Researchers at UT Southwestern Medical Center have identified the specific molecular characteristics that allow the enzyme NSUN2 to recognize and modify RNA. The findings, published in the journal Nature, clarify how this enzyme selects its targets, a mechanism previously unclear due to the enzyme's ability to interact with numerous different RNA types.
NSUN2 is an enzyme that adds a chemical mark known as 5-methylcytosine to various RNA molecules. This modification influences how cells process genetic information. The enzyme has been linked to significant health issues, including its overexpression in several cancers, particularly lung cancer, and mutations in the gene encoding NSUN2 being associated with intellectual disabilities such as Dubowitz-like syndrome.
To understand the selection process, the research team utilized cryo-electron microscopy to capture three-dimensional structures of NSUN2 bound to RNA at different stages of methylation. These structures demonstrated that the enzyme identifies targets through a combination of RNA shape and specific sequence patterns. Specifically, NSUN2 prefers RNA molecules that feature two stem-like regions arranged in a particular orientation, along with a short sequence motif near the modification site.
The team validated these structural observations through biochemical experiments. They designed a shortened RNA molecule that retained the essential features required for recognition by NSUN2. The results confirmed that these identified features are both necessary and sufficient for an RNA molecule to become a direct target of the enzyme.
The study also provided new insights into transfer RNA, one of the most abundant RNA types in cells. When bound to NSUN2, transfer RNA adopted a shape distinct from its classic L-shaped structure, indicating that this molecule can assume more dynamic forms than previously understood.
Yunsun Nam, a professor of biochemistry and biophysics at UT Southwestern and corresponding author of the study, stated that identifying these specific molecular targets closes a knowledge gap regarding how NSUN2 disrupts normal gene expression. Nam, who is also a member of the Harold C. Simmons Comprehensive Cancer Center and an investigator in the Peter O'Donnell Jr. Brain Institute, noted that these findings could help researchers investigate how abnormal RNA modification contributes to disease and lay the groundwork for therapies targeting NSUN2.
