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Nucleic Acids Research Advance Access first published online on October 1, 2008
This version published online on October 1, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn626
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Gene regulation, Chromatin and Epigenetics

A novel DNA sequence periodicity decodes nucleosome positioning

Kaifu Chen1,2, Qingshu Meng1,2, Lina Ma1,2, Qingyou Liu3, Petrus Tang4, Chungshung Chiu5, Songnian Hu1 and Jun Yu1,*

1Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 2Graduate University of Chinese Academy of Sciences, Beijing, 3Animal Reproduction Institute, Guangxi Key laboratory of subtropical Bioresource Conservation and Vitalization, Guangxi University, Nanning, 4Bioinformatics Center/Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan and 5Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan, China

*To whom correspondence should be addressed. Tel: +86 10 8299 5357; Fax: +86 10 8299 5373; Email: junyu{at}big.ac.cn

Received June 16, 2008. Revised August 16, 2008. Accepted September 12, 2008.

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.


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