title: Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns.
abstract: 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.
authors.affiliation: 1 Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, Ontario, Canada .|2 Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada .
authors.forename: Doo
authors.initials: D
authors.lastname: Yang
authors.affiliation: 1 Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, Ontario, Canada .|2 Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada .
authors.forename: Ilya
authors.initials: I
authors.lastname: Ioshikhes
mesh_terms: D000818:Animals; D042002:Chromatin Assembly and Disassembly; D018900:Dinucleotide Repeats; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D006657:Histones / Q000378:metabolism*; D009707:Nucleosomes / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D006657:Histones; D009707:Nucleosomes
keywords: histone variants; nucleosome positioning sequence patterns; nucleosomes.