title: A novel DNA sequence periodicity decodes nucleosome positioning.
abstract: There have been two types of well-characterized DNA sequence periodicities; both are found to be associated with important molecular mechanisms. One is a 3-nt periodicity corresponding to codon triplets, the other is a 10.5-nt periodicity related to the structure of DNA helixes. In the process of analyzing the genome and transcriptome of Trichomonas vaginalis, we observed a 120.9-nt periodicity along DNA sequences. Different from the 3- and 10.5-nt periodicities, this novel periodicity originates near the 5'-end of transcripts, extends along the direction of transcription, and weakens gradually along transcripts. As a result, codon usage as well as amino acid composition is constrained by this periodicity. Similar periodicities were also identified in other organisms, but with variable length associated with the length of nucleosome units. We validated this association experimentally in T. vaginalis, and demonstrated that the periodicity manifests nucleotide variations between linker-DNA and wrapping-DNA along nucleosome array. We conclude that this novel DNA sequence periodicity is a signature of nucleosome organization suggesting that nucleosomes are well-positioned with regularity, especially near the 5'-end of transcripts.
authors.affiliation: Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Graduate University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Kaifu
authors.initials: K
authors.lastname: Chen
authors.forename: Qingshu
authors.initials: Q
authors.lastname: Meng
authors.forename: Lina
authors.initials: L
authors.lastname: Ma
authors.forename: Qingyou
authors.initials: Q
authors.lastname: Liu
authors.forename: Petrus
authors.initials: P
authors.lastname: Tang
authors.forename: Chungshung
authors.initials: C
authors.lastname: Chiu
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000596:Amino Acids / Q000032:analysis; D000818:Animals; D001483:Base Sequence; D003062:Codon; D004247:DNA / Q000737:chemistry*; D016054:DNA, Protozoan / Q000737:chemistry; D009707:Nucleosomes / Q000737:chemistry*; D009711:Nucleotides / Q000032:analysis; D010507:Periodicity; D017422:Sequence Analysis, DNA; D014246:Trichomonas vaginalis / Q000235:genetics*
chemical_list: D000596:Amino Acids; D003062:Codon; D016054:DNA, Protozoan; D009707:Nucleosomes; D009711:Nucleotides; D004247:DNA