Twofold symmetries in nucleotide distribution in large domains of Saccharomyces cerevisiae Chromosome I

Abstract

Single stranded chains of biological DNA show a widespread occurrence of parity for complementary nucleotides, i.e., A=T, G=C. This has been referred to as A-T, G-C symmetry. A distinction must be made between this, which this paper calls mirror symmetry, and twofold symmetry, where complementary nucleotide parity occurs between two segments, of the same length and equidistant from a symmetry center, along a single-stranded DNA chain. I have analysed the sequence of Chromosome I of Saccharomyces cerevisiae for the occurrence of complementary nucleotide symmetry. Open reading frame (ORF) sequences made up 63% of the total chromosome length and most of them were asymmetric for both A-T and G-C. The sign of A-T asymmetry was correlated with transcriptional orientation (A>T for sense and A<T for antisense ORFs), whereas G-C asymmetry was not. However, long single-stranded segments of Chromosome I were A-T mirror symmetric because they contained similar frequencies of ORFs in both transcriptional orientations. The same results were obtained with the AA-TT pair of complementary dinucleotides. Profiling of AA-TT symmetry along Chromosome I showed this chromosome to be organized as a succession of five domains that were twofold symmetric for AA-TT, placed between two subtelomeric regions without clear symmetry properties. This pattern was destroyed when ORF sequences were randomly repositioned along the chromosome. Based on the above findings, an architectural model is proposed for Chromosome I, in which the twofold symmetric domains, from 30 to 50 kb long, correspond to chromosome loops.