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Whole Genome Tiling Array Analysis of Bacterial Genome pp. 301-316 $100.00
Authors:  (Takeshi Akama, Kazunari Tanigawa, Kazuaki Nakamura, Akira Kawashima, Huhehasi Wu, Mariko Sue, Aya Yoshihara, Yuko Ishido, Norihisa Ishii, Koichi Suzuki, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan)
Abstract:
Microarrays have facilitated transcriptome analysis through the use of probes that target a large number of genes. However, only known or predicted genes can be examined in such experiments; it is not possible to analyze the RNA expression of non-coding regions and potential pseudogenes that do not have the appropriate annotation. Tiling arrays have become a useful tool for the analysis of whole genome or chromosome expression, and have been used to uncover novel RNA expression patterns. The genome size of microbes, as well as the proportion of non-coding regions, is much smaller than that of eukaryotes. Therefore, RNA expression from these regions has been extensively studied. The tiling array has facilitated far more in-depth transcriptome analysis, including non-coding regions, than previous techniques such as shotgun cloning. A yeast tiling array analysis identified 98 novel non-coding RNAs. The technique has identified unexpected gene activity in a number of areas, and in some cases has served to elucidate entire microbial metabolic processes, as exemplified by caloric restriction or oxidative stress in Escherichia coli (E. coli). Moreover, RNA expression profiling has been valuable in the analysis of pathogenic bacteria. Analyses of changes in RNA expression upon infection of host macrophages has identified genes related to oxidative stress, proliferation and other unknown functions in Yersinia pestis and Salmonella enterica serovar Typhi. DNA microarray analysis has also found genes involved in the acid stress response and transcriptional hierarchy of the flagellar system. 


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Whole Genome Tiling Array Analysis of Bacterial Genome pp. 301-316