Signaling to Chromatin through Histone Modifications

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Chromatin Structure: A Repeating Unit of Histones and DNA

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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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Epigenetic Treatments for Cognitive Impairments

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Psychological stress increases histone H3 phosphorylation in adult dentate gyrus granule neurons: involvement in a glucocorticoid receptor‐dependent behavioural response

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Transforming Growth Factor-β1 Inhibits Non-pathogenic Gramnegative Bacteria-induced NF-κB Recruitment to the Interleukin-6 Gene Promoter in Intestinal Epithelial Cells through Modulation of Histone Acetylation

Haller, D., Holt, L. C., Kim, S. C., Schwabe, R. F., Sartor, R. B., & Jobin, C. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300075200 · Cited by 127

Holding it together: chromatin in the Archaea

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Statins Control Oxidized LDL-Mediated Histone Modifications and Gene Expression in Cultured Human Endothelial Cells

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NuA4 Subunit Yng2 Function in Intra-S-Phase DNA Damage Response

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HANP1/H1T2, a Novel Histone H1-Like Protein Involved in Nuclear Formation and Sperm Fertility

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Glucocorticoids, epigenetic control and stress resilience

Reul, J. M. H. M., Collins, A., Saliba, R. S., Mifsud, K. R., Carter, S. D., Gutièrrez‐Mecinas, M., Qian, X., & Linthorst, A. C. E. (2014) · Neurobiology of Stress · doi:10.1016/j.ynstr.2014.10.001 · Cited by 124

An increasingly complex code

Spotswood, H. T., & Turner, B. M. (2002) · Journal of Clinical Investigation · doi:10.1172/jci16547 · Cited by 146

More than just tails: intrinsic disorder in histone proteins

Peng, Z., Mizianty, M. J., Xue, B., Kurgan, L., & Uversky, V. N. (2012) · Molecular BioSystems · doi:10.1039/c2mb25102g · Cited by 127

Dynamic and Transient Remodeling of the Macrophage IL-10 Promoter during Transcription

Zhang, X., Edwards, J. P., & Mosser, D. M. (2006) · The Journal of Immunology · doi:10.4049/jimmunol.177.2.1282 · Cited by 122

Brain-Penetrant LSD1 Inhibitors Can Block Memory Consolidation

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Synergistic Coactivator Function by Coactivator-associated Arginine Methyltransferase (CARM) 1 and β-Catenin with Two Different Classes of DNA-binding Transcriptional Activators

Koh, S. S., Li, H., Lee, Y., Widelitz, R. B., Chuong, C., & Stallcup, M. R. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m110865200 · Cited by 122

The promise and perils of HDAC inhibitors in neurodegeneration

Didonna, A., & Opal, P. (2014) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.147 · Cited by 123

The roles of protein–protein interactions and protein methylation in transcriptional activation by nuclear receptors and their coactivators

Stallcup, M. R., Kim, J. H., Teyssier, C., Lee, Y., Ma, H., & Chen, D. (2003) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/s0960-0760(03)00222-x · Cited by 121

Histone H2A.Z Acetylation Modulates an Essential Charge Patch

Ren, Q., & Gorovsky, M. A. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00269-6 · Cited by 117

Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcriptionPreprint

Loyola, A., LeRoy, G., Wang, Y.-H., & Reinberg, D. (2001) · Genes & Development · doi:10.1101/gad.937401 · Cited by 120

Lysine acetylation of the Mycobacterium tuberculosis HU protein modulates its DNA binding and genome organization

Ghosh, S., Padmanabhan, B., Anand, C., & Nagaraja, V. (2016) · Molecular Microbiology · doi:10.1111/mmi.13339 · Cited by 118

Signal transduction in prostate cancer progression

Gioeli, D. G. (2005) · Clinical Science · doi:10.1042/cs20040329 · Cited by 117

Facile synthesis of site-specifically acetylated and methylated histone proteins: Reagents for evaluation of the histone code hypothesis

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Drosophila Sir2 Is Required for Heterochromatic Silencing and by Euchromatic Hairy/E(Spl) bHLH Repressors in Segmentation and Sex Determination

Rosenberg, M. I., & Parkhurst, S. M. (2002) · Cell · doi:10.1016/s0092-8674(02)00732-8 · Cited by 118

Novelty stress induces phospho‐acetylation of histone H3 in rat dentate gyrus granule neurons through coincident signalling via the N‐methyl‐d‐aspartate receptor and the glucocorticoid receptor: relevance for c‐fos induction

Chandramohan, Y., Droste, S. K., & Reul, J. M. H. M. (2007) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2006.04396.x · Cited by 117

Consequences of lead exposure, and it’s emerging role as an epigenetic modifier in the aging brain

Eid, A., & Zawia, N. (2016) · NeuroToxicology · doi:10.1016/j.neuro.2016.04.006 · Cited by 121

Vitamin A regulation of gene expression: molecular mechanism of a prototype gene

McGrane, M. M. (2007) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2006.10.006 · Cited by 115

Evidence for a reduced transcriptional state during hibernation in ground squirrels

Morin, P., & Storey, K. B. (2006) · Cryobiology · doi:10.1016/j.cryobiol.2006