HIPS-Talk:“Transcriptome Sequencing for Deciphering Transcriptional Regulatory Networks in Actinobacteria“
Due to the recent developments in increasing throughput and decreasing prices, transcriptome analysis is moving from "classical" microarray hybridization to the massive parallel sequencing of cDNA that is generated from RNA (RNA-Seq). We have designed advanced techniques for the full resolution of bacterial transcriptomes by RNA-Seq. These techniques were applied to Corynebacterium glutamicum, a model organism for industrial biotechnology and for other Actinobacteria, including organisms relevant for the production of secondary metabolites as well as important human pathogens.
The RNA-Seq techniques can be used for generating a "static" transcriptome, giving all transcribed elements with a single-nucleotide resolution and allows determination of 5'- and 3'-ends of transcripts, promoters, operon structures, small RNAs, and antisense transcripts. With this technique, we identified more than 2,000 promoters in C. glutamicum and were able to describe the promoter "logic" in this organism precisely. In addition, the comprehensive determination of antisense RNAs unraveled a novel mechanism for gene expression regulation in this organism.
RNA-Seq is also ideal for quantitative analysis of transcription (the "dynamic" transcriptome), due to its resolution, its independence of gene-specific hybridization probes, and its almost unlimited dynamic range. The RNA-Seq technology can not only be applied to bacterial transcriptomes in vivo, but also in vitro transcription can be brought to the genome-wide level and analyzed by this method, allowing a background-free identification of promoter motifs responsible for sigma factor recognition and description of single nucleotides that confer sigma factor specificity.
The presentation will provide examples for all mentioned research topics and will show the broad applicability of RNA-Seq for different organisms and numerous scientific applications.
Gebäude und Raum
Blg E8.1, Seminarraum (Erdgeschoss)
Prof. Dr. Jörn Kalinowski is adjunct (apl.) professor at Bielefeld University, Center for Biotechnology (CeBiTec). He has more than 30 years of experience in DNA sequencing and microbial genetics and more than 20 years of experience in bioinformatics and bacterial genomics. He is the head of the "Technology Platform Genomics" (TPG) at CeBiTec. Up to now, he has published more than 200 papers, several book chapters, and is inventor in more than 70 patents.
The CeBiTec of Bielefeld University integrates research from all natural sciences departments, namely biology, chemistry, physics, and the technical faculty that comprises biotechnology and bioinformatics. Several renowned scientists in these fields work together under one roof, with a focus on cross-discipline research projects. A structural pillar of the CeBiTec are the technology platforms, that exist for genomics and post-genomics (TPG), for bioinformatics ("Bioinformatics Ressource Facility," BRF) and for fermentation. The TPG includes high-throughput technology for genomics, transcriptomics, proteomics and metabolomics research, for generating multiple omics datasets from different levels of cellular information for genome-based systems biology studies. All kinds of genomes, ranging from animals to plants, bacteria and archaea as well as metagenomes and transcriptomes have been sequenced here.
Jörn Kalinowskis research interests comprise genome- and metagenome-based microbial biotechnology with a strong focus on systems and synthetic biology approaches. In addition, he is offering all kinds of collaborations on the (meta)genome and (meta)transcriptome sequencing/analysis sector.
Prof. Dr. Andriy Luzhetskyy
- Metabolisches Engineering von Aktinomyzeten - Dr. Andriy Luzhetskyy