RNA secondary structure and compensatory evolution

The classic concept of epistatic fitness interactions between genes has bee n extended to study interactions within gene regions, especially between nu cleotides that are important in maintaining pre-mRNA/mRNA secondary structu res. It is shown that the majority of linkage disequilibria found within th e Drosophila Adh gene are likely to be caused by epistatic selection operat ing on RNA secondary structures. A recently proposed method of RNA secondar y structure prediction based on DNA sequence comparisons is reviewed and ap plied to several types of RNAs, including tRNA, rRNA, and mRNA. The pattern s of covariation in these RNAs are analyzed based on Kimura's compensatory evolution model. The results suggest that this model describes the substitu tion process in the pairing regions (helices) of RNA secondary structures w ell when the helices are evolutionarily conserved and thermodynamically sta ble, but fails in some other cases. Epistatic selection maintaining pre-mRN A/mRNA secondary structures is compared to weak selective forces that deter mine features such as base composition and synonymous codon usage. The rela tionships among these forces and their relative strengths are addressed. Fi nally, our mutagenesis experiments using the Drosophila Adh locus are revie wed. These experiments analyze long-range compensatory interactions between the 5' and 3' ends of Adh mRNA, the different constraints on secondary str uctures in introns and exons, and the possible role of secondary structures in RNA splicing.