Direct Detection of Abortive RNA Transcripts in Vivo

Identifying Abortive Initiation During transcription initiation in vitro, the RNA polymerase enzyme typically engages in cycles of synthesis and release of short RNA transcripts (“abortive initiation”) before breaking interactions with promoter DNA and beginning transcription elongation. Using hybridization methods developed to detect microRNAs, Goldman et al. (p. 927) directly detected products of abortive initiation in bacterial cells in vivo. Abortive initiation increased when interactions between RNA polymerase and the promoter were strengthened or when transcription was prevented. Thus, products of abortive initiation may help to regulate gene expression. RNA polymerase engages in abortive transcription in bacteria, a process that may help to regulate gene expression. 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.