Genome-wide Identification and Conservation of Unannotated Transcription Start Sites within a Bacterial Genus (2013)

W. Shao, M. N. Price, A. M. Deutschbauer, M. F. Romine, A. P. Arkin


Recent studies have revealed unexpected complexity in bacterial transcription. Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the prevalence and evolutionary conservation of unexpected TSSs. Using high-resolution "tiling" microarrays and 5’-end RNA sequencing, we identified 2,531 TSSs in MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that 30% of the sense-orientated internal TSSs (iTSSs) were conserved. In addition, sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are selected for and under direct regulatory control. Evolutionary conservation was also detected for "orphan" TSSs that were intergenic and far from annotated genes (nTSSs). Some of the nTSSs drove the expression of putative non-coding RNAs. To the contrary, most of the antisense TSSs that were located inside CDSs (aTSSs) had neither conserved transcription nor conserved promoter sequences. Overall, our findings demonstrate that most antisense transcription is not under selection within a bacterial genus. In contrast, other "unexpected" transcription, such as iTSSs and nTSSs, were conserved and thus likely functional.

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This work conducted by ENIGMA -- Ecosystems and Networks Integrated with Genes and Molecular Assemblies -- was supported by the Office of Science, Office of Biological and Environmental Research, of the U. S. Department of Energy under Contract No. DE-AC02-05CH11231.