On the Relationship between DNA Periodicity and Local Chromatin Structure

DNA periodicity and its relationship to the formation of nucleosomes has been investigated extensively using autocorrelation and Fourier transform methods. We provide a precise treatment of the mathematical foundation for this type of analysis, and we apply the resulting method to quantify dinucleotide periodicity in several datasets. We begin by demonstrating, via simulation, the sensitivity of our method relative to previous methods. We then provide evidence of pervasive ∼10 bp periodicity in S. cerevisiae, with stronger periodicity in sequences associated with positioned nucleosomes. In human, although repeat-masked sequences do not exhibit significant periodicity on average, we find that experimentally determined nucleosome positions show a periodicity of the AA dinucleotide similar to that found in S. cerevisiae. Furthermore, transcription start sites in the human genome are marked by a sharp drop in the 10 bp periodicity of the AA dinucleotide, while occupied CTCF sites are surrounded by a local increase.