Link to the complete list of our publications.
We analyzed how fast the RNA polymerase moves along the gene to synthesize RNA. This speed can be a critical checkpoint in controlling the amount of transcription and co-transcriptional RNA processing, but has only been measured in a small number of genes. Here, we used a chemical inhibitor of P-TEFb kinase that prevents RNA polymerase escape from the promoter to visualize the clearance of RNA polymerase along the gene. By analyzing the the time-course of this clearance, we measured the elongation rates of up to a thousand genes at once.
We showed that the RNA polymerase at the promoter are stably paused, although they are not infinitely stable and can be terminated. This termination was a consequence of increased turnover of RNA polymerase at the promoter rather than a control mechanism during heat-shock response in a major Drosophila heat-shock gene Hsp70.
This is a broad-spectrum review paper on the mechanisms of RNA polymerase elongation, and the factors affecting this process of productive RNA synthesis.
This paper demonstrates PRO-seq and PRO-cap methods to map genome-wide RNA polymerases and their start sites in base-pair resolution. We identified different modes of RNA polymerase pausing, and showed how promoter DNA sequences direct early transcription in Drosophila cells.