A method for extracting period~10 modulations from DNA sequence correlations applied to the Drosophila melanogaster genome.

Abstract

Nucleosome DNA packaging and positioning within the Drosophila melanogaster genome imposes a weak modulation, with a period of about 10 bp in the genomic composition correlations. We present formalism for extracting such modulations from an irreducible set of six correlation functions calculated along the D. melanogaster genome. These modulations were seen to be stronger for the irreducible self-correlation C(zz)(k) (strong-weak binding). Using an FFT procedure, we show that the period~10 modulation extracted from such self-correlation is viewed to be an oscillation with period~10.9 overmodulated by an oscillation with period~153. This behavior of the modulation reflects the organization of the eukaryotic genomic DNA. But, since the period~10 modulation dies for k ~150, the constraints imposed by the nucleosome arrangement over the nucleosome sequence composition must be weak, provided that such constraints are the sources for the modulations.