Full member of the DoktoratsKolleg RNA Biology from 2007 until 2016
Andrés Mágán Garcia
Ivana Bilusic: “Antisense RNAs in E. coli”
DK RNA Biology Alumni:
Adam Weiss: “In search of cis-acting RNA regulators of RNA polymerase II”
Nadezda Tukhtubaeva: “Transcriptional regulation in bacteria: exploring the world of RNA aptamers”
Martina Dötsch: “RNA structural remodeling by RNA annealer proteins and RNA chaperones”
Bob Zimmermann: “Computational and Biochemical Analyses of Genomic Aptamers in Multiple Species”
Katarzyna Matylla Kulinska: “Function and expression of human alpha satellites”
Krzysztof Chylinski (PhD student with Emmanuelle Charpentier, Helmholtz Center for Infection Research, Braunschweig): “The bacterial immunity system CRISPR/Cas: evolution and mechanisms of action.”
RNA is at the center of all steps of gene expression. Cells can be defined by their transcriptomes, not by their genomes. We are interested in discovering many regulatory elements that are part of the RNA regulon and in identifying their interacting partners and their targets. To achieve this goal we adapted the classical SELEX procedure to be used in combination with genome sequences and deep sequencing. Genomic systematic evolution of ligands by exponential enrichment (SELEX) allows the isolation of protein binding RNAs independently of computational predictions and expression conditions. We used genomic SELEX with an E. coli library to isolate RNA aptamers against RNA polymerase and the regulator protein Hfq. We further selected RNA polymerase II binding aptamers from the yeast and human genomes. These experiments delivered thousands of genomic RNA aptamers that regulate gene expression. We are currently analyzing the mode of action of these aptamers.
Another focus in our laboratory deals with proteins that promote RNA folding: RNA chaperones. As model examples we are analyzing the mode of action of the E. coli protein StpA and the HIV-1 Tat peptide. While StpA promotes RNA annealing and strand exchange, HIV-1 Tat only promotes RNA annealing. Using biochemical and biophysical methods (NMR) we study the structural dynamics of both RNA and protein.