Different types of pausing modes during transcription initiation.
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.1and from Lerner, Chung et al.2In 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.
a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.
Eitan
0000-0002-3791-5277
E
Lerner
a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.
Antonino
0000-0002-9348-1397
A
Ingargiola
b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA.
Jookyung J
0000-0002-6551-2870
JJ
Lee
b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA.
Sergei
0000-0002-3517-3003
S
Borukhov
a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.
Xavier
0000-0001-6602-7693
X
Michalet
a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.|c Molecular Biology Institute , University of California , Los Angeles , CA , USA.|d Department of Physiology , University of California , Los Angeles , CA , USA.
Shimon
0000-0002-0720-5426
S
Weiss
D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer; D008957:Models, Genetic; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D000072760:Single Molecule Imaging / Q000379:methods; D061785:Transcription Initiation, Genetic
D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases
abortive initiation; backtracking; promoter escape; single-molecule FRET; transcription initiation; transcription pausing