The mechanism of variability in transcription start site selection
Libing Yu,
Jared T Winkelman,
Chirangini Pukhrambam,
Terence R Strick,
Bryce E Nickels,
Richard H Ebright
Affiliations
Libing Yu
Department of Chemistry, Rutgers University, Piscataway, United States; Waksman Institute, Rutgers University, Piscataway, United States
Jared T Winkelman
Department of Chemistry, Rutgers University, Piscataway, United States; Waksman Institute, Rutgers University, Piscataway, United States; Department of Genetics, Rutgers University, Piscataway, United States
Chirangini Pukhrambam
Waksman Institute, Rutgers University, Piscataway, United States; Department of Genetics, Rutgers University, Piscataway, United States
Terence R Strick
Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France; Programme Equipe Labellisées, Ligue Contre le Cancer, Paris, France; Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Paris, France
Bryce E Nickels
Waksman Institute, Rutgers University, Piscataway, United States; Department of Genetics, Rutgers University, Piscataway, United States
During transcription initiation, RNA polymerase (RNAP) binds to promoter DNA, unwinds promoter DNA to form an RNAP-promoter open complex (RPo) containing a single-stranded ‘transcription bubble,’ and selects a transcription start site (TSS). TSS selection occurs at different positions within the promoter region, depending on promoter sequence and initiating-substrate concentration. Variability in TSS selection has been proposed to involve DNA ‘scrunching’ and ‘anti-scrunching,’ the hallmarks of which are: (i) forward and reverse movement of the RNAP leading edge, but not trailing edge, relative to DNA, and (ii) expansion and contraction of the transcription bubble. Here, using in vitro and in vivo protein-DNA photocrosslinking and single-molecule nanomanipulation, we show bacterial TSS selection exhibits both hallmarks of scrunching and anti-scrunching, and we define energetics of scrunching and anti-scrunching. The results establish the mechanism of TSS selection by bacterial RNAP and suggest a general mechanism for TSS selection by bacterial, archaeal, and eukaryotic RNAP.
