Signaling to Chromatin through Histone Modifications

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Signaling—2000 and Beyond

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IAP family proteins---suppressors of apoptosisPreprint

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Megabase Chromatin Domains Involved in DNA Double-Strand Breaks in Vivo

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CREB: A Stimulus-Induced Transcription Factor Activated by A Diverse Array of Extracellular Signals

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Phosphorylated CREB binds specifically to the nuclear protein CBP

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Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation

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Histone deacetylase inhibitors: new drugs for the treatment of inflammatory diseases?

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Function and regulation of the transcription factors of the Myc/Max/Mad network

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A Nitric Oxide Signaling Pathway Controls CREB-Mediated Gene Expression in Neurons

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PKM2 Regulates Chromosome Segregation and Mitosis Progression of Tumor Cells

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The Constantly Changing Face of Chromatin

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Environmental epigenetics of asthma: An update

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Mammalian circadian clock and metabolism – the epigenetic link

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Chromatin Docking and Exchange Activity Enhancement of RCC1 by Histones H2A and H2B

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The IκB Kinase Regulates Chromatin Structure during Reconsolidation of Conditioned Fear Memories

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Histone Modifications and Cancer

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TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION IN INFLAMMATION

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Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

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Histone deacetylase 6 binds polyubiquitin through its zinc finger (PAZ domain) and copurifies with deubiquitinating enzymes

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Major chromatin remodeling in the germinal vesicle (GV) of mammalian oocytes is dispensable for global transcriptional silencing but required for centromeric heterochromatin function

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The Human Transient Receptor Potential Vanilloid Type 6 Distal Promoter Contains Multiple Vitamin D Receptor Binding Sites that Mediate Activation by 1,25-Dihydroxyvitamin D3 in Intestinal Cells

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Multilevel regulation of the circadian clock

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Breaching the DNA damage checkpoint via PF-00477736, a novel small-molecule inhibitor of checkpoint kinase 1

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The epigenetic landscape of addiction

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Epigenetic Cross-Talk between DNA Methylation and Histone Modifications in Human Cancers

Kondo, Y. (2009) · Yonsei Medical Journal · doi:10.3349/ymj.2009.50.4.455 · Cited by 226

Mechanism for Nucleocytoplasmic Shuttling of Histone Deacetylase 7

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Intrinsically disordered proteins play diverse roles in cell signaling

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SMRT Derepression by the IκB Kinase α

Hoberg, J. E., Yeung, F., & Mayo, M. W. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.10.010 · Cited by 220

A tale of histone modifications.

Grant, P. A. (2001) · Genome biology · doi:10.1186/gb-2001-2-4-reviews0003 · Cited by 213

The JIL-1 Tandem Kinase Mediates Histone H3 Phosphorylation and Is Required for Maintenance of Chromatin Structure in Drosophila

Wang, Y., Zhang, W., Jin, Y., Johansen, J., & Johansen, K. M. (2001) · Cell · doi:10.1016/s0092-8674(01)00325-7 · Cited by 213

Histone Modifications and Chromatin Remodeling during Bacterial Infections

Hamon, M. A., & Cossart, P. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.07.009 · Cited by 222

Deficient in DNA Methylation 1 (DDM1) Defines a Novel Family of Chromatin-remodeling Factors

Brzeski, J., & Jerzmanowski, A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m209260200 · Cited by 210

Posttranslational Protein Modification inArchaea

Eichler, J., & Adams, M. W. W. (2005) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.69.3.393-425.2005 · Cited by 211

Reversible S-glutathionylation of Cys374 regulates actin filament formation by inducing structural changes in the actin molecule

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A Peek into the Complex Realm of Histone Phosphorylation

Banerjee, T., & Chakravarti, D. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05631-11 · Cited by 228

Histone levels are regulated by phosphorylation and ubiquitylation-dependent proteolysis

Singh, R. K., Kabbaj, M.-H. M., Paik, J., & Gunjan, A. (2009) · Nature Cell Biology · doi:10.1038/ncb1903 · Cited by 204

Regulation of heterochromatin by histone methylation and small RNAs

Grewal, S. I. S., & Rice, J. C. (2004) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2004.04.002 · Cited by 207

Genome-Wide Analysis of DNA Methylation Differences in Muscle and Fat from Monozygotic Twins Discordant for Type 2 Diabetes

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A Comprehensive View of the Epigenetic Landscape. Part II: Histone Post-translational Modification, Nucleosome Level, and Chromatin Regulation by ncRNAs

Sadakierska−Chudy, A., & Filip, M. (2014) · Neurotoxicity Research · doi:10.1007/s12640-014-9508-6 · Cited by 202

