Alignment of (dA)·(dT) Homopolymer Tracts in Gene Flanking Sequences Suggests Nucleosomal Periodicity in D. discoideum DNA

Abstract

It has been shown that the frequency versus size distribution of A and T overlapping and non- overlapping homopolymer tracts of N>5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report we demonstrate, that a spatial periodicity exists in long A and T tracts (N> 10) in long flanking sequences by scored alignments of those tracts (N> 10) with the nucleosomal repeat. A tract spacing was found at 185–190 bp that corresponds to a maximum alignment score. This is exactly the average spacing of D. discoideum nucleosomes determined experimentally. A majority of A and T tracts in flanking sequences are often spaced by short DNA stretches and the total length of adjacent A and T tracts plus the interrupting short DNA stretch corresponds closely to the average experimentally measured nucleosomal linker DNA size in D. discoideum-42 bp. These data suggest a model which has A and T runs of N> 10 bp in flanking DNA of D. discoideum organized in a regular phase with nonhomopolymer sequences along the DNA. This model has functional implications for A and T tracts, suggesting that they are found in nucleosomal linker DNA regions of chromatin during some necessary portion(s) of the life of the cell.