BIRMINGHAM, Ala. – RNA transcription is a vital genomic process, wherein a cell replicates the DNA sequence of a gene into an RNA copy.

In research recently published in Nucleic Acids Research, University of Alabama at Birmingham's Professor Jun Zhang, Ph.D., alongside his team, explores the novel role of the protein SRSF1 in binding and unwinding intricate RNA Guanine-quadruplex structures (GQ).

GQs are highly structured elements found in both DNA and RNA sequences. These G-quadruplexes consist of four guanine-rich bases, aligned in a planar conformation called a G-tetrad, connected via Hoogsteen hydrogen bonds. A fully formed GQ tends to feature multiple layers of G-tetrads.

In healthy cellular environments, GQs are typically unwound, ensuring RNA information is available for proper protein synthesis. GQs play a role in adjusting the level of protein expression. Unfortunately, their considerable stability can lead to complications, particularly within cells, making the unwinding of GQs a strenuous task.

For instance, if a GQ remains unresolved, the ribosome’s passage can be blocked, halting protein production. This regulation is critical, particularly when the protein in question has a cancer-suppressing function. Failure to unwind GQs can promote the replication of harmful cells, including cancerous ones.

“This is significant because advancing our knowledge on how to open GQ structures more efficiently could create new treatment opportunities for various diseases,” Zhang explained. “No simple external mechanism currently exists for unwinding these structures within cells.”

Zhang's research team focused on the extensive Ser/Arg-rich (SR) family of proteins.

This protein family, consisting of 12 members, is recognized for its involvement in RNA-binding, specifically during RNA splicing. Notably, SRSF1 oversees the splicing of over 1,500 different mRNA transcripts.

“Splicing errors can contribute to disease development, including cancer,” Zhang noted. “In fact, misregulated splicing accounts for around 60 percent of known diseases.”

Each SR protein holds one or two N-terminal RNA recognition motifs (RRMs), alongside a phosphorylatable C-terminal section abundant in repetitive Arg/Ser dipeptides (RS).

Zhang's lab was the first to successfully solubilize full-length SRSF1 in its native form. This allowed the team to probe SRSF1’s RNA-binding landscape, revealing SRSF1's preference for purine-rich sequences over pyrimidine-rich ones.

Utilizing fluorescence resonance energy transfer (FRET) between fluorescent markers Cy3 and Cy5, Zhang’s team observed a notable Cy5 signal reduction when SRSF1 was introduced. This finding indicates that SRSF1 binds cooperatively to ARPC2 GQ and successfully unravels the GQ structure.

“Our discoveries lay the groundwork for further exploration into the broader roles that SR proteins, such as SRSF1, play in RNA splicing and translation,” said Zhang. “This deeper understanding helps us clarify how proteins are regulated within cells.”

The other contributors to this study include postdoctoral scholar Naiduwadura Ivon Upekala De Silva, undergraduate researcher Nathan Lehman, and graduate students Talia Fargason, Trenton Paul, and Zihan Zhang.

This research received funding from the National Institutes of Health under grant R35, awarded to Professor Zhang.

Journal

Nucleic Acids Research

DOI

10.1093/nar/gkae213

Method of Research

Data/statistical analysis

Subject of Research

Cells

Article Title

Discovering a New Role of SRSF1 in RNA G-Quadruplex Binding and Unfolding

Article Publication Date

April 3, 2024

COI Statement

No conflicts of interest declared.