ERK Activation Following Macrophage FcγR Ligation Leads to Chromatin Modifications at the IL-10 Locus

Lucas, M., Zhang, X., Prasanna, V., & Mosser, D. M. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.175.1.469 · Cited by 197

Fluoxetine and Cocaine Induce the Epigenetic Factors MeCP2 and MBD1 in Adult Rat Brain

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Isolation and Characterization of Mammalian HDAC10, a Novel Histone Deacetylase

Kao, H.-Y., Lee, C.-H., Komarov, A., Han, C. C., & Evans, R. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m108931200 · Cited by 193

Histone code pathway involving H3 S28 phosphorylation and K27 acetylation activates transcription and antagonizes polycomb silencing

Lau, P. N. I., & Cheung, P. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012798108 · Cited by 191

UPTAKE, LOCALIZATION, AND NONCARBOXYLASE ROLES OF BIOTIN

Zempleni, J. (2005) · Annual Review of Nutrition · doi:10.1146/annurev.nutr.25.121304.131724 · Cited by 193

Serine-arginine protein kinases: a small protein kinase family with a large cellular presence

Giannakouŕos, T., Nikolakaki, E., Mylonis, I., & Georgatsou, E. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2010.07987.x · Cited by 192

MAP kinase‐mediated phosphoacetylation of histone H3 and inducible gene regulation

Clayton, A. L., & Mahadevan, L. C. (2003) · FEBS Letters · doi:10.1016/s0014-5793(03)00451-4 · Cited by 189

The Transcriptional Co-activators CREB-binding Protein (CBP) and p300 Play a Critical Role in Cardiac Hypertrophy That Is Dependent on Their Histone Acetyltransferase Activity

Gusterson, R. J., Jazrawi, E., Adcock, I. M., & Latchman, D. S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211762200 · Cited by 186

Chromatin Remodeling, Measured by a Novel Real-Time Polymerase Chain Reaction Assay, Across the Proximal Promoter Region of the IL-2 Gene

Rao, S., Procko, E., & Shannon, M. F. (2001) · The Journal of Immunology · doi:10.4049/jimmunol.167.8.4494 · Cited by 188

REST Repression of Neuronal Genes Requires Components of the hSWI·SNF Complex

Battaglioli, E., Andrés, M. E., Rose, D. W., Chenoweth, J. G., Rosenfeld, M. G., Anderson, M. E., & Mandel, G. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m205691200 · Cited by 195

The TRPM7 Chanzyme Is Cleaved to Release a Chromatin-Modifying Kinase

Krapivinsky, G. B., Krapivinsky, L., Manasian, Y., & Clapham, D. E. (2014) · Cell · doi:10.1016/j.cell.2014.03.046 · Cited by 181

Endotoxin Tolerance Disrupts Chromatin Remodeling and NF-κB Transactivation at the IL-1β Promoter

Chan, C., Li, L., McCall, C. E., & Yoza, B. K. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.175.1.461 · Cited by 180

Chromatin unfolding and activation by HMGN**The nomenclature of the HMG protein superfamily has been recently revised (see Ref. 12 and http://www.informatics.jax.org/mgihome/nomen/genefamilies/hmgfamily.shtml). chromosomal proteins

Bustin, M. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01855-2 · Cited by 177

Targeted recruitment of a histone H4-specific methyltransferase by the transcription factor YY1Preprint

Rezai‐Zadeh, N., Zhang, X. M., Namour, F., Fejér, G., Wen, Y., Yao, Y., Győry, I., Wright, K. L., & Seto, E. (2003) · Genes & Development · doi:10.1101/gad.1068003 · Cited by 178

Coupling cAMP Signaling to Transcription in the Liver: Pivotal Role of CREB and CREM

Servillo, G., Fazia, M. A. D., & Sassone‐Corsi, P. (2002) · Experimental Cell Research · doi:10.1006/excr.2002.5491 · Cited by 175

HATs on and beyond chromatin

Chen, H.-W., Tini, M., & Evans, R. M. (2001) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(00)00200-3 · Cited by 178

Synergy among Nuclear Receptor Coactivators: Selective Requirement for Protein Methyltransferase and Acetyltransferase Activities

Lee, Y., Koh, S. S., Zhang, X., Cheng, X., & Stallcup, M. R. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.11.3621-3632.2002 · Cited by 181

Sirtuins: Molecular Traffic Lights in the Crossroad of Oxidative Stress, Chromatin Remodeling, and Transcription

Rajendran, R., Garva, R., Krstic–Demonacos, M., & Demonacos, C. (2011) · BioMed Research International · doi:10.1155/2011/368276 · Cited by 180

