Folding of DNA into a quadruple helix might regulate cellular organisation and gene expression

Researchers at Imperial have found that a protein linked to a rare age-accelerating disease can form liquid droplets in the laboratory when bound to a quadruplex helix DNA structure that has been linked to the regulation of gene expression and the development of ovarian cancer chemoresistance.

Most people are familiar with DNA as a double helix. But under certain conditions, stretches of DNA can fold into compact, three-dimensional quadruple helical structures known as G-quadruplexes. These structures are found in regions of the genome that control which genes are switched on, and researchers have long suspected they play an active role in regulating gene expression, a process known to be compromised during ageing and cancer development.

Indeed, previous work from the same group showed that G-quadruplex structures accumulate in ovarian cancer cells as they become resistant to chemotherapy, and that the largest changes in gene expression were linked to clusters of these structures working together across long stretches of DNA. That work raised a key question: how might these clusters actually drive changes in gene expression at a mechanistic level?

In a new study published in Nucleic Acids Research, researchers in the Di Antonio group at Imperial's Department of Chemistry report that a protein linked with a rare age-accelerating disease known as Cockayne Syndrome B (CSB) can form liquid droplets at unusually low concentrations, particularly when bound to multimolecular G-quadruplex (mG4) structures.

It's fascinating how the control of gene expression is still shrouded in a lot of mystery, despite being one of the key processes to maintain cellular homeostasis. This new angle — that CSB binds mG4 and undergoes phase separation — may indeed shed some light on a previously overlooked aspect of transcriptional regulation. Naura Antariksa ICB-CDT PhD Student

The team found that mG4s can substantially alter the ability of the CSB protein to form droplets inside cells, affecting how different parts of the genome are organised. For example, the researchers have shown that these droplets can preferentially select DNA structures containing mG4s, suggesting that cells may use this process to selectively activate certain genes.

Dr Marco Di Antonio commented, "Understanding the fundamental mechanisms leading to unbalanced gene expression in ageing and diseases will be key to underpinning new therapeutic modalities to target these diseases. Our work represents a new paradigm in this area, whereby the interaction between proteins and specific DNA structures, rather than sequences, can directly affect protein localisation and transcriptional control”

Given the relevance of mG4s in key processes like the development of ovarian cancer chemoresistance, these observations might represent a druggable pathway to manipulate gene expression in otherwise unanticipated ways.

The next steps will focus on validating these findings in living cells and therapeutically relevant models, including new potential targets in other cancers where multimolecular G4s could play a role.

Recognition of multimolecular G-quadruplex regulates phase separation of Cockayne Syndrome B by Antariksa et al. is published in Nucleic Acids Research.