Different types of pausing modes during transcription initiation

Eitan Lerner, Antonino Ingargiola, Jookyung J. Lee, Sergei Borukhov, Xavier Michalet, Shimon Weiss*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

11 Scopus citations


In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al.1 and from Lerner, Chung et al.2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1–2 nucleotide backtracking of a 7-mer transcript.

Original languageAmerican English
Pages (from-to)242-253
Number of pages12
Issue number4
StatePublished - 8 Aug 2017
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2017 Taylor & Francis.


  • abortive initiation
  • backtracking
  • promoter escape
  • single-molecule FRET
  • transcription initiation
  • transcription pausing


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