Central project: Deep sequencing as a tool for prokaryotic RNA research

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Project Z will foster research in SPP1258 by providing the resources for next-generation sequencing using, e.g., 454, Solexa, or SOLiD technology. So-called deep sequencing or RNA-seq approaches have recently begun to give unprecedented insight into the diversity of cellular RNA species and the organization of prokaryotic transcriptomes. Pilot studies using RNA-seq proved very successful in several SPP1258 projects, yet the full potential of the new technologies remains to be exploited. Project Z will facilitate both comprehensive discovery and the necessary in-depths analyses of already discovered RNA molecules. Approaches will include genome-wide RNA profiling to establish RNA atlases from multiple growth and stress conditions, settle 5’ or 3’ ends of cellular RNA, and reveal conditional RNA processing; RNA-protein interaction maps to understand binding specificities and action of ancillary proteins in vivo, and to improve biocomputational target predictions; high-throughput RNA structure probing in vitro or in vivo, not only of sRNAs and mRNAs but also of metabolite-responsive RNA before and after ligand binding; novel mutagenesis techniques to identify chromosomal co-factors of regulatory RNAs, and critical residues within such RNAs required for activity or protein binding.