DFG Forschergruppe Unravelling the prokaryotic immune system Bioinformatic analyses of CRISPR elements

Description of the project:
Prokaryotes acquire immunity against phages and viruses through a gene silencing pathway mediated by clusters of regularly interspaced short palindromic repeats, co-called CRISPR non-coding RNAs. The project aims to elucidate the mechanism underlying the processing of CRISPR-transcripts, targeting specificity of mature crRNA, and acquisition of new spacers using advanced bioinformatics tools. A complex of CRISPR-associated (CAS) proteins is known to process the CRISPR-transcripts and binds to a sequence/structure motif within the direct repeats. We use two approaches to predict the important secondary structure elements (1) We will analyse families of all known CRISPR repeats. (2) We will investigate the influence of the context sequence (flanking spacers) on the repeat structure and calculate structure quality measures for each occurrence. Mature crRNA targets either single-stranded RNA or double-stranded DNA. We will scan metagenomic data for novel proto-spacers, which are invading DNA/RNA that match a CRISPR-spacer and represent a putative target. With this set of proto-spacers, we will determine characteristic features of targeting single-stranded RNA, e.g. the interaction hybridization strength, accessibility of the target site, and various kinetic features. Based on experimental data for RNA-DNA interaction, we will also develop a novel classification approach for RNA-DAN interaction. Current data indicates an R-loop interaction, and we will combine sequence-based features of DNA-duplex stability with features from the predicted R-loop interaction.

Additional information: http://www.bioinf.uni-freiburg.de
contact person: Prof. Dr. Rolf Backofen
Phone: 0761 203 7461
Email: backofen@informatik.uni-freiburg.de
Start of project: 2012
End of project: 2014
Project Management:
Albert-Ludwigs-University Freiburg
Prof. Dr. Rolf Backofen

Actual Research Report