Thursday, March 18, 2010

Terminator™ Exonuclease helps unravel the mysteries of the Helicobacter pylori transcriptome

Helicobacter pylori infects about 50% of the human population, and is implicated in inflammation, ulcers, and gastric cancer. Sharma et al.* used a novel approach--differential RNA-Seq (dRNA-Seq)--that selects for the 5’ ends of primary transcripts to construct a genome-wide map of transcriptional start sites (TSS) and operons. Their analysis revealed the unexpected complexity of the H. pylori transcriptome, and demonstrated that the dRNA-Seq method has wide-ranging potential for studying gene expression in pathogenic organisms.

A key component of the dRNA-Seq method is the discrimination of primary transcripts (with 5’-triphosphate ends) from processed ones (with 5’-monophosphate ends). The authors used Terminator™ Exonuclease to enrich a total bacterial RNA preparation in primary transcripts. Terminator Exonuclease degrades transcripts that have a 5’-monophosphate end, but not those that have a 5’-triphosphate, 5’-capped, or 5’-hydroxyl end. The authors conclude that:
Other RNA-seq studies detected termini of bacterial transcripts but could not unequivocally assign TSS due to lack of 5’ group discrimination. As 5’-[triphosphate] ends mark native transcripts in all eubacteria, dRNA-seq should help improve the genome annotations of other organisms, alone or through metatranscriptomics.*Sharma, C. et al. (2010). The primary transcriptome of the major human pathogen Helicobacter pylori Nature, 464 (7286), 250-255 DOI: 10.1038/nature08756

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