Nucleosomes are implicated in transcriptional regulation as well as in packing 
and stabilizing the DNA. Nucleosome positions affect the transcription by 
impeding or facilitating the binding of transcription factors. The DNA sequence, 
especially the periodic occurrences of dinucleotides, is a major factor that 
affects the nucleosome positioning. We analyzed the Drosophila DNA sequences 
bound by H2A and H2A.Z nucleosomes. Periodic patterns of dinucleotides 
(weak-weak/strong-strong or purine-purine/pyrimidine-pyrimidine) were identified 
as WW/SS and RR/YY nucleosome positioning sequence (NPS) patterns. The WW/SS NPS 
pattern of the H2A nucleosome has a 10-bp period of weak-weak/strong-strong 
(W = A or T; S = G or C) dinucleotides. The 10-bp periodicity, however, is 
disrupted in the middle of the sequence. At the dyad, the SS dinucleotide is 
preferred. On the other hand, the RR/YY NPS pattern has an 18-bp periodicity of 
purine-purine/pyrimidine-pyrimidine (R = A or G; Y = T or C) dinucleotides. The 
NPS patterns from H2A.Z nucleosomes differ from the NPS patterns from H2A 
nucleosomes. The RR/YY pattern of H2A.Z nucleosomes has major peaks shifted by 
10 bp deviated from the H2A nucleosome pattern. The H2A and H2A.Z nucleosomes 
have different sequence preferences. The shifted peaks coincide with DNA regions 
interacting with the histone loops.