Kinases and chromatin structure

References

• Badeaux AI, Shi Y. Emerging roles for chromatin as a signal integration and storage platform. Nat Rev Mol Cell Biol 2013; 14:211 - 24; http://dx.doi.org/10.1038/nrm3545
   Web of Science ®Google Scholar
• Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, Kouzarides T. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 2010; 143:470 - 84; http://dx.doi.org/10.1016/j.cell.2010.10.012; PMID: 21029866
   PubMed Web of Science ®Google Scholar
• Eberl HC, Spruijt CG, Kelstrup CD, Vermeulen M, Mann M. A map of general and specialized chromatin readers in mouse tissues generated by label-free interaction proteomics. Mol Cell 2013; 49:368 - 78; http://dx.doi.org/10.1016/j.molcel.2012.10.026; PMID: 23201125
   PubMed Web of Science ®Google Scholar
• Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, et al, ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489:57 - 74; http://dx.doi.org/10.1038/nature11247; PMID: 22955616
   PubMed Web of Science ®Google Scholar
• Fischle W, Wang Y, Allis CD. Binary switches and modification cassettes in histone biology and beyond. Nature 2003; 425:475 - 9; http://dx.doi.org/10.1038/nature02017; PMID: 14523437
   PubMed Web of Science ®Google Scholar
• Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293:1074 - 80; http://dx.doi.org/10.1126/science.1063127; PMID: 11498575
   PubMed Web of Science ®Google Scholar
• Smith E, Shilatifard A. The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes. Mol Cell 2010; 40:689 - 701; http://dx.doi.org/10.1016/j.molcel.2010.11.031; PMID: 21145479
   PubMed Web of Science ®Google Scholar
• Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 2013; 152:1146 - 59; http://dx.doi.org/10.1016/j.cell.2013.02.004; PMID: 23434322
   PubMed Web of Science ®Google Scholar
• Suganuma T, Workman JL. Chromatin and signaling. Curr Opin Cell Biol 2013; 25:322 - 6; http://dx.doi.org/10.1016/j.ceb.2013.02.016; PMID: 23498660
   PubMed Web of Science ®Google Scholar
• Suganuma T, Workman JL. Signals and combinatorial functions of histone modifications. Annu Rev Biochem 2011; 80:473 - 99; http://dx.doi.org/10.1146/annurev-biochem-061809-175347; PMID: 21529160
   PubMed Web of Science ®Google Scholar
• Turner BM. Defining an epigenetic code. Nat Cell Biol 2007; 9:2 - 6; http://dx.doi.org/10.1038/ncb0107-2; PMID: 17199124
   PubMed Web of Science ®Google Scholar
• Weiner A, Chen HV, Liu CL, Rahat A, Klien A, Soares L, et al. Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol 2012; 10:e1001369; http://dx.doi.org/10.1371/journal.pbio.1001369; PMID: 22912562
   PubMedGoogle Scholar
• Collins RT, Treisman JE. Osa-containing Brahma chromatin remodeling complexes are required for the repression of wingless target genes. Genes Dev 2000; 14:3140 - 52; http://dx.doi.org/10.1101/gad.854300; PMID: 11124806
   PubMed Web of Science ®Google Scholar
• Miotto B, Sagnier T, Berenger H, Bohmann D, Pradel J, Graba Y. Chameau HAT and DRpd3 HDAC function as antagonistic cofactors of JNK/AP-1-dependent transcription during Drosophila metamorphosis. Genes Dev 2006; 20:101 - 12; http://dx.doi.org/10.1101/gad.359506; PMID: 16391236
   PubMed Web of Science ®Google Scholar
• von Zelewsky T, Palladino F, Brunschwig K, Tobler H, Hajnal A, Müller F. The C. elegans Mi-2 chromatin-remodelling proteins function in vulval cell fate determination. Development 2000; 127:5277 - 84; PMID: 11076750
   PubMed Web of Science ®Google Scholar
• Rottbauer W, Saurin AJ, Lickert H, Shen X, Burns CG, Wo ZG, et al. Reptin and pontin antagonistically regulate heart growth in zebrafish embryos. Cell 2002; 111:661 - 72; http://dx.doi.org/10.1016/S0092-8674(02)01112-1; PMID: 12464178
   PubMed Web of Science ®Google Scholar
• Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 1999; 23:185 - 8; http://dx.doi.org/10.1038/13810; PMID: 10508514
   PubMed Web of Science ®Google Scholar
• Gibbons RJ, Picketts DJ, Villard L, Higgs DR. Mutations in a putative global transcriptional regulator cause X-linked mental retardation with alpha-thalassemia (ATR-X syndrome). Cell 1995; 80:837 - 45; http://dx.doi.org/10.1016/0092-8674(95)90287-2; PMID: 7697714
   PubMed Web of Science ®Google Scholar
• Hansen RS, Wijmenga C, Luo P, Stanek AM, Canfield TK, Weemaes CM, et al. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci U S A 1999; 96:14412 - 7; http://dx.doi.org/10.1073/pnas.96.25.14412; PMID: 10588719
   PubMed Web of Science ®Google Scholar
• Kasprzyk L, Defossez PA, Miotto B. [Epigenetic regulation in neuronal differentiation and brain function]. Biol Aujourdhui 2013; 207:1 - 17; http://dx.doi.org/10.1051/jbio/2013001; PMID: 23694721
   PubMedGoogle Scholar
• Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS, et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010; 468:839 - 43; http://dx.doi.org/10.1038/nature09586; PMID: 21057493
   PubMed Web of Science ®Google Scholar
• Petrij F, Giles RH, Dauwerse HG, Saris JJ, Hennekam RC, Masuno M, et al. Rubinstein-Taybi syndrome caused by mutations in the transcriptional co-activator CBP. Nature 1995; 376:348 - 51; http://dx.doi.org/10.1038/376348a0; PMID: 7630403
   PubMed Web of Science ®Google Scholar
• Trivier E, De Cesare D, Jacquot S, Pannetier S, Zackai E, Young I, et al. Mutations in the kinase Rsk-2 associated with Coffin-Lowry syndrome. Nature 1996; 384:567 - 70; http://dx.doi.org/10.1038/384567a0; PMID: 8955270
   PubMed Web of Science ®Google Scholar
• Villard L, Gecz J, Mattéi JF, Fontés M, Saugier-Veber P, Munnich A, et al. XNP mutation in a large family with Juberg-Marsidi syndrome. Nat Genet 1996; 12:359 - 60; http://dx.doi.org/10.1038/ng0496-359; PMID: 8630485
   PubMed Web of Science ®Google Scholar
• Latham JA, Chosed RJ, Wang S, Dent SY. Chromatin signaling to kinetochores: transregulation of Dam1 methylation by histone H2B ubiquitination. Cell 2011; 146:709 - 19; http://dx.doi.org/10.1016/j.cell.2011.07.025; PMID: 21884933
   PubMed Web of Science ®Google Scholar
• Kaidi A, Jackson SP. KAT5 tyrosine phosphorylation couples chromatin sensing to ATM signalling. Nature 2013; 498:70 - 4; http://dx.doi.org/10.1038/nature12201; PMID: 23708966
   PubMed Web of Science ®Google Scholar
• Klein AM, Zaganjor E, Cobb MH. Chromatin-tethered MAPKs. Curr Opin Cell Biol 2013; 25:272 - 7; http://dx.doi.org/10.1016/j.ceb.2013.01.002; PMID: 23434067
   PubMed Web of Science ®Google Scholar
• Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C. A chromatin-modifying function of JNK during stem cell differentiation. Nat Genet 2012; 44:94 - 100; http://dx.doi.org/10.1038/ng.1036; PMID: 22179133
   PubMed Web of Science ®Google Scholar
• Suganuma T, Mushegian A, Swanson SK, Abmayr SM, Florens L, Washburn MP, et al. The ATAC acetyltransferase complex coordinates MAP kinases to regulate JNK target genes. Cell 2010; 142:726 - 36; http://dx.doi.org/10.1016/j.cell.2010.07.045; PMID: 20813260
   PubMed Web of Science ®Google Scholar
• Ura S, Nishina H, Gotoh Y, Katada T. Activation of the c-Jun N-terminal kinase pathway by MST1 is essential and sufficient for the induction of chromatin condensation during apoptosis. Mol Cell Biol 2007; 27:5514 - 22; http://dx.doi.org/10.1128/MCB.00199-07; PMID: 17548476
   PubMed Web of Science ®Google Scholar
• Kim T, Yoon J, Cho H, Lee WB, Kim J, Song YH, et al. Downregulation of lipopolysaccharide response in Drosophila by negative crosstalk between the AP1 and NF-kappaB signaling modules. Nat Immunol 2005; 6:211 - 8; http://dx.doi.org/10.1038/ni1159; PMID: 15640802
