Unlocking the Pause: A new player in gene transcription
The human body is an immensely complex biological machine composed of diverse and specialised cells, tissues, and organs. Remarkably, this diversity can originate from a single fertilised egg, that contains within its DNA the complement of genes necessary to guide the development of a fully functioning organism. To achieve this remarkable feat cells must be able to use specific complements of genes at the right time and place during development, and do so in an extremely precise manner. At the molecular level this relies on controlling how RNA Polymerase II transcribes the gene-encoded information into messenger RNA molecules.
Key to this whole information control process is the ability to guide and define the activity of RNA Polymerase II at genes. RNA Polymerase II initiates transcription at the beginning of the gene, then pauses, and, upon receiving certain regulatory signals, proceeds into productive elongation eventually reaching the end of the gene and terminating. We don’t fully understand the peculiar ‘pause’ step where RNA Polymerase II stops transcribing and awaits signals that are fundamental in deciding whether transcription should continue and whether the messenger RNA should be made or not.
In new work published in the journal Molecular Cell, the Klose lab has now discovered a critical mechanism, that controls how RNA Polymerase II is released from this ‘pause’ state. Using a combination of rapid protein degradation technology and biochemical approaches, coupled with calibrated genomics, transcriptomics, and live-cell imaging, they reveal that the PNUTS-PP1 phosphatase complex is a central determinant in releasing RNA Polymerase II from its paused state. This discovery was highly unexpected as PNUTS-PP1 was previously only thought to be associated with controlling the final stages of transcription, when transcription needs to be terminated. Importantly, they show that this new role for the PNUTS-PP1 complex in releasing RNA Polymerase II from its paused state relies on its phosphatase activity. This enzymatic activity allows PNUTS-PP1 to remove phosphate from other protein factors, which changes, or regulates, how they function in transcription. Importantly, PNUTS-PP1 appears to achieve its influence on transcription pause release by regulating the phosphorylation of several key proteins that allow RNA Polymerase II to exit from pausing and enter into productive gene transcription. Identifying these PNUTS-PP1 phosphatase targets was done in collaboration with the Kettenbach lab, who are experts in tracking down phosphorylation of phosphatase targets using mass spectrometry approaches. Together this exciting new discovery sheds fundamental insight into how the pause step in transcription is controlled, revealing an essential new player in the process of deciding whether genes should be made or not.
This work was supported by the Wellcome Trust in the UK and the NIH in the USA. It was a highly collaborative team effort spearheaded by Jessica Kelley and Emilia Dimitrova with valuable contributions from other members of the Klose and Kettenbach labs.
DOI: 10.1016/j.molcel.2024.10.045
Emilia Dimitrova
17th January 2025
