Mentz, Almut; Neshat, Armin; Pfeifer-Sancar, Katharina; Pühler, Alfred; Rückert, Christian; Kalinowski, Jörn: Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. In: BMC Genomics. Jg.14 H. 1. 2013
Inhalt
- Results
- Detection of potential sRNA genes in C. glutamicum ATCC 13032 by transcriptome sequencing and read-mapping
- Characterization of potential sRNA genes with the help of bioinformatic promoter analysis
- Classification of potential sRNA genes by their positions relative to annotated protein-coding sequences
- Detection of small C. glutamicum genes encoding small proteins
- Analysis of cis-antisense RNA genes, located within protein-coding genes
- Bioinformatic analysis of sequence and structural conservation of trans-encoded sRNAs in C. glutamicum ATCC 13032
- Experimental validation of three trans-encoded sRNAs by Northern blotting of stress-specific RNA samples and detailed structure analysis
- Discussion
- Conclusions
- Methods
- Preparation of cDNA libraries for RNA-Sequencing
- Preparation of two different cDNA libraries for sequencing
- Bioinformatics analysis
- Detection of transcription start sites
- Promoter search using primary 5′-end data
- Rho-independent terminator search
- ORF and RBS prediction
- Prediction of secondary structure conservation
- Other tools and software
- Northern blot
- Additional files
- Abbreviations
- Competing interests
- Authors’ contributions
- Acknowledgements
- Author details
- References