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

Project Z将通过为下一代测序提供资源来促进SPP 1258的研究，例如，454、Solexa或SOLiD技术。所谓的深度测序或RNA-seq方法最近开始对细胞RNA物种的多样性和原核转录组的组织提供前所未有的见解。使用RNA-seq的试点研究在几个SPP 1258项目中证明非常成功，但新技术的全部潜力仍有待开发。 Project Z将促进对已经发现的RNA分子的全面发现和必要的深入分析。方法将包括全基因组RNA分析，以建立来自多种生长和应激条件的RNA图谱，解决细胞RNA的5'或3'末端，并揭示条件RNA加工; RNA-蛋白质相互作用图谱，以了解体内辅助蛋白的结合特异性和作用，并改善生物计算靶点预测;在体外或体内探测高通量RNA结构，不仅探测sRNA和mRNA，而且探测配体结合之前和之后的代谢物响应性RNA;新的诱变技术来鉴定调节RNA的染色体辅因子，以及这些RNA中活性或蛋白质结合所需的关键残基。

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.