Transcriptional pausing without backtracking

Transcriptional pausing by multisubunit RNA polymerases (RNAPs) plays key roles in gene regulation by coordinating RNAP movement with interactions of regulators and folding of the nascent RNA and, in metazoans, by helping program cycles of promoter-proximal transcription that poise RNAPII for gene expression (1, 2). However, mechanistic understanding of pausing is incomplete. Proposed mechanisms can be divided broadly into 2 classes (Fig. 1): backtrack pausing, in which reverse translocation of RNAP dislodges the transcript 3′ end from the active site and thereby prevents RNA synthesis; and (ii) nonbacktrack pausing, in which conformational rearrangements in the RNAP active site block the nucleotide addition cycle. Only a single example of nonbacktrack pausing, one for which the pause lifetime is increased by a nascent RNA hairpin, has been studied in biochemical detail (refs. 3 and 4 and references therein). Considerable disagreement exists over the contribution of nonbacktrack pauses to the ubiquitous pausing observed during both ensemble and single-molecule in vitro transcription experiments (5–9). An article in this issue of PNAS by Kireeva and Kashlev (10) now provides definitive evidence that, at least for bacterial RNAPs, significant nonbacktrack pausing occurs even without the contribution of pause RNA hairpins.