The frequency of two-base tracts in eukaryotic genomes

Abstract

The frequency of two-base tracts is surveyed in a wide range of eukaryotic genomes using the special program TRACTS. All three two-base families are surveyed: R.Y (A,G.C,T), K.M (A,C.G,T), and S;W (A.T and G.C). Data for the human beta-globin complex, for the tobacco chloroplast, and for 247 nt mammalian promoter regions are presented. All two-base tracts longer than three or four bases are overrepresented to an extent surpassing by far their occurrence in a randomized DNA population in the majority of the genomic regions analyzed; 20-30 long tracts are quite frequent, against the statistical odds. R.Y tracts are found at the largest excess, K.M tract to a slightly lesser extent, while S.W tracts are found at a moderate yet significant excess. The majority of the tracts manifest only a limited extent of tandem repeat structures. The idea that the two base tracts serve as unwinding elements is considered.

Cruciform structures and functions

“…Timsit and D. Moras 1982;Pardue et al 1987;Huijser et al 1987;Yagil, 1993) but (CA) n tracts are not detectable in bacteria (Gross & Garrard, 1986). They are involved in multiple biological functions (Rodgers, 1983) such as the control of gene expression (Hamada et al 1984;Braaten et al 1988;Cowie & Myers, 1988) or in enhancement of recombination (Treco & Arnheim, 1986;.…”

Distributions of Dimeric Tandem Repeats in Non-coding and Coding DNA Sequences

“…The probability distribution functions for the length of special classes of repeats have been studied in many publications (see e.g. Marx et al, 1993;Yagil, 1993;Stallings et al, 1991;Dokholyan et al, 1997Dokholyan et al, , 1998. Bell & Jurka (1997) studied the length distributions of dimeric tandem repeats of rodent and primate DNA.…”

The over-representation of binary DNA tracts in seven sequenced chromosomes

“…Thus, K.M tracts were found in large excess in the human β globin complex and in organelle DNA [13], as well as in yeast chromosome 3 [14]. The data in Tables 4 and 5 show that these findings can be extended to the wider range of phyla studied here.…”

“…The S tracts, found in high concentrations in certain regions, are well studied as CpG islands [12]. The abundance of these combinations was previously established in an assortment of mammalian genes [13] and in a yeast chromosome [14]. In bacteria, the W motif, rather than the R.Y motif, was found to be the predominating binary motif [15,16].…”