, 2009; Toledo-Arana et al., 2009). An alternative use of high-throughput sequencing has been in the sequencing of immunoprecipitated RNA or DNA (IP-seq), which is an alternative to ChIP-on-chip experiments (Wade et al., 2007). A recent example of such an approach has

been the simultaneous identification of sRNA and mRNA of S. enterica serovar Typhimurium, which were bound to the RNA chaperone Hfq (Sittka et al., 2008). The rapid developments in sequencing technologies allow one to obtain very PLX3397 high-definition transcription snapshots, and these will, undoubtedly, significantly increase our insights in transcriptional and post-transcriptional events in microorganisms. Besides the increased insight into the process of transcription, it will also help in improving or correcting the annotation of

genome sequences (Denoeud et al., 2008). Identification of the 5′ and 3′ boundaries of mRNA species will inform us of the most likely translation initiation codon, especially in those cases where a ribosome-binding site is not apparent (Moll et al., 2002). Next to technical challenges, the rapid increases in knowledge Dasatinib chemical structure will be accompanied by new problems, as with previous breakthroughs in functional genomics (like genome sequencing and microarrays). Several issues may require action from the scientific community, and some of these are highlighted below. 1 Differentiation of transcriptional

and post-transcriptional events. The sequencing-based approaches used for determining the bacterial transcriptomics to date are not able to distinguish between de novo transcription and post-transcriptional events, as they only record the levels of RNA (cDNA) present. This is a weakness shared with microarray technology. Alternative approaches such as those used for genome-wide determination of transcription start sites by 5′ rapid amplification of cDNA ends (RACE) and 5′-serial analysis of gene expression approaches (Hashimoto Gefitinib clinical trial et al., 2004, 2009). These approaches use techniques distinguishing between primary (capped) RNA species, which result from de novo transcription, and processed (uncapped) RNA species. The combination with standard RNA-seq allows for specific identification of primary transcripts, and could be coupled to the use of rifampicin to inhibit transcription for the study of RNA stability (Mosteller & Yanofsky, 1970). Historically, research on microbial transcription focused on protein-based signal transduction and regulatory systems, and mRNA was seen as a relatively inert information carrier. However, the conventional view of RNA has changed in the last decade due to the discovery of regulatory and catalytic RNA activity (Waters & Storz, 2009).