   PubMed Web of Science ®Google Scholar
• Hattori A, Mizuno T, Akamatsu M, Hisamoto N, Matsumoto K. The Caenorhabditis elegans JNK signaling pathway activates expression of stress response genes by derepressing the Fos/HDAC repressor complex. PLoS Genet 2013; 9:e1003315; http://dx.doi.org/10.1371/journal.pgen.1003315; PMID: 23437011
   PubMedGoogle Scholar
• Miotto B, Struhl K. HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1. Genes Dev 2008; 22:2633 - 8; http://dx.doi.org/10.1101/gad.1674108; PMID: 18832067
   PubMed Web of Science ®Google Scholar
• Miotto B, Struhl K. JNK1 phosphorylation of Cdt1 inhibits recruitment of HBO1 histone acetylase and blocks replication licensing in response to stress. Mol Cell 2011; 44:62 - 71; http://dx.doi.org/10.1016/j.molcel.2011.06.021; PMID: 21856198
   PubMed Web of Science ®Google Scholar
• Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA. Activated signal transduction kinases frequently occupy target genes. Science 2006; 313:533 - 6; http://dx.doi.org/10.1126/science.1127677; PMID: 16873666
   PubMed Web of Science ®Google Scholar
• Duch A, Felipe-Abrio I, Barroso S, Yaakov G, García-Rubio M, Aguilera A, et al. Coordinated control of replication and transcription by a SAPK protects genomic integrity. Nature 2013; 493:116 - 9; http://dx.doi.org/10.1038/nature11675; PMID: 23178807
   PubMed Web of Science ®Google Scholar
• Bungard D, Fuerth BJ, Zeng PY, Faubert B, Maas NL, Viollet B, et al. Signaling kinase AMPK activates stress-promoted transcription via histone H2B phosphorylation. Science 2010; 329:1201 - 5; http://dx.doi.org/10.1126/science.1191241; PMID: 20647423
   PubMed Web of Science ®Google Scholar
• Dawson MA, Bannister AJ, Göttgens B, Foster SD, Bartke T, Green AR, et al. JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Nature 2009; 461:819 - 22; http://dx.doi.org/10.1038/nature08448; PMID: 19783980
   PubMed Web of Science ®Google Scholar
• Gehani SS, Agrawal-Singh S, Dietrich N, Christophersen NS, Helin K, Hansen K. Polycomb group protein displacement and gene activation through MSK-dependent H3K27me3S28 phosphorylation. Mol Cell 2010; 39:886 - 900; http://dx.doi.org/10.1016/j.molcel.2010.08.020; PMID: 20864036
   PubMed Web of Science ®Google Scholar
• Göke J, Chan YS, Yan J, Vingron M, Ng HH. Genome-wide Kinase-Chromatin Interactions Reveal the Regulatory Network of ERK Signaling in Human Embryonic Stem Cells. Mol Cell 2013; 50:844 - 55; http://dx.doi.org/10.1016/j.molcel.2013.04.030; PMID: 23727019
   PubMed Web of Science ®Google Scholar
• Sutcliffe EL, Bunting KL, He YQ, Li J, Phetsouphanh C, Seddiki N, et al. Chromatin-associated protein kinase C-θ regulates an inducible gene expression program and microRNAs in human T lymphocytes. Mol Cell 2011; 41:704 - 19; http://dx.doi.org/10.1016/j.molcel.2011.02.030; PMID: 21419345
   PubMed Web of Science ®Google Scholar
• Rosenfeld MG, Lunyak VV, Glass CK. Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. Genes Dev 2006; 20:1405 - 28; http://dx.doi.org/10.1101/gad.1424806; PMID: 16751179
   PubMed Web of Science ®Google Scholar
• American Association for Cancer Research Human Epigenome Task Force, European Union, Network of Excellence, Scientific Advisory Board. Moving AHEAD with an international human epigenome project. Nature 2008; 454:711 - 5; http://dx.doi.org/10.1038/454711a; PMID: 18685699
   PubMed Web of Science ®Google Scholar
• Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al, The NIH Roadmap Epigenomics Mapping Consortium. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 2010; 28:1045 - 8; http://dx.doi.org/10.1038/nbt1010-1045; PMID: 20944595
   PubMed Web of Science ®Google Scholar
