RNA Polymerase Pausing during Initial Transcription

Mol Cell. 2016 Sep 15;63(6):939-50. doi: 10.1016/j.molcel.2016.08.011. Epub 2016 Sep 8.


In bacteria, RNA polymerase (RNAP) initiates transcription by synthesizing short transcripts that are either released or extended to allow RNAP to escape from the promoter. The mechanism of initial transcription is unclear due to the presence of transient intermediates and molecular heterogeneity. Here, we studied initial transcription on a lac promoter using single-molecule fluorescence observations of DNA scrunching on immobilized transcription complexes. Our work revealed a long pause ("initiation pause," ∼20 s) after synthesis of a 6-mer RNA; such pauses can serve as regulatory checkpoints. Region sigma 3.2, which contains a loop blocking the RNA exit channel, was a major pausing determinant. We also obtained evidence for RNA backtracking during abortive initial transcription and for additional pausing prior to escape. We summarized our work in a model for initial transcription, in which pausing is controlled by a complex set of determinants that modulate the transition from a 6- to a 7-nt RNA.

Keywords: DNA scrunching; RNA polymerase; initial transcription; promoter escape; single-molecule FRET; transcriptional pausing.

MeSH terms

  • Base Sequence
  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Fluorescence Resonance Energy Transfer
  • Lac Operon
  • Nucleic Acid Synthesis Inhibitors / pharmacology
  • Promoter Regions, Genetic
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Messenger / antagonists & inhibitors
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics*
  • Rifampin / pharmacology
  • Single Molecule Imaging / methods
  • Time Factors
  • Transcription, Genetic*


  • Escherichia coli Proteins
  • Nucleic Acid Synthesis Inhibitors
  • RNA, Bacterial
  • RNA, Messenger
  • DNA-Directed RNA Polymerases
  • Rifampin