Characteristics of the Large (dA).(dT) Homopolymer Tracts in D. discoideum Gene Flanking and Intron Sequences

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Abstract
D. discoideum, the slime mold, is one of the most AT rich eukaryotic genomes known. In this paper we examine this organism's database for overlapping N-tuples of high frequency and find A and T tracts possess among the highest frequencies in flanking sequences but not in coding sequences. We examined both overlapping and non-overlapping frequencies of the A T, G and C homopolymer tracts of 2>N>6. Overlapping (dG)·(dC) and (dA)·(dT) tracts occur at greater frequencies than expected, based on random occurrence. Long (dA)·(dT) tracts of N< 10 occur at well above expected frequencies in flanking and intron regions, while (dG)·(dC) tracts above N=5 are rarely found. Some of the implications of these findings for tract origins in slip-strand replication and for chromatin stucture are discussed.