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学科主题: 医学信息学
题名:
Systematic identification of Class I HDAC substrates
作者: Li, Tingting1; Song, Boyan2; Wu, Zheng1; Lu, Ming1; Zhu, Wei-Guo2
关键词: Class I HDACs ; deacetylation ; prediction ; sequence feature ; specificity
刊名: BRIEFINGS IN BIOINFORMATICS
发表日期: 2014-11-01
DOI: 10.1093/bib/bbt060
卷: 15, 期:6, 页:963-972
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology
类目[WOS]: Biochemical Research Methods ; Mathematical & Computational Biology
研究领域[WOS]: Biochemistry & Molecular Biology ; Mathematical & Computational Biology
关键词[WOS]: HUMAN HISTONE DEACETYLASE ; SUPPORT VECTOR MACHINES ; LARGE GENE LISTS ; LYSINE ACETYLATION ; TRANSCRIPTION FACTORS ; BETA ENHANCEOSOME ; SIRT1 ; CLONING ; PHOSPHORYLATION ; PGC-1-ALPHA
英文摘要:

Lysine acetylation is a common post-translational modification of histone and non-histone proteins. This process has an important function in regulating transcriptional activities and other biological processes. Although several computer programs have been developed to predict protein acetylation sites, deacetylases responsible for known or predicted acetylation sites remain unknown. In this research, Class I histone deacetylases (HDACs) substrates were manually obtained, and sequence features of deacetylation sites were analyzed. We found that three members of Class I HDACs (HDAC1, HDAC2 and HDAC3) shared similar sequence features. Therefore, a method was proposed to identify the substrates of Class I HDACs. We evaluated the efficiency of the prediction based on P-value distribution analysis and leave-one-out test. To validate the result of the prediction, we overexpressed Class I HDACs in cells and detected the acetylation levels of potential substrates. In the experiment, five of the seven predicted proteins were deacetylated by Class I HDACs. These results suggested that our method could effectively predict protein deacetylation sites. The work has been integrated to the website ASEB, which was freely available at http://cmbi.bjmu.edu.cn/huac.

语种: 英语
所属项目编号: 2011CBA01104 ; 2012AA020401 ; 60905014 ; 31030041
项目资助者: National Basic Research Program of China ; National High-Tech Research and Development Program of China ; National Natural Science Foundation of China
WOS记录号: WOS:000345386100008
Citation statistics:
内容类型: 期刊论文
版本: 出版稿
URI标识: http://ir.bjmu.edu.cn/handle/400002259/65670
Appears in Collections:基础医学院_医学信息学系_期刊论文

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作者单位: 1.Peking Univ, Hlth Sci Ctr, Dept Biomed Informat, Beijing 100191, Peoples R China
2.Peking Univ, Hlth Sci Ctr, Dept Biochem & Mol Biol, Beijing 100191, Peoples R China

Recommended Citation:
Li, Tingting,Song, Boyan,Wu, Zheng,et al. Systematic identification of Class I HDAC substrates[J]. BRIEFINGS IN BIOINFORMATICS,2014,15(6):963-972.
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