Direct Detection of Abortive RNA Transcripts in Vivo
Seth R. Goldman,1
Richard H. Ebright,2
Bryce E. Nickels1,*
During transcription initiation in vitro, prokaryotic and eukaryotic
RNA polymerase (RNAP) can engage in abortive initiation—the
synthesis and release of short (2 to 15 nucleotides) RNA transcripts—before
productive initiation. It has not been known whether abortive
initiation occurs in vivo. Using hybridization with locked nucleic
acid probes, we directly detected abortive transcripts in bacteria.
In addition, we show that in vivo abortive initiation shows
characteristics of in vitro abortive initiation: Abortive initiation
increases upon stabilizing interactions between RNAP and either
promoter DNA or sigma factor, and also upon deleting elongation
factor GreA. Abortive transcripts may have functional roles
in regulating gene expression in vivo.
2 Department of Chemistry, Waksman Institute, and Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA.
* To whom correspondence should be addressed. E-mail: bnickels{at}waksman.rutgers.edu
