Transcriptonal analysis of L. plantarum WCFS1

Title: Transcriptonal analysis of L. plantarum WCFS1


Background: Microarray analysis of genomes is the major technique to study the transcriptional activity of genes under changing conditions. Although these microarrays mainly focus on the transcription of protein conding genes, it has been shown for many organisms, that the transcriptome is not only compromised by protein coding genes, but that more and more other regions of the genome are being expressed (e.g. identification of non-coding RNAs (ncRNAs), often functioning as regulatory RNAs). 


Goal: Recently a new microarray platform has been designed and employed at NIZO food research. This microarray covers the complete genome of L. plantarum in a tiling fashion (partially overlapping probes, covering the full chromosome and plasmids). This tiling array provides a wealth of information on the transcription products and transcriptional process of L. plantarum. Full coverage of the genomes allows identification of transcription start sites, non-coding, or antisense transcribed small RNAs and unusual long untranslated regions up- or downstream of protein coding genes. The main goal of this project is to exploit this information and give a biological interpretation to the data (e.g. the cause of a large untranslated region (regulatory motif?), or correlation of known promoter locations with transcription start sites gathered from the microarray).

 Student tasks and tools used/to be learned:

-         Scripting (e.g. Python, Perl)

-         Webscripting (e.g. cgi)

-         Database design and mining (e.g. MySQL)

-         Motif searching tools (e.g. MEME, MAST, alignment programs)

-         Statistics (e.g. R)

 Supervisors:Michiel Wels, Christof Francke (support from Roland Siezen en Michiel Kleerebezem??)