Transcription initiation is arguably the single most important process for the regulation of gene expression in all organisms.  In bacteria, it is a widely accepted dogma that regulated transcription initiation at a promoter sequence controls only the adjacent transcription unit (i.e., a gene or operon).  In contrast, this paper demonstrates the feasibility of a new mechanism by which production of multiple RNAs from nearby operons is coupled to the binding of an individual RNA polymerase molecule to a promoter.

The new mechanism was hypothesized based on the recent discovery in vitro of a post-termination state of the bacterial RNA polymerase in which the polymerase slides randomly on DNA after terminating transcription of one RNA and can reinitiate transcription on a nearby promoter, producing another RNA. Despite these observations, it was unclear whether the hypothesized mechanism could operate efficiently over the time and distance scales necessary to couple nearby operons in a bacterial genome in vivo. Now-graduated Ph.D. student Debora Tenenbaum and collaborators tested this idea by developing a mathematical theory based on a diffusion-to-capture mechanism. The theory quantitatively predicts the efficacy of operon coupling in terms of rate constants that were previously unknown but which the authors measured in single-molecule biophysics experiments. This combination of theory and experiment shows that the mechanism operates on the length and time scales needed to function in bacterial genomes. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA.

DNA transcription is the most important nexus of gene regulation in all living organisms.  In recent years, single-molecule experiments have given us a new window into the mechanisms of transcription and have revealed novel, previously unsuspected molecular behaviors and mechanisms.  Ph.D. student Tim Harden used multi-color single-molecule fluorescence imaging to reveal a completely new transcription cycle for bacterial RNA polymerase.  Harden and co-authors showed that an RNA polymerase molecule in vitro frequently (in >90% of transcription events) remains bound to DNA and may again initiate transcription after it has terminated the first round of transcription.  Even more unexpectedly, this “secondary initiation” is not restricted to the same RNA.  After the first round, the polymerase can scan thousands of basepairs along the DNA and can initiate at a different start site, frequently one that is oriented in the opposite direction and produces an antisense transcript.

To complement the single-molecule studies in vitro, the manuscript reports new analyses of whole-transcriptome cellular RNAs revealed by the Rend-seq method that measures transcript initiation and termination frequencies across the genome with single basepair resolution.  These provide evidence that the new transcription cycle may be responsible for initiating antisense transcription at hundreds of genomic locations in the two widely divergent bacterial species examined.  The work defines a new mechanism for the regulated production of antisense RNAs, many of which are now recognized as important agents of gene-specific regulation through control of transcription, mRNA decay, and translation.  In addition, the new transcription cycle provides a mechanism through which transcription initiation can be controlled not just through feedback networks involving multiple genes, but also through production of multiple different primary transcripts consequent to a single RNA polymerase-to-DNA recruitment event.