Transcriptional Induction of MKP-1 in Response to Stress Is Associated with Histone H3 Phosphorylation-Acetylation

Li, J., Gorospe, M., Hutter, D., Barnes, J., Keyse, S. M., & Liu, Y. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.23.8213-8224.2001 · Cited by 173

Regulation of Mammalian Oocyte Maturation

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Evidence of DNA damage in Alzheimer disease: phosphorylation of histone H2AX in astrocytes

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Expression and purification of recombinant human histones

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Regulation of gene expression by biotin☆ (review)

Rodrı́guez-Meléndez, R., & Zempleni, J. (2003) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2003.07.001 · Cited by 167

Sox9 and p300 Cooperatively Regulate Chromatin-mediated Transcription

Furumatsu, T., Tsuda, M., Yoshida, K., Taniguchi, N., Ito, T., Hashimoto, M., Ito, T., & Asahara, H. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m502409200 · Cited by 168

Epigenetics, brain evolution and behaviour

Keverne, E. B., & Curley, J. P. (2008) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2008.03.001 · Cited by 168

Combinatorial Control of Smooth Muscle–Specific Gene Expression

Kumar, M. S., & Owens, G. K. (2003) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/01.atv.0000065197.07635.ba · Cited by 164

Histone Deacetylase Inhibitors Decrease Cocaine But Not Sucrose Self-Administration in Rats

Romieu, P., Host, L., Gobaille, S., Sandner, G., Aunis, D., & Zwiller, J. (2008) · Journal of Neuroscience · doi:10.1523/jneurosci.0379-08.2008 · Cited by 162

Orchestration of chromatin-based processes: mind the TRRAP

Murr, R., Vaissière, T., Sawan, C., Shukla, V., & Herceg, Z. (2007) · Oncogene · doi:10.1038/sj.onc.1210605 · Cited by 174

14‐3‐3 Proteins recognize a histone code at histone H3 and are required for transcriptional activation

Winter, S., Simboeck, E., Fischle, W., Zupkovitz, G., Dohnal, I., Mechtler, K., Ammerer, G., & Seiser, C. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601954 · Cited by 160

Metabolic and mitogenic signal transduction in human skeletal muscle after intense cycling exercise

Yu, M., Stepto, N. K., Chibalin, A., Fryer, L. G. D., Carling, D., Krook, A., Hawley, J. A., & Zierath, J. R. (2003) · The Journal of Physiology · doi:10.1113/jphysiol.2002.034223 · Cited by 160

Histone deacetylase (HDAC) inhibition improves myocardial function and prevents cardiac remodeling in diabetic mice

Chen, Y., Du, J., Zhao, Y., Zhang, L., Lv, G., Zhuang, S., Qin, G., & Zhao, T. C. (2015) · Cardiovascular Diabetology · doi:10.1186/s12933-015-0262-8 · Cited by 156

Structure of Alba: an archaeal chromatin protein modulated by acetylation

Wardleworth, B. N., Russell, R. J. M., Bell, S. D., Taylor, G. L., & White, M. F. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf465 · Cited by 156

Conserved Enzymatic Production and Biological Effect of O-Acetyl-ADP-ribose by Silent Information Regulator 2-like NAD+-dependent Deacetylases

Borra, M. T., O'Neill, F. J., Jackson, M. D., Marshall, B. L., Verdin, E. M., Foltz, K. R., & Denu, J. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m111830200 · Cited by 155

Interactive Effects of HDAC Inhibitors and TRAIL on Apoptosis Are Associated with Changes in Mitochondrial Functions and Expressions of Cell Cycle Regulatory Genes in Multiple Myeloma

Fandy, T. E., Shankar, S., Ross, D. D., Sausville, E. A., & Srivastava, R. K. (2005) · Neoplasia · doi:10.1593/neo.04655 · Cited by 156

Adenovirus E1A: remodelling the host cell, a life or death experience

Gallimore, P. H., & Turnell, A. S. (2001) · Oncogene · doi:10.1038/sj.onc.1204913 · Cited by 159

Chromatin Organization in the Mammalian Nucleus

Gilbert, N., Gilchrist, S., & Bickmore, W. A. (2004) · International review of cytology · doi:10.1016/s0074-7696(04)42007-5 · Cited by 156

Epigenetic regulation and cancer (Review)

CHEN, Q. W., Zhu, X., Li, Y., & Meng, Z. (2013) · Oncology Reports · doi:10.3892/or.2013.2913 · Cited by 150

When Signaling Kinases Meet Histones and Histone Modifiers in the Nucleus

Baek, S. H. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.03.022 · Cited by 149

