G-quadruplexes (G4s) are non-canonical nucleic acid secondary structures formed by guanine-rich sequences that play crucial roles in regulating gene expression. This research investigates how IGF2BP1 protein specifically recognizes and binds to G-quadruplex structures in the 3' untranslated region (3'UTR) of the CCN1 gene, influencing its expression and cellular functions.
As the lead computational analyst for this project, I conducted comprehensive bioinformatics analyses, analyzed proteomics data, and helped design further experiments to understand the molecular mechanisms of G-quadruplex-mediated gene regulation. This work provides new insights into post-transcriptional regulation and the functional importance of RNA secondary structures.
Computational identification and validation of G-quadruplex forming sequences in the CCN1 3'UTR
Characterization of IGF2BP1 binding specificity to G-quadruplex structures
Comprehensive analysis of protein complexes associated with G-quadruplex structures
Integration of computational predictions with experimental validation
CCN1 (Cellular Communication Network Factor 1) is a matricellular protein involved in cell adhesion, migration, proliferation, and survival. Its dysregulation is associated with various pathological conditions including cancer, fibrosis, and inflammatory diseases. Understanding the regulatory mechanisms controlling CCN1 expression is therefore of significant biomedical importance.
G-quadruplexes are four-stranded nucleic acid structures formed by sequences rich in guanine. These structures are stabilized by Hoogsteen hydrogen bonding between guanines arranged in planar tetrads. In RNA, G-quadruplexes can regulate various processes including translation, RNA stability, and localization.
IGF2BP1 (Insulin-like Growth Factor 2 mRNA-Binding Protein 1) is an RNA-binding protein that regulates mRNA stability, localization, and translation. It plays crucial roles in embryonic development and is often reactivated in cancer, where it promotes oncogenic processes.
The 3'UTR of mRNAs contains regulatory elements that control gene expression post-transcriptionally. G-quadruplex structures in 3'UTRs can serve as binding platforms for specific proteins, influencing mRNA fate and protein production.
Utilized multiple computational tools including QGRS Mapper and G4Hunter to identify potential G-quadruplex forming sequences in the CCN1 3'UTR. Analyzed sequence conservation across species to identify evolutionarily preserved G4 motifs.
Performed molecular modeling of predicted G-quadruplex structures using computational tools to understand their topology and stability. Analyzed different G4 conformations and their potential for protein recognition.
Analyzed mass spectrometry data to identify proteins specifically enriched in G-quadruplex pull-down experiments. Performed statistical analysis to distinguish specific binders from background proteins.
Constructed protein-protein interaction networks to understand the functional relationships between G4-binding proteins. Identified regulatory modules and pathways affected by G-quadruplex-mediated regulation.
Analyzed gene expression data to correlate CCN1 levels with IGF2BP1 expression across different cellular contexts and cancer types, revealing the biological relevance of this regulatory mechanism.
Identified and validated a stable G-quadruplex structure in the CCN1 3'UTR that serves as a regulatory element. This structure is conserved across mammalian species, suggesting functional importance.
Demonstrated that IGF2BP1 specifically recognizes and binds to the G-quadruplex structure in CCN1 3'UTR, distinguishing it from linear RNA sequences. This binding stabilizes the mRNA and enhances CCN1 expression.
Revealed that IGF2BP1-G4 interaction positively regulates CCN1 expression, with disruption of the G-quadruplex structure leading to decreased CCN1 levels and altered cellular functions.
Showed that modulation of the IGF2BP1-G4-CCN1 axis affects cell migration, proliferation, and survival, particularly in cancer cells where this pathway is often dysregulated.
This research contributes to our understanding of RNA-based gene regulation and has implications for both basic biology and therapeutic development.
Established a new paradigm for post-transcriptional regulation where G-quadruplex structures serve as specific recognition elements for RNA-binding proteins, expanding our understanding of 3'UTR-mediated gene control.
The IGF2BP1-G4-CCN1 axis represents a potential therapeutic target, particularly in cancers where IGF2BP1 is overexpressed. Small molecules targeting this interaction could modulate CCN1 levels for therapeutic benefit.
The expression correlation between IGF2BP1 and CCN1 could serve as a biomarker for disease states, particularly in cancers and fibrotic diseases where both proteins are dysregulated.
This work suggests that G-quadruplex-protein interactions may be a widespread regulatory mechanism, opening new avenues for investigating similar structures in other disease-relevant genes.
Biochemistry (2024)
Abstract: The 3' untranslated regions (3'UTRs) of mRNAs are critical for regulating mRNA stability, localization, and translation. Here, we report that IGF2BP1 specifically binds to a G-quadruplex structure in the 3'UTR of CCN1 mRNA, enhancing its stability and expression. Using a combination of biophysical, biochemical, and cellular approaches, we demonstrate that this interaction is crucial for CCN1-mediated cellular functions including migration and proliferation. Our proteomics analysis reveals that IGF2BP1 is the primary G-quadruplex-binding protein for this element. Disruption of the G-quadruplex structure or depletion of IGF2BP1 leads to decreased CCN1 expression and impaired cellular functions. These findings establish a new regulatory mechanism where G-quadruplex structures serve as platforms for specific protein recognition in post-transcriptional gene regulation.
Expanding the analysis to identify all G-quadruplex structures in 3'UTRs that are recognized by IGF2BP1 and other RNA-binding proteins, creating a comprehensive map of G4-mediated regulation.
Developing small molecule inhibitors that can specifically disrupt the IGF2BP1-G4 interaction as potential therapeutic agents for cancers where this pathway is dysregulated.
Determining the high-resolution structure of the IGF2BP1-G4 complex to understand the molecular basis of recognition and guide rational drug design efforts.
Investigating the IGF2BP1-G4-CCN1 axis in patient samples to validate its relevance in human disease and explore its potential as a therapeutic target or biomarker.
If you're interested in learning more about G-quadruplex biology, RNA-protein interactions, or computational approaches to studying RNA structure, feel free to reach out.