A cross-species view of transcription termination in bacteria

To adapt to environmental changes, bacteria strictly regulate their gene expression through versatile regulatory mechanisms at both the transcriptional and post-transcriptional levels. In addition to the extensively-studied transcription initiation regulation by transcription factors, there are regulatory mechanisms reshaping the 3’ termini of initiated and already transcribed transcripts, involving termination factors, attenuators, riboswitches, and ribonucleases. To study the evolutionary conservation of these mechanisms and their dynamics under various growth conditions, the 3’ termini of gene transcripts need to be explicitly determined. Recent data generated by tailored RNA-seq approaches, aimed to globally identify the 3’ termini, are limited to only a few bacteria and a few growth conditions. To this end, we developed a computational approach to determine with high accuracy transcript 3’ termini from sequencing data generated by the RNAtag-seq protocol. Our method exploits a signal identified in the RNAtag-seq data, without the need for special experimental manipulations. The ample RNAtag-seq data available for many bacterial pathogens, grown under various stress and virulence-inducing conditions, enable us to use our computational method for constructing an atlas of 3’ termini across bacteria and growth conditions, and to study them from an evolutionary point of view.