A novel DNA sequence periodicity decodes nucleosome positioning

Kaifu Chen, Qingshu Meng, Lina Ma, Qingyou Liu, Petrus Tang, Chungshung Chiu, Songnian Hu, Jun Yu

Research output: Contribution to journalArticle

28 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)6228-6236
Number of pages9
JournalNucleic Acids Research
Volume36
Issue number19
DOIs
StatePublished - 2008

ASJC Scopus subject areas

  • Genetics

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