Alignment of (dA).(dT) homopolymer tracts in gene flanking sequences suggests nucleosomal periodicity in D. discoideum DNA.
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.
Department of Chemistry, University of Massachusetts Lowell 01854.
K A
KA
Marx
S T
ST
Hess
R D
RD
Blake
D000818:Animals; D001483:Base Sequence; D004271:DNA, Fungal / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D016208:Databases, Factual; D004023:Dictyostelium / Q000235:genetics*; D005800:Genes, Fungal; D008040:Genetic Linkage; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics*; D010507:Periodicity; D011067:Poly dA-dT / Q000235:genetics*; D016415:Sequence Alignment
D004271:DNA, Fungal; D004275:DNA, Ribosomal; D009707:Nucleosomes; D011067:Poly dA-dT