Building the Connectivity Map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry

被引：40
作者：
Creech, Amanda L. [1 ]
Taylor, Jordan E. [1 ]
Maier, Verena K. [2 ]
Wu, Xiaoyun [1 ]
Feeney, Caitlin M. [1 ]
Udeshi, Namrata D. [1 ]
Peach, Sally E. [1 ]
Boehm, Jesse S. [1 ]
Lee, Jeannie T. [2 ,3 ]
Carr, Steven A. [1 ]
Jaffe, Jacob D. [1 ]
机构：
[1] Broad Inst MIT & Harvard Univ, Cambridge, MA 02142 USA
[2] Harvard Univ, Massachusetts Gen Hosp, Sch Med, Boston, MA 02114 USA
[3] Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02114 USA
来源：
METHODS | 2015年 / 72卷
关键词：
Histones; Chromatin; Epigenetics; Proteomics; Mass spectrometry; SILAC; H3; LYSINE; 27; HISTONE H3; METHYLATION; EZH2; MUTATIONS;
D O I：
10.1016/j.ymeth.2014.10.033
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Epigenetic control of genome function is an important regulatory mechanism in diverse processes such as lineage commitment and environmental sensing, and in disease etiologies ranging from neuropsychiatric disorders to cancer. Here we report a robust, high-throughput targeted, quantitative mass spectrometry (MS) method to rapidly profile modifications of the core histones of chromatin that compose the epigenetic landscape, enabling comparisons among cells with differing genetic backgrounds, genomic perturbations, and drug treatments. (C) 2014 ElsevierInc. All rights reserved.
引用
收藏
页码：57 / 64
页数：8
相关论文
共 13 条
  • [1] Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders
    Ernst, Thomas
    Chase, Andrew J.
    Score, Joannah
    Hidalgo-Curtis, Claire E.
    Bryant, Catherine
    Jones, Amy V.
    Waghorn, Katherine
    Zoi, Katerina
    Ross, Fiona M.
    Reiter, Andreas
    Hochhaus, Andreas
    Drexler, Hans G.
    Duncombe, Andrew
    Cervantes, Francisco
    Oscier, David
    Boultwood, Jacqueline
    Grand, Francis H.
    Cross, Nicholas C. P.
    [J]. NATURE GENETICS, 2010, 42 (08) : 722 - U109
  • [2] The ENCODE (ENCyclopedia of DNA elements) Project
    Feingold, EA
    Good, PJ
    Guyer, MS
    Kamholz, S
    Liefer, L
    Wetterstrand, K
    Collins, FS
    Gingeras, TR
    Kampa, D
    Sekinger, EA
    Cheng, J
    Hirsch, H
    Ghosh, S
    Zhu, Z
    Pate, S
    Piccolboni, A
    Yang, A
    Tammana, H
    Bekiranov, S
    Kapranov, P
    Harrison, R
    Church, G
    Struhl, K
    Ren, B
    Kim, TH
    Barrera, LO
    Qu, C
    Van Calcar, S
    Luna, R
    Glass, CK
    Rosenfeld, MG
    Guigo, R
    Antonarakis, SE
    Birney, E
    Brent, M
    Pachter, L
    Reymond, A
    Dermitzakis, ET
    Dewey, C
    Keefe, D
    Denoeud, F
    Lagarde, J
    Ashurst, J
    Hubbard, T
    Wesselink, JJ
    Castelo, R
    Eyras, E
    Myers, RM
    Sidow, A
    Batzoglou, S
    [J]. SCIENCE, 2004, 306 (5696) : 636 - 640
  • [3] Chemical derivatization of histones for facilitated analysis by mass spectrometry
    Garcia, Benjamin A.
    Mollah, Sahana
    Ueberheide, Beatrix M.
    Busby, Scott A.
    Muratore, Tara L.
    Shabanowitz, Jeffrey
    Hunt, Donald F.
    [J]. NATURE PROTOCOLS, 2007, 2 (04) : 933 - 938
  • [4] METHOD OF THE YEAR Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry
    Gillette, Michael A.
    Carr, Steven A.
    [J]. NATURE METHODS, 2013, 10 (01) : 28 - 34
  • [5] Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia
    Jaffe, Jacob D.
    Wang, Yan
    Chan, Ho Man
    Zhang, Jinghui
    Huether, Robert
    Kryukov, Gregory V.
    Bhang, Hyo-eun C.
    Taylor, Jordan E.
    Hu, Min
    Englund, Nathan P.
    Yan, Feng
    Wang, Zhaofu
    McDonald, E. Robert, III
    Wei, Lei
    Ma, Jing
    Easton, John
    Yu, Zhengtian
    deBeaumount, Rosalie
    Gibaja, Veronica
    Venkatesan, Kavitha
    Schlegel, Robert
    Sellers, William R.
    Keen, Nicholas
    Liu, Jun
    Caponigro, Giordano
    Barretina, Jordi
    Cooke, Vesselina G.
    Mullighan, Charles
    Carr, Steven A.
    Downing, James R.
    Garraway, Levi A.
    Stegmeier, Frank
    [J]. NATURE GENETICS, 2013, 45 (11) : 1386 - +
  • [6] The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease
    Lamb, Justin
    Crawford, Emily D.
    Peck, David
    Modell, Joshua W.
    Blat, Irene C.
    Wrobel, Matthew J.
    Lerner, Jim
    Brunet, Jean-Philippe
    Subramanian, Aravind
    Ross, Kenneth N.
    Reich, Michael
    Hieronymus, Haley
    Wei, Guo
    Armstrong, Scott A.
    Haggarty, Stephen J.
    Clemons, Paul A.
    Wei, Ru
    Carr, Steven A.
    Lander, Eric S.
    Golub, Todd R.
    [J]. SCIENCE, 2006, 313 (5795) : 1929 - 1935
  • [7] Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
    MacLean, Brendan
    Tomazela, Daniela M.
    Shulman, Nicholas
    Chambers, Matthew
    Finney, Gregory L.
    Frewen, Barbara
    Kern, Randall
    Tabb, David L.
    Liebler, Daniel C.
    MacCoss, Michael J.
    [J]. BIOINFORMATICS, 2010, 26 (07) : 966 - 968
  • [8] The Polycomb complex PRC2 and its mark in life
    Margueron, Raphael
    Reinberg, Danny
    [J]. NATURE, 2011, 469 (7330) : 343 - 349
  • [9] Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules
    Peach, Sally E.
    Rudomin, Emily L.
    Udeshi, Namrata D.
    Carr, Steven A.
    Jaffe, Jacob D.
    [J]. MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (05) : 128 - 137
  • [10] EZH1 Mediates Methylation on Histone H3 Lysine 27 and Complements EZH2 in Maintaining Stem Cell Identity and Executing Pluripotency
    Shen, Xiaohua
    Liu, Yingchun
    Hsu, Yu-Jung
    Fujiwara, Yuko
    Kim, Jonghwan
    Mao, Xiaohong
    Yuan, Guo-Cheng
    Orkin, Stuart H.
    [J]. MOLECULAR CELL, 2008, 32 (04) : 491 - 502
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