Kasaju, M. | Search bioRxiv

bioRxiv2026

The role of a G-quadruplex structure in mediating the interactions of miR-1249-3p with the 3-UTR of the HNRNPK mRNA

Heterogenous nuclear riboprotein K (hnRNP K) is an important regulator of multiple signaling pathways involved in DNA repair and function whose expression has been found to be mis-regulated in many cancers and neurological diseases. The expression regulation of hnRNP K is not fully understood however it has been shown that the microRNA miR-1249-3p targets its mRNA 3-untranslated region (UTR), regulating its translation. In this study we identified a guanosine-rich sequence in the HNRNPK 3-UTR within the miR-1249-3p binding site that has the potential to form a G-quadruplex (GQ) structure. By using various biophysical methods, we show that this sequence forms a parallel GQ structure which modulates the binding of miR-1249-3p to HNRNPK 3-UTR in vitro. Additionally, using luciferase reporter assays, we determined that this GQ structure affects the hnRNP K protein expression, suggesting modulation of the binding interaction of miR-1249-3p to the 3-UTR of HNRNPK. This HNRNPK mRNA GQ-miR binding axis is an unexplored mechanism of regulation, offering a novel therapeutic target for diseases caused by abnormal hnRNP K expression.

biochemistry↗

bioRxiv2025

G-Quadruplex and i-Motif Structures in the SHMT1 5UTR Modulate Gene Expression

Multiple sclerosis (MS) is a fatal neurodegenerative disease that progresses by eroding the myelin sheath and exposing the neuron, leading to neuronal degradation and death. While MS remains without an effective treatment or cure, studies have identified genes that are dysregulated in MS patients and predicted to be involved with disease progression. These genes are primarily involved in controlling DNA methylation: a process required for regulating gene expression, which is critical for cellular health. Having identified potential genetic risk factors, research is focused on how to manipulate the expression of these genes by offsetting DNA methylation errors in patients through the targeting of DNA and RNA secondary structure formation. Serine hydroxy methyltransferase 1 (SHMT1), a key player in DNA methylation, was determined to be upregulated in MS patients. Here, we identified and characterized a hybrid 3+1 G-quadruplex (GQ) and i-motif (iM) structures in the SHMT1 DNA 5 untranslated region and a parallel GQ in the corresponding mRNA. Additionally, we found that the GQ/iM structures suppress the mRNA levels and protein expression of a reporter gene. Together, these data suggest that GQ/iM structures are necessary for SHMT1 regulation, which could serve as a target for therapeutic intervention for MS patients.

biochemistry↗