Unbiased proteomic screen for binding proteins to modified lysines on histone H3

被引:34
作者
Chan, Doug W. [1 ]
Wang, Yi [2 ]
Wu, Meng [3 ]
Wong, Jiemin [3 ]
Qin, Jun [2 ]
Zhao, Yingming [4 ]
机构
[1] ProTech Lab Inc, Houston, TX 77054 USA
[2] Baylor Coll Med, Ctr Mol Discovery Verna & Mars McLean, Dept Biochem & Mol Biol, Dept Mol & Cellular Biol, Houston, TX 77030 USA
[3] E China Normal Univ, Coll Life Sci, Inst Biomed Sci, Shanghai 200062, Peoples R China
[4] Univ Texas SW Med Ctr Dallas, Dept Biochem, Dallas, TX 75390 USA
基金
美国国家卫生研究院;
关键词
Epigenetics; Histone code effectors; Histone modifications; Proteomics; MASS-SPECTROMETRY; POSTTRANSLATIONAL MODIFICATIONS; CELL-CULTURE; CHROMATIN MODIFICATIONS; DNA METHYLATION; GENE REPRESSION; MECP1; COMPLEX; AMINO-ACIDS; PHD FINGER; TRANSCRIPTION;
D O I
10.1002/pmic.200800600
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We report a sensitive peptide pull-down approach in combination with protein identification by LC-MS/MS and qualitative abundance measurements by spectrum counting to identify proteins binding to histone H3 tail containing dimethyl lysine 4 (H3K4me2), dimethyl lysine 9 (H3K9me2), or acetyl lysine 9 (H3K9ac). Our study identified 86 nuclear proteins that associate with the histone H3 tail peptides examined, including seven known direct binders and 16 putative direct binders with conserved PHD finger, bromodomain, and WD40 domains. The reliability of our proteomic screen is supported by the fact that more than one-third of the proteins identified were previously described to associate with histone H3 tail directly or indirectly. To our knowledge, the results presented here are the most comprehensive analysis of H3K4me2, H3K9me2, and H3K9ac associated proteins and will provide a useful resource for researchers studying the mechanisms of histone code effector proteins.
引用
收藏
页码:2343 / 2354
页数:12
相关论文
共 52 条
[1]   Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain [J].
Bannister, AJ ;
Zegerman, P ;
Partridge, JF ;
Miska, EA ;
Thomas, JO ;
Allshire, RC ;
Kouzarides, T .
NATURE, 2001, 410 (6824) :120-124
[2]   Quantitative proteomic analysis of posttranslational modifications of human histones [J].
Beck, Hans Christian ;
Nielsen, Eva C. ;
Matthiesen, Rune ;
Jensen, Lars H. ;
Sehested, Maxwell ;
Finn, Paul ;
Grauslund, Morten ;
Hansen, Anne Maria ;
Jensen, Ole Norregaard .
MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (07) :1314-1325
[3]   The complex language of chromatin regulation during transcription [J].
Berger, Shelley L. .
NATURE, 2007, 447 (7143) :407-412
[4]   Stable-isotope-assisted MALDI-TOF mass spectrometry for accurate determination of nucleotide compositions of PCR products [J].
Chen, X ;
Fei, ZD ;
Smith, LM ;
Bradbury, EM ;
Majidi, V .
ANALYTICAL CHEMISTRY, 1999, 71 (15) :3118-3125
[5]   Lysine propionylation and butyrylation are novel post-translational modifications in histones [J].
Chen, Yue ;
Sprung, Robert ;
Tang, Yi ;
Ball, Haydn ;
Sangras, Bhavani ;
Kim, Sung Chan ;
Falck, John R. ;
Peng, Junmin ;
Gu, Wei ;
Zhao, Yingming .
MOLECULAR & CELLULAR PROTEOMICS, 2007, 6 (05) :812-819
[6]   Acetylation and chromosomal functions [J].
Cheung, WL ;
Briggs, SD ;
Allis, CD .
CURRENT OPINION IN CELL BIOLOGY, 2000, 12 (03) :326-333
[7]   Mapping post-translational modifications of the histone variant macroH2A1 using tandem mass spectrometry [J].
Chu, FX ;
Nusinow, DA ;
Chalkely, RJ ;
Plath, K ;
Panning, B ;
Burlingame, AL .
MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (01) :194-203
[8]   ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor [J].
Citterio, E ;
Van Den Boom, V ;
Schnitzler, G ;
Kanaar, R ;
Bonte, E ;
Kingston, RE ;
Hoeijmakers, JHJ ;
Vermeulen, W .
MOLECULAR AND CELLULAR BIOLOGY, 2000, 20 (20) :7643-7653
[9]   Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes [J].
Cox, Brian ;
Kislinger, Thomas ;
Wigle, Dennis A. ;
Kannan, Anitha ;
Brown, Kevin ;
Okubo, Tadashi ;
Hogan, Brigid ;
Jurisica, Igor ;
Frey, Brendan ;
Rossant, Janet ;
Emili, Andrew .
MOLECULAR SYSTEMS BIOLOGY, 2007, 3 (1)
[10]   The yeast PH domain proteins Slm1 and Slm2 are targets of sphingolipid signaling during the response to heat stress [J].
Daquinag, Alexes ;
Fadri, Maria ;
Jung, Sung Yun ;
Qin, Jun ;
Kunz, Jeannette .
MOLECULAR AND CELLULAR BIOLOGY, 2007, 27 (02) :633-650