RNA polymerase II (Pol II) pausing downstream of gene promoters has emerged as a widespread phenomenon in eukaryotic gene expression. Pausing could prime signal-responsive genes for rapid activation; alternatively, it might serve as a checkpoint that allows recruitment of the RNA-processing machinery. Although the phenomenon—originally described 20 years ago in Drosophila melanogaster heat-shock genes—has gained acceptance as a core element of transcription in higher eukaryotes, the status of Pol II at the pause site has remained ambiguous. In a recent study, Core et al. address the transcriptional status of promoter-associated Pol II by using global run-on sequencing (GRO-seq). This method, which relies on the detection of nascent RNA, allows precise determination of the position, amount and orientation of transcriptionally engaged polymerases genome wide. By producing matched GRO-seq data sets in the presence or absence of Sarkosyl and quantitatively comparing those to Pol II ChIP-chip and ChIP-seq results, the authors confirm that a high degree of stable pausing occurs near promoters and show that most, if not all, of the promoter-associated polymerase is in a transcriptionally engaged state rather than being part of a postrecruitment preinitiation complex. In conjunction with several earlier studies, this work cements the dynamic state of the paused polymerase complex as a key tunable element of gene expression regulation. (Cell Rep. doi:10.1016/j.celrep.2012.08.034, published online 25 October 2012)