Identification of Novel Non-Coding Small RNAs from Streptococcus Pneumoniae TIGR4 Using High-Resolution Genome Tiling Arrays

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Identification of Novel Non-Coding Small RNAs from Streptococcus Pneumoniae TIGR4 Using High-Resolution Genome Tiling Arrays

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dc.contributor.author Kumar, Ranjit
dc.contributor.author Swiatlo, Edwin
dc.contributor.author Burgess, Shane C
dc.contributor.author Lawrence, Mark L
dc.contributor.author Nanduri, Bindu
dc.contributor.author Shah, Pratik
dc.date.accessioned 2011-03-17T13:30:58Z
dc.date.issued 2010
dc.identifier.citation Kumar, Ranjit, Pratik Shah, Edwin Swiatlo, Shane C. Burgess, Mark L. Lawrence, and Bindu Nanduri. 2010. Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics 11:350. en_US
dc.identifier.issn 1471-2164 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:4743183
dc.description.abstract Background: The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studies have shown that non-coding transcripts participate in a broad range of cellular functions like gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Streptococcus pneumoniae (pneumococcus), an obligate human respiratory pathogen responsible for significant worldwide morbidity and mortality. Tiling microarrays enable genome wide mRNA profiling as well as identification of novel transcripts at a high-resolution. Results: Here, we describe a high-resolution transcription map of the S. pneumoniae clinical isolate TIGR4 using genomic tiling arrays. Our results indicate that approximately 66% of the genome is expressed under our experimental conditions. We identified a total of 50 non-coding small RNAs (sRNAs) from the intergenic regions, of which 36 had no predicted function. Half of the identified sRNA sequences were found to be unique to S. pneumoniae genome. We identified eight overrepresented sequence motifs among sRNA sequences that correspond to sRNAs in different functional categories. Tiling arrays also identified approximately 202 operon structures in the genome. Conclusions: In summary, the pneumococcal operon structures and novel sRNAs identified in this study enhance our understanding of the complexity and extent of the pneumococcal 'expressed' genome. Furthermore, the results of this study open up new avenues of research for understanding the complex RNA regulatory network governing S. pneumoniae physiology and virulence. en_US
dc.language.iso en_US en_US
dc.publisher BioMed Central en_US
dc.relation.isversionof doi:10.1186/1471-2164-11-350 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887815/pdf/ en_US
dash.license LAA
dc.title Identification of Novel Non-Coding Small RNAs from Streptococcus Pneumoniae TIGR4 Using High-Resolution Genome Tiling Arrays en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal BMC Genomics en_US
dash.depositing.author Shah, Pratik
dc.date.available 2011-03-17T13:30:58Z
dash.affiliation.other HMS^Microbiology and Molecular Genetics en_US

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