title: Sequence signatures of nucleosome positioning in Caenorhabditis elegans.
abstract: Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine (AG) gradient from the 5'-end to the 3'-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model (HMM) algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Kaifu
authors.initials: K
authors.lastname: Chen
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Meng
authors.initials: M
authors.lastname: Yang
authors.forename: Jiucheng
authors.initials: J
authors.lastname: Liu
authors.forename: Chengqi
authors.initials: C
authors.lastname: Xin
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D018509:DNA, Helminth / Q000737:chemistry* / Q000378:metabolism*; D049751:Genome, Helminth; D008390:Markov Chains; D009707:Nucleosomes / Q000378:metabolism*; D011687:Purines / Q000032:analysis; D011743:Pyrimidines / Q000032:analysis; D017422:Sequence Analysis, DNA
chemical_list: D018509:DNA, Helminth; D009707:Nucleosomes; D011687:Purines; D011743:Pyrimidines; C030986:pyrimidine; C030985:purine