Link to the complete list of our publications.
In cell stress, cytoplasmic RNA are known to be sequestered to RNA granules. We investigated whether there is transcript specificity in this stress induced RNA granulation. We used subcellar fractionation, RNA sequencing, and RNA FISH to discover that certain mRNAs (e.g. Brca1) are more prone to relocalize in RNA granules. These transcripts tend to be longer, have more AU-rich elements, and are enriched with genes that affect cell survival and apoptosis.
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.