The Simon lab in collaboration with the Steitz lab recently developed a new technique and published their findings in Molecular Cell. The technique, Start-TimeLapse-seq (STL-seq), is a method that captures the kinetics of short, capped RNA turnover. Using STL-seq, the Simon lab was able to determine the effects of pausing kinetics on transcriptional control.
During transcription, RNA polymerase II (RNA Pol II) must copy DNA to make RNA which is then later used to make protein. This process usually happens rapidly, but the cell can also control if the RNA Pol II starts creating RNA through a process called ‘promoter-proximal pausing.’ This pausing is where the RNA pol II stalls 20-60 bp downstream of the transcription start site and forms a complex with a short nascent transcript on the chromatin. In order for transcription to proceed, the RNA Pol II has to be released from the promoter-proximal pausing site so it can continue into the elongation step of transcription. Previous studies have shown, though, that not all paused RNA Pol II molecules are released, and some RNA Pol II molecules are prematurely terminated and removed from the DNA.
While this regulatory process is critical to cellular function, the kinetics of the promoter-proximal pausing has not been well characterized due to technical limitations. However, the STL-seq technique developed by the Simon lab allows for the kinetics of the pausing to be observed. The Simon lab made many interesting discoveries with this STL-Seq such as the fact that four of five initiated transcripts are terminated at the pause site on average. They also found that pause-release rates can be highly variable, but overall turnover is similar between species suggesting that pausing mechanics could be conserved across metazoans.
This new method will be critical to better understanding the regulatory functions of proximal-promotor pausing and overall transcription regulation.
Read the full article in Molecular Cell: https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00686-9
By Jake Thrasher