Introns and GC-content

After the thorough examination of introns and their splicing effects, this journal, Introns structure patterns of variation in nucleotide composition in Arabidopsis thaliana and rice protein-coding genes, by Ressayre et al. explores how introns can influence the nucleotide composition (GC content). As the title suggests the authors looked at two plants species that that offered the best annotated gene structures among plants with A. thaliana being GC-poor and rice being GC-rich, respectively.

The authors wanted to investigate the potential role of introns in GC-content variation in plant genes. They focused on the link between intron presence and GC-content. They observed tight links between intron presence and variation in GC-content into a negative correlation between intron number and GC-content. The intron/exon structure was shown to effect nucleotide, codon, and amino acid compositions.

The results of their experimentation and numerous calculations revealed that introns impede the increase in GC-content. They found this by comparing intron infused in 5’ UTR and 5’ UTR without introns. They found that the genes with the introns were smaller compared to the genes without the introns.

In the experiment the authors looked at internal and external coding regions and how they interacted introns. Introns appear to delimit gene space in three different regions, one internal and the other external. They observed lower variation in GC-content in internal sequences, this resulted in a more complex pattern along the genes with negative correlations. Gene intron number is expected to be a strong determinant of CDS GC-content. The introns have more effect in GC-rich regions but have less of an effect in GC-poor regions.

The authors concluded that gene intron number and precise gene-intron architecture are required to properly describe patterns of variation in GC content. The GC-content is correlated with many genomic features such as recombination rates, splicing mechanisms, and nucleosome positioning. They propose that the effects of introns on the GC-content have a long-range effect on those genomic features. They suggest that an intron barrier exists that explains the peculiarities of GC-content. The intron acts as barriers in recombination or extension of conversion for external GC-content. This intron barrier can increase the GC-content of external genes while acting as a constraitn on internal GC-content. In regards to internal GC-content the introns can suppress the increase in the spreading. While the presence of introns has effects on GC-content without the introns the GC-content would be more susceptible to evolutionary change that could negatively impact the organism.

The previous journal articles have discussed how introns can be beneficial via splicing and regulation. This one looked at how the physical presence of introns affected the architecture of the GC-content in these plants, the authors mentioned other plants and how their architecture varies to produce variants of the genes studied. From these journals I see how the introns have a legitimate influence in the structure and expression of genes. Much smaller compared to exons but enough to have a positive or negative impact.

Sources:

Ressayre, A., Glemin, S., Montalent, P., Serre-Giardi, L., Dillmann, C., & Joets, J. (2015). Introns structure patterns of variation in nucleotide composition in Arabidopsis thaliana and rice protein-coding gene. Genome Biology and Evolution. PMCID: PMC4684703