CDK9-dependent RNA polymerase II pausing controls transcription initiation

Genes can contain the coded instructions to make proteins. These instructions must first be copied, or transcribed, into an intermediate molecule called a messenger RNA by an enzyme known as RNA polymerase II. Shortly after it begins, this enzyme – which is called Pol II for short – pauses, and it only starts again after it recruits other proteins, including one called CDK9. The number of RNA copies made of a gene depends upon how many Pol II enzymes begin transcription. Pol II pausing also has an effect – if the enzymes pause for longer, less messenger RNA is transcribed. But why does this happen? One hypothesis is that paused Pol II enzymes interfere with other Pol II enzymes initiating transcription. Yet, until recently it was not possible to measure if this actually happens in living cells. Now, Gressel, Schwalb et al. used a new biochemical method together with a compound that blocks CDK9 to measure pausing and transcription initiation for active genes in living human cells. The CDK9 inhibitor was used to make Pol II enzymes pause for longer than normal. Gressel, Schwalb et al. found that different genes responded differently to CDK9 inhibition, meaning that some remained paused for longer than others. The number of Pol II enzymes that initiated transcription was calculated by measuring how many RNA copies had been made locally at that the site of transcription. These experiments showed that blocking the release of paused Pol II strongly reduced the number of RNA copies made. Gressel, Schwalb et al. conclude that Pol II pausing can control initiation of transcription. Cells may use Pol II pausing to adjust how many copies of an RNA are made, helping to ensure that different cell types make the appropriate number of RNA copies from a gene. Many diseases are associated with gene transcription being incorrectly regulated. This and future studies will help scientists to better understand how Pol II pausing contributes to the control of transcription in both normal and diseased cells.