• Weiner A, Chen HV, Liu CL, Rahat A, Klien A, Soares L, et al. Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol 2012; 10:e1001369; http://dx.doi.org/10.1371/journal.pbio.1001369; PMID: 22912562
   PubMedGoogle Scholar
• Zanton SJ, Pugh BF. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev 2006; 20:2250 - 65; http://dx.doi.org/10.1101/gad.1437506; PMID: 16912275
   PubMed Web of Science ®Google Scholar
• Proft M, Struhl K. Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell 2002; 9:1307 - 17; http://dx.doi.org/10.1016/S1097-2765(02)00557-9; PMID: 12086627
   PubMed Web of Science ®Google Scholar
• Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 2005; 102:10604 - 9; http://dx.doi.org/10.1073/pnas.0500398102; PMID: 16009939
   PubMed Web of Science ®Google Scholar
• Shiloh Y, Ziv Y. The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol 2013; 14:197 - 210; http://dx.doi.org/10.1038/nrm3546
   Web of Science ®Google Scholar
• Uziel T, Lerenthal Y, Moyal L, Andegeko Y, Mittelman L, Shiloh Y. Requirement of the MRN complex for ATM activation by DNA damage. EMBO J 2003; 22:5612 - 21; http://dx.doi.org/10.1093/emboj/cdg541; PMID: 14532133
   PubMed Web of Science ®Google Scholar
• Lee JH, Paull TT. Direct activation of the ATM protein kinase by the Mre11/Rad50/Nbs1 complex. Science 2004; 304:93 - 6; http://dx.doi.org/10.1126/science.1091496; PMID: 15064416
   PubMed Web of Science ®Google Scholar
• Lee JH, Paull TT. ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science 2005; 308:551 - 4; http://dx.doi.org/10.1126/science.1108297; PMID: 15790808
   PubMed Web of Science ®Google Scholar
• Falck J, Coates J, Jackson SP. Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage. Nature 2005; 434:605 - 11; http://dx.doi.org/10.1038/nature03442; PMID: 15758953
   PubMed Web of Science ®Google Scholar
• Kim YC, Gerlitz G, Furusawa T, Catez F, Nussenzweig A, Oh KS, et al. Activation of ATM depends on chromatin interactions occurring before induction of DNA damage. Nat Cell Biol 2009; 11:92 - 6; http://dx.doi.org/10.1038/ncb1817; PMID: 19079244
   PubMed Web of Science ®Google Scholar
• Lukas J, Lukas C, Bartek J. More than just a focus: The chromatin response to DNA damage and its role in genome integrity maintenance. Nat Cell Biol 2011; 13:1161 - 9; http://dx.doi.org/10.1038/ncb2344; PMID: 21968989
   PubMed Web of Science ®Google Scholar
• Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M, Bonner WM. A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr Biol 2000; 10:886 - 95; http://dx.doi.org/10.1016/S0960-9822(00)00610-2; PMID: 10959836
   PubMed Web of Science ®Google Scholar
• Sun Y, Jiang X, Chen S, Fernandes N, Price BD. A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. Proc Natl Acad Sci U S A 2005; 102:13182 - 7; http://dx.doi.org/10.1073/pnas.0504211102; PMID: 16141325
   PubMed Web of Science ®Google Scholar
• Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007; 316:1160 - 6; http://dx.doi.org/10.1126/science.1140321; PMID: 17525332
   PubMed Web of Science ®Google Scholar
• Ayoub N, Jeyasekharan AD, Bernal JA, Venkitaraman AR. HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response. Nature 2008; 453:682 - 6; http://dx.doi.org/10.1038/nature06875; PMID: 18438399
   PubMed Web of Science ®Google Scholar
• Zhang K, Lin W, Latham JA, Riefler GM, Schumacher JM, Chan C, et al. The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation. Cell 2005; 122:723 - 34; http://dx.doi.org/10.1016/j.cell.2005.06.021; PMID: 16143104
   PubMed Web of Science ®Google Scholar
• Kouzarides T. Acetylation: a regulatory modification to rival phosphorylation?. EMBO J 2000; 19:1176 - 9; http://dx.doi.org/10.1093/emboj/19.6.1176; PMID: 10716917
   PubMed Web of Science ®Google Scholar