A novel dna sequence periodicity decodes nucleosome positioning
文献类型：期刊论文
| 作者 | Chen, Kaifu1,2; Meng, Qingshu1,2; Ma, Lina1,2; Liu, Qingyou3; Tang, Petrus4; Chiu, Chungshung5; Hu, Songnian1; Yu, Jun1 |
| 刊名 | Nucleic acids research
 |
| 出版日期 | 2008-11-01 |
| 卷号 | 36期号:19页码:6228-6236 |
| ISSN号 | 0305-1048 |
| DOI | 10.1093/nar/gkn626 |
| 通讯作者 | Yu, jun(junyu@big.ac.cn) |
| 英文摘要 | 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. |
| WOS关键词 | TRICHOMONAS-VAGINALIS ; ARCHAEAL NUCLEOSOMES ; EFFECTIVE NUMBER ; CODON USAGE ; SACCHAROMYCES-CEREVISIAE ; GIARDIA-INTESTINALIS ; MICROCOCCAL NUCLEASE ; GENOME SEQUENCE ; CHROMATIN ; HISTONE |
| WOS研究方向 | Biochemistry & Molecular Biology |
| WOS类目 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000260983000027 |
| 出版者 | OXFORD UNIV PRESS |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2386238 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Yu, Jun |
| 作者单位 | 1.Chinese Acad Sci, Beijing Inst Genom, Key Lab Genome Sci & Informat, Beijing 100864, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing, Peoples R China 3.Guangxi Univ, Guangxi Key Lab Subtrop Bioresource Conservat & V, Anim Reprod Inst, Nanning 530004, Peoples R China 4.Chang Gung Univ, Bioinformat Ctr, Mol Med Res Ctr, Tao Yuan 333, Taiwan 5.Chang Gung Mem Hosp, Mol Infect Dis Res Ctr, Tao Yuan 333, Taiwan |
| 推荐引用方式 GB/T 7714 | Chen, Kaifu,Meng, Qingshu,Ma, Lina,et al. A novel dna sequence periodicity decodes nucleosome positioning[J]. Nucleic acids research,2008,36(19):6228-6236. |
| APA | Chen, Kaifu.,Meng, Qingshu.,Ma, Lina.,Liu, Qingyou.,Tang, Petrus.,...&Yu, Jun.(2008).A novel dna sequence periodicity decodes nucleosome positioning.Nucleic acids research,36(19),6228-6236. |
| MLA | Chen, Kaifu,et al."A novel dna sequence periodicity decodes nucleosome positioning".Nucleic acids research 36.19(2008):6228-6236. |
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来源：中国科学院大学
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