Over the past few years several important oral pathogens have been fully or partially sequenced. These genetic sequences hold a tremendous amount of biological information and valuable data to be explored and analyzed. Microarray is one of the best technologies that directly capitalize on the genomic sequence information. By designing DNA probes based on the genomic sequences, microarray can monitor the expression of tens of thousands of genes or specific sequences in parallel, making it a great tool for systemic studies. Microarray can also provide experimental validation for the computationally predicted genes including protein-coding or non-coding ones. Through a collaborative effort between NIDCR and NIAID-PFGRC located at TIGR, oligonucleotide genomic DNA microarrays for 5 of the completed oral pathogens have been made freely available to the research community. While proven invaluable to the research communities, these microarrays were designed based on computer-predicted open reading frames (ORFs) only, and are limited to gene expression studies only in the protein-coding regions. This application aims to explore the use of a commercially available high-density oligonucleotide array that can accommodate a total of 385,000 probes on a single slide. This array platform allows the design of tiling arrays that contains probes covering every nucleotide of a typical bacterial genome. The use of genomic tiling arrays permits true genome-wide monitoring of all the RNA molecules in parallel including both ORFs and intergenic regions, thus capable of detecting both protein-coding RNAs (mRNAs) and non-coding RNAs (ncRNAs). The significance of this application is two-fold: it will provide experimental validation for genomic annotations and it will detect potential ncRNAs that may play important roles in disease mechanism for these pathogens. The long term objective is to provide comprehensive transcriptome information for all the oral pathogens to foster hypothesis-drive studies among the research communities. The specific goal of this application is to define the transcriptome for one of the most studied oral pathogen Porphyromonas gingivalis.
Three specific aims are proposed to achieve this goal.
Aim 1 - Define transcriptome profiling of P. gingivalis using high-density tiling microarrays;
Aim 2 -Experimentally annotate P. gingivalis genomes;
Aim 3 - Construct the oral pathogen transcriptome and ncRNA databases. Successful completion of this research project will provide a wealth of information that will help us understand better about oral infectious diseases including tooth decay and gum disease. Studies proposed in this application will specifically identify important genetic traits of oral pathogens that cause these diseases. By understanding more about these traits, better treatment and prevention methods can be developed.
Successful completion of this research project will provide a wealth of information that will help us understand better about oral infectious diseases including tooth decay and gum disease. Studies proposed in this application will specifically identify important genetic traits of oral pathogens that cause these diseases. By understanding more about these traits, better treatment and prevention methods can be developed.
| Hovik, Hedda; Yu, Wen-Han; Olsen, Ingar et al. (2012) Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83. J Bacteriol 194:100-14 |
| Yu, Wen-Han; Hovik, Hedda; Olsen, Ingar et al. (2011) Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays. BMC Mol Biol 12:3 |
| Yu, Wen-Han; Hovik, Hedda; Chen, Tsute (2010) A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data. Bioinformatics 26:1423-30 |
| Hovik, Hedda; Chen, Tsute (2010) Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. BMC Bioinformatics 11:82 |
