Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans

查看全文 作　　者：Kaifu [1,2]Chen;Lei [1,2]Wang;Meng [1]Yang;Jiucheng [1,2]Liu;Chengqi [1,2]Xin;Songnian [1]Hu;Jun [1]Yu

机构地区：[1]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China;[2]Graduate University of Chinese Academy of Sciences, Beijing 100049, China.

出　　处：《Genomics, Proteomics & Bioinformatics》索引2010年第8卷第2期,共11页

基　　金：supported by the National Basic Re-search Program (973 Program) from the Ministry of Science;Technology of the People’s Republic of China (2006CB910404 to JY) 摘　　要：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. 关键词：DNA序列定位计算核小体签名线虫隐马尔可夫模型解码算法 GC含量

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Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans

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