The availability of 25 completed Archaea genomic sequences has provided a wealth of data on the gene content, the metabolic potential and the evolutionary relatedness of Archaea. These data have also made it possible to combine genome level enquiries, such as DNA array analysis of transcription, with biochemical and genetic approaches in the study of archaeal physiology. This project will use tiled DNA arrays to generate a map of the transcription activity for the metabolically versatile and experimentally tractable model archaeon, Haloferax volcanii. An international community of expert researchers will provide RNAs from cells grown under a variety of conditions, and from specific mutant strains, to assemble a library of data describing the transcription response of this organism. This approach has the advantage that the entire genome, both proposed coding and intergenic regions, will be queried providing an unbiased and comprehensive map of transcription activity. Results will be released to the community upon completion of the experiments through a designated public web site to encourage collaboration in the analyses of these data and to foster future experimentation with this organism. The tiled DNA array method will also address a new emerging problem, the identification small RNA-encoding genes that lack highly conserved sequences, and plans are proposed to use these arrays in the analyses of the DNA or RNA interactions of nucleic acid binding proteins. Finally, data from these studies will be used to develop new teaching tools, highlighting differences in statistical analyses and data interpretation for gene-based and tiled arrays, through ongoing interactions with colleagues at a predominately undergraduate teaching institution.
