Researchers from UNSW Sydney and the MRC Laboratory of Molecular Biology in Cambridge, UK, have discovered how cells regulate the quality and quantity of RNA production, to ensure their proper development and survival.

Their findings, published in Molecular Cell, reveal how cells carefully monitor and control the levels of RNA Polymerase II (Pol II), the molecular machine responsible for reading genetic instructions in DNA and transcribing it into RNA, specifically messenger RNA (mRNA) which is essential for protein production.   

"Our research show how cells control the abundance of RNA production machinery,” said co-lead investigator Scott Berry, from UNSW’s School of Biomedical Sciences, the UNSW RNA Institute and the EMBL Australia Node in Single Molecule Science.

“This is likely a crucial cellular function, as there are multiple layers of this mechanism which we found act at different stages of the RNA production process.”

The international collaboration between the Berry Lab at UNSW and Dr Ana Tufegdžić Vidaković’s lab in Cambridge discovered how two molecular components, ARMC5 and the Integrator complex, work in parallel to manage Pol II levels, to maintain accurate, efficient gene transcription. 

The two components essentially act as a quality and quantity checkpoint, by removing faulty or excess Pol II before it can cause potential problems. 

The Integrator complex and ARMC5 act as a checkpoint, recycling and degrading faulty and excess Pol II to maintain accurate, efficient gene transcription. Image: Elfy Chiang/MRC LMB

Understanding of RNA production processes key for treatments

The findings will inform therapies to modulate Pol II, which may be used to treat excessive and poorly controlled gene expression in cancer, or to alleviate the effects of abnormal RNA processing in neurodegenerative diseases, Dr Berry said.

“It’s important that have a good understanding of these molecules, how they interact with each other, and how the transcription processes are adapted, so that when, for example, a viral infection meddles with RNA processing, we can pinpoint the step that has been interfered with, and understand how the cell adapts to this,” he said.

"This also has a role to play in the context of cancer therapies. With cancer, transcription proteins are commonly mutated and that affects transcription in very curious ways, which we can't really understand until we know how the different stages of the transcription process are linked in normal, healthy cells.” 

The research originated from the complementary interests of the two lead investigators: Dr Berry's work on Pol II homeostasis and Dr Vidaković's work on how molecular modifications regulate the cellular functions of Pol II. Their team combined cutting-edge imaging experiments driven by Alexander Gillis at UNSW, with biochemistry and genomics analyses from Roberta Cacioppo, Iván Shlamovitz and Andrew Zeller in Cambridge.

How the checkpoint for RNA production works

ARMC5 and the Integrator complex work in parallel to remove faulty or excess Poll II. The Integrator complex is focused on recycling the polymerase, while ARMC5 is focused on degrading it.  

“In order to make an RNA transcript, the polymerase must bind to the genetic instructions stored in DNA and then decide, is it going to make that RNA transcript, or is it just going to be recycled back to the pool? That is what the Integrator complex does.

“But then during that recycling phase, ARMC5 can also act to degrade the polymerase, if it is defective or if there is too much of it. It is about controlling the levels to keep them optimal for the cell to function properly.”

The parallel processes can compensate for one another when needed, to prevent excess or defective Pol II from being deployed, but work best in tandem, Dr Berry said. 

When the ARMC5 protein is lost, defective Pol II accumulates in the cells. This excess is either prevented from binding to genes, or, if bound, is prevented from progressing beyond a specific region of the gene known as the “pausing zone”, where the Integrator complex recycles defective molecules. 

On the other hand, when the Integrator is lost, a lot of Pol II can get stuck on the genome, as it is unable to be recycled, and it becomes unable to move forward.  

“These molecules are really integral to proper cell functioning, and the role played by each becomes even more important, should the other fail,” Dr Berry said. 

“By better understanding how optimal levels of Pol II are maintained, we’ll be able to improve the therapies that are turned to when gene transcription goes wrong.”