NAR Molecular Biology Database Collection entry number 1306
Xue, Yu; Liu, Zexian; Wang, Yongbo; Gao, Tianshun; Pan, Zhicheng; Cheng, Han; Yang, Qing; Cheng, Zhongyi; Guo, Anyuan; Ren, Jian
1Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027.
2Department of Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
3Department of Medicine, Molecular Oncology Group, McGill University Health Center and McGill Cancer Center, McGill University, Montr‚al, Quebec, H3A 1A1, Canada.
4School of Life Sciences, Sun Yat-sen University (SYSU), Guangzhou 510275, China.

Database Description

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the CPLA (Compendium of Protein Lysine Acetylation, http://cpla.biocuckoo.org) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7,151 experimentally identified acetylation sites in 3,311 targets. Combined with protein-protein interaction (PPI) information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1,862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0).


The authors thank Dr. Michael Galperin for his helpful suggestions. This work was supported by National Basic Research Program (973 project) (2006CB933300, 2007CB947401), National Natural Science Foundation of China (90919001, 30700138, 30900835, 30830036, 30721002), and Chinese Academy of Sciences (INFO-115-C01-SDB4-36, KSCX2-YW-R-139).

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