{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T12:17:24Z","timestamp":1769343444585,"version":"3.49.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":5092,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100005222","name":"Jyv\u00e4skyl\u00e4n Yliopisto","doi-asserted-by":"publisher","award":["2006CB910404"],"award-info":[{"award-number":["2006CB910404"]}],"id":[{"id":"10.13039\/501100005222","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2032-end to the 3\u2032-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.<\/jats:p>","DOI":"10.1016\/s1672-0229(10)60010-1","type":"journal-article","created":{"date-parts":[[2010,8,5]],"date-time":"2010-08-05T09:10:46Z","timestamp":1280999446000},"page":"92-102","source":"Crossref","is-referenced-by-count":11,"title":["Sequence Signatures of Nucleosome Positioning in <i>Caenorhabditis Elegans<\/i>"],"prefix":"10.1093","volume":"8","author":[{"given":"Kaifu","family":"Chen","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meng","family":"Yang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiucheng","family":"Liu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengqi","family":"Xin","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Songnian","family":"Hu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Yu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,8,4]]},"reference":[{"key":"2024051008272827800_bib1","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/nature03686","article-title":"X-ray structure of a tetranucleosome and its implications for the chromatin fibre","volume":"436","author":"Schalch","year":"2005","journal-title":"Nature"},{"key":"2024051008272827800_bib2","first-page":"105","article-title":"The crystal structure of the nucleosome core particle by contrast variation","volume":"27","author":"Bentley","year":"1984","journal-title":"Basic Life Sci."},{"key":"2024051008272827800_bib3","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/0022-2836(84)90382-6","article-title":"Crystal structure of the nucleosome core particle at 16 A resolution","volume":"176","author":"Bentley","year":"1984","journal-title":"J. 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