Role of the ERK/MSK1 signalling pathway in chromatin remodelling and brain responses to drugs of abuse

Brami‐Cherrier, K., Roze, E. F., Girault, J., Bétuing, S., & Caboche, J. (2009) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2009.05879.x · Cited by 156

Dual action on promoter demethylation and chromatin by an isothiocyanate restored GSTP1 silenced in prostate cancer

Wang, L. G., Beklemisheva, A. A., Liu, X. M., Ferrari, A. C., Feng, J. Q., & Chiao, J.-W. (2006) · Molecular Carcinogenesis · doi:10.1002/mc.20258 · Cited by 148

Making memories of stressful events: a journey along epigenetic, gene transcription, and signaling pathways

Reul, J. M. H. M. (2014) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2014.00005 · Cited by 147

Epigenetic Silencing of Tumor Necrosis Factor α during Endotoxin Tolerance

Gazzar, M. E., Yoza, B. K., Hu, J., Cousart, S. L., & McCall, C. E. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m704584200 · Cited by 145

Time-lapse Imaging Reveals Dynamic Relocalization of PP1γ throughout the Mammalian Cell Cycle

Trinkle‐Mulcahy, L., Andrews, P. D., Wickramasinghe, S. R., Sleeman, J., Prescott, A. R., Lam, Y. W., Lyon, C. E., Swedlow, J. R., & Lamond, A. I. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-07-0376 · Cited by 145

Epigenetic considerations in aquaculture

Gavery, M. R., & Roberts, S. (2017) · PeerJ · doi:10.7717/peerj.4147 · Cited by 148

Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB

Yang, X., Tajkhorshid, E., & Chen, L. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.01343-09 · Cited by 149

Inhibition of histone deacetylases triggers pharmacologic preconditioning effects against myocardial ischemic injury

Zhao, T., Cheng, G., Zhang, L., TSENG, Y., & PADBURY, J. (2007) · Cardiovascular Research · doi:10.1016/j.cardiores.2007.08.010 · Cited by 142

Direct Association with Inner Centromere Protein (INCENP) Activates the Novel Chromosomal Passenger Protein, Aurora-C

Li, X., Sakashita, G., Matsuzaki, H., Sugimoto, K., Kimura, K., Hanaoka, F., Taniguchi, H., Furukawa, K., & Urano, T. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m403029200 · Cited by 142

p21‐activated kinase 1 interacts with and phosphorylates histone H3 in breast cancer cells

Li, F., Adam, L., Vadlamudi, R. K., Zhou, H., Sen, S., Chernoff, J., Mandal, M., & Kumar, R. (2002) · EMBO Reports · doi:10.1093/embo-reports/kvf157 · Cited by 142

TheS. pombeaurora-related kinase Ark1 associates with mitotic structures in a stage dependent manner and is required for chromosome segregation

Petersen, J., Paris, J., Willer, M., Philippe, M., & Hagan, I. (2001) · Journal of Cell Science · doi:10.1242/jcs.114.24.4371 · Cited by 141

Epigenetic regulation of smooth muscle cell plasticity

Liu, R., Leslie, K. L., & Martin, K. A. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.06.004 · Cited by 142

Aberrant histone acetylation, altered transcription, and retinal degeneration in a Drosophila model of polyglutamine disease are rescued by CREB-binding proteinPreprint

Taylor, J. P., Taye, A. A., Campbell, C. E., Kazemi‐Esfarjani, P., Fischbeck, K. H., & Min, K. (2003) · Genes & Development · doi:10.1101/gad.1087503 · Cited by 143

Apoptotic Release of Histones from Nucleosomes

Wu, D., Ingram, A. J., Lahti, J. M., Mazza, B., Grenet, J. A., Kapoor, A., Liu, L., Kidd, V. J., & Tang, D. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109219200 · Cited by 139

ISWI Remodeling Complexes inXenopusEgg Extracts: Identification as Major Chromosomal Components that Are Regulated by INCENP-aurora B

MacCallum, D. E., Losada, A., Kobayashi, R., & Hirano, T. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.01-09-0441 · Cited by 137

Epigenetic regulation of female puberty

Lomniczi, A., Wright, H., & Ojeda, S. R. (2015) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2014.08.003 · Cited by 136

Epigenetic programming of the neuroendocrine stress response by adult life stress

Dirven, B. C. J., Homberg, J. R., Kozicz, T., & Henckens, M. J. A. G. (2017) · Journal of Molecular Endocrinology · doi:10.1530/jme-17-0019 · Cited by 135

Chapter 1 Chromatin Structure and the Regulation of Gene Expression: The Lessons of PEV in Drosophila

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