Analytical expression of the purine/pyrimidine autocorrelation function after and before random mutations

Area of Science:

• Genetics
• Evolutionary Biology
• Bioinformatics

Background:

• The mutation process, specifically purine-pyrimidine substitutions (transversions), is a fundamental mechanism in evolutionary genetics.
• Understanding motif occurrence in DNA sequences is crucial for deciphering evolutionary processes and gene function.

Purpose of the Study:

• To derive and apply analytical expressions for motif and d-motif occurrence probabilities under transversions in DNA sequences.
• To investigate the evolutionary history of genes by analyzing motif patterns and their periodicity.

Main Methods:

• Developed analytical expressions to calculate motif and d-motif probabilities on the purine/pyrimidine (R/Y) alphabet under transversions.
• Applied these expressions to analyze autocorrelation functions (d-motif probabilities) in various gene types (chloroplast, mitochondrial, nuclear, prokaryotic, RNA, noncoding).
• Reversed the evolutionary process using back transversions to infer primitive gene characteristics.

Main Results:

• Protein-coding genes in chloroplasts and mitochondria show a preferential YRY(N)6YRY motif with modulo 3 periodicity.
• Most other genes (RNA, noncoding) also favor YRY(N)6YRY, but without strict periodicity.
• Protein-coding genes in eukaryotic nuclei and prokaryotes favor YRY(N)0YRY, but revert to YRY(N)6YRY with modulo 3 periodicity after simulated back transversions, indicating similarity to primitive genes.

Conclusions:

• Actual chloroplast and mitochondrial protein-coding genes resemble primitive nuclear and prokaryotic protein-coding genes.
• The study provides the first results on the mutation process within a proposed model of DNA sequence evolution.
• Genes evolve through initial oligonucleotide mixing followed by mutation, with observed motif patterns reflecting this history.