, RNA helicases and nucleases to form ribonucleoprotein complexes. These complexesplay a key role in the regulation of spatial and temporal changes in protein synthesis bycontrolling transport, storage and translation of mRNAs. Deregulation and failed coordinationof these mechanisms contribute to pathophysiologicial development and conditions. Aprerequisite for a systems level understanding of post-transcriptional regulation is atranscriptome-wide high-resolution map of the RNA-protein contacts that allows us to studyhow these interactions control the fate of cytoplasmic RNA. To achieve this goal we use anovel crosslinking-immunoprecipitation approach (PAR-CLIP) in combination with massivelyparallel sequencing to identify functional RNA-protein interactions at single-nucleotideresolution.Post-transcriptional regulation by RNA-bindingproteinsMammalian genomes encode several hundred RNAbindingproteins, each containing one or multipledomains able to recognize target mRNA in a sequenceand/orstructure-dependent manner. The association ofthese proteins with RNA regulates the biogenesis andtranslation of RNA. For a large number of RNA-bindingproteins the target mRNAs and their function in RNAmetabolism are unknown, limiting our understandingof post-transcriptional regulatory processes.In particular, we are interested in RNA-binding proteinsthat positively and negatively modulate the activity ofmicroRNAs. By combining maps of functional RNA-proteininteractions with cell-based and biochemicalassays, we determine the dynamic assembly of RNAbindingproteins and microRNAs on their target mRNAsas well as the elements and mechanisms guidingmRNA maturation, localization, turnover and proteinsynthesis.Specificity and function of RNA helicasesRNA helicases are a family of highly conserved proteinsthat utilize NTP hydrolysis to unwind RNA structuresand/or remodeling of ribonucleoprotein complexes.RNA helicases participate in all biological processesthat involve RNA metabolism, including transcription,splicing and translation and have been implicated indisease states such as tumorgenesis and the replicationof viruses. We are using our crosslinking-immunoprecipitationapproach to define functional interactions ofhelicases and RNA that are typically transient in nature.The identification of RNA target sites provides a foundationfor biochemical and reverse genetic approachesto investigate the remodeling mechanism of ribonucleoproteincomplexes by helicases. These studies will provideinsights into the determinants of target RNA selection,functional interactions with other RNA-interactingproteins and the physiological role of RNA helicases.62 Cardiovascular and Metabolic Disease Research