- Student wanted for Master project -
RNA-binding proteins (RBPs) and small regulatory RNAs have been shown to be important regulatory of gene expression by acting together at post-transcriptional level and influencing several pathways in the cell.
In collaboration with the experimental group of Dr. Benedikt Beckmann at IRI (Humboldt University Berlin) we want to investigate the role of RBPs, as well as sRNAs in Salmonella infection. In order to understand if bacterial sRNAs or RBPs directly influence human targets during the infection process, we first need to identify/annotate such regulatory elements in the Salmonella genome. While some RBPs are known and have been well characterized, the whole repertoire of RBPs in Salmonella, as well as the sRNAs important for pathogenicity, still remain largely uncharacterized.
One of the first goals of the project is to develop a computational pipeline to automatically annotate RBPs, as well as sRNAs in the Salmonella genome making use of gene finding methods, as well as comparative analysis with a related species, E.coli.
A second step would be to investigate if bacterial RBPs contain sequence/structure motifs which are similar to human RBP motifs and are potentially able to mimic human protein functions by competing for binding to human mRNAs and non-coding RNAs.
If you are interested in the Bioinformatics analysis as part of this inter-disciplinary project please contact Prof. Annalisa Marisco.