Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome (Ju et al., Nature 2024)
Mtb transcriptome profiling by SEnd-seq. (A) Circos plot showing the transcriptomic profile of log-phase Mtb cells. Outer circle: gene annotation; middle circle: RNA coverage; inner circle: TSS intensity. Red and blue represent positive and negative strands, respectively. (B) SEnd-seq data track for an example Mtb genomic region showing total RNA coverage (summed from signals on both strands), aligned SEnd-seq reads (red lines: positive-strand RNA; blue lines: negative-strand RNA), and TSSs (sense: orange arrows; antisense: purple arrows). (C) Working model of Mtb transcription showing s-dependent TSS-proximal stalling and translation-stimulated elongation.
Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that inflicts major health and economic costs around the world. Mtb encounters a diversity of environments during its life cycle and responds to these changes by reprogramming its transcriptional output. In collaboration with the Rock Lab and the Darst-Campbell Lab, we study the mechanism of Mtb transcription using genomic and biochemical methods. Surprisingly, we find that the RNA coverage for Mtb transcription units frequently displays a drop-off within 200-500 nucleotides downstream of the transcription start site, yielding an accumulation of incomplete transcripts. We show that these short RNAs mostly remain associated with paused elongation complexes, and that the sigma factor plays a critical role in early RNAP pausing. Furthermore, we find evidence for transcription-translation coupling in Mtb that promotes its transcriptional processivity. In sum, our results reveal pervasive promoter-proximal pausing of the Mtb transcription machinery that is reminiscent of eukaryotic Pol II, a new paradigm for understanding mycobacterial gene regulation that could be exploited for developing TB therapeutics.