Relationship between gene compactness and base composition in rice and human genome

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Gene structure and expression levels are linked to genome organization, but this relationship differs between species.
• In humans, highly expressed genes are shorter, favoring transcriptional and translational economy.
• In plants like rice, highly expressed genes are often longer, indicating different evolutionary forces.

Purpose of the Study:

• To investigate the influence of GC composition on genome organization in rice and human genes.
• To compare gene compactness and secondary structure stability in relation to expression levels and GC content across species.

Main Methods:

• Comparative analysis of gene organization, GC content, and expression levels in rice and human genomes.
• Assessment of pre-mRNA secondary structure stability for GC-rich genes in both species.
• Examination of the impact of intronic sequences on mRNA secondary structure.

Main Results:

• In GC-rich rice genes, highly expressed genes are less compact than lowly expressed genes; no difference was observed in GC-poor genes.
• Human gene compactness is not influenced by GC composition concerning expression levels.
• Highly expressed rice GC-rich pre-mRNA exhibits less stable secondary structures, which stabilize upon intronic sequence removal.

Conclusions:

• Long introns in GC-rich rice genes may enhance transcriptional efficiency by modulating pre-mRNA secondary structure.
• Evolutionary mechanisms driving genome organization differ significantly between rice and human genomes.
• GC composition and gene expression play a crucial role in shaping genome architecture in plants, contrasting with findings in humans.