Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Intramolecular G-quadruplexes (G4s) are nucleic acid secondary structures implicated in various cellular processes.
• Existing research on G4s predominantly focuses on mammals and yeast, with plant G4s being largely understudied.
• G4s have been linked to genomic instability but also to the regulation of transcription and translation.

Purpose of the Study:

• To investigate the sequence variability of predicted G4s (pG4s) in plant genomes, specifically *Arabidopsis thaliana* and *Oryza sativa*.
• To compare plant pG4 variability with human data and analyze differences across gene structural elements.
• To assess the functional relevance of plant pG4s by examining sequence conservation and substitution preferences.

Main Methods:

• Analysis of whole-genome sequencing (WGS) data from *Arabidopsis thaliana* and *Oryza sativa*.
• Focus on single nucleotide variability within sequences predicted to form G4 structures (pG4s) in protein-coding transcripts.
• Comparative analysis with human G4 data and examination of pG4s located at 5'UTR/CDS junctions.

Main Results:

• Plant pG4s exhibit non-uniform sequence variability across different gene structural elements.
• Abundant AUG-containing pG4s at 5'UTR/CDS junctions in plants show remarkable conservation, suggesting functional importance.
• Sequence substitutions that decrease G4 formation probability are evolutionarily favored over neutral or stabilizing changes.

Conclusions:

• Plant G-quadruplexes, particularly those near translation start sites, are functionally relevant and under selective pressure.
• The distinct variability patterns of plant pG4s highlight their unique roles in gene regulation compared to other genomic regions.
• Evolutionary analysis supports the functional significance of G4 structures in plants, challenging previous assumptions about their instability.