A team of chemical modifiers to regulate the essential mechanisms of life

Scientists at the Gladstone Institutes made a key observation regarding one of the most fundamental biological processes: gene transcription.

The role of a gene is to provide a cell with instructions for creating a specific protein. The first step in this process is called transcription, during which time DNA is copied into RNA. The scribe is an enzyme called RNA polymerase II, but the polymerase does not work alone. Several proteins interact with the long tail of the polymerase to produce chemical modifications that regulate critical steps in the processing of cellular RNA.

For decades, scientists have thought that a modification, phosphorylation, was directing the exposure. Its function is so essential that it occurs when transcribing a gene in cells ranging from yeast to human. In 2013, Melanie Ott, MD, Ph.D., principal investigator at Gladstone, discovered that another alteration, called acetylation, is also occurring on the regulatory tail of the polymerase during gene transcription in organisms more complexes such as mammals. Nobody knew what acetylation was doing, until now.

"There is so much evidence that phosphorylation plays an important role in transcription in many different species," said Ott, who published a new article on the subject in the scientific journal Molecular Cell. "We show that acetylation provides a unique way for higher order species to regulate thousands of genes – previously we only knew about it – we now know how it works."

Three waves of modifications

Ott's team revealed that the acetylation and phosphorylation team was intended to guide the RNA polymerase during the different stages of transcription.

To begin transcribing a gene, the tail of the polymerase must be labeled by phosphorylation at a specific location. However, in order for the polymerase to continue and terminate the copy of RNA, this mark must be removed. In the new article, Ott and his colleagues show that the essential role of acetylation is to recruit a family of proteins called polymerase RPRD, containing an enzyme that can erase phosphorylation.

"Our report is the first to indicate that acetylation enhances the binding of RPRD proteins to the polymerase," said Ibraheem Ali, Ph.D., a postdoctoral researcher in Ott's lab, first author of the new document. "What we think is that RPRD proteins bind to the acetylation mark, which helps remove the first phosphorylation so that the polymerase can move on to the next phase of transcription."

The team also discovered that another protein was recruited into the polymerase to remove the acetylation mark. This step may be necessary to allow a second phosphorylation to occur at a different site on the tail of the polymerase, which is necessary to restart the next step of transcription.

"We imagine it happens in three waves," says Ali. "The first wave is the first phosphorylation.The second wave is acetylation, and the presence of the second wave forces the first wave to subside.Then, as acetylation is suppressed, a second phosphorylation can occur, which is the third wave.At the time all these waves have passed, you have a gene fully transcribed. "

By regulating genes in this phased approach, cells can quickly and efficiently coordinate gene expression by creating controls at different stages. This extra level of regulation is particularly useful in cells that frequently change function and respond to external stimuli, such as immune cells or during the development of the body.

The clinical potential of acetylation

The question that now arises is why higher-level organizations need these waves of modifications while yeast can work without them.

"That's the big question we always want to answer," says Ott, also a professor in the Department of Medicine at UC San Francisco (UCSF). "We think that's because higher organisms have much longer and complex genes, so we think that acetylation has evolved to allow cells to carefully regulate this transition between initiation and the completion of the transcription process. "

It is also possible that RPRD proteins may be a new target for stopping tumor growth, indicating that the discovery may have potential implications for cancer treatments. Drugs blocking the interaction between acetylation and another family of proteins containing so-called bromodomains already exist and have become a promising anti-cancer therapy.

"Cancer drugs are essentially trying to slow down the cells that divide too quickly," says Nevan Krogan, co-author, Ph.D., principal investigator at Gladstone, director of UCSF's Quantitative Biosciences Institute, and professor of molecular pharmacology at UCSF. 39; UCSF. "If you can regulate transcription through the interaction between acetylation and RPRD proteins, you might be able to come up with a new therapy that would slow cell proliferation."

However, the revelation that acetylation is so important for gene transcription also raises concerns about the potential side effects of targeting such a fundamental process.

"The fact that phosphorylation and acetylation of the tail of the polymerase are so closely related indicates that we need to think of many other problems when developing drugs that target these processes," Ott adds. "Before we begin to administer these drugs to patients, we need to better understand the fundamental processes that are influenced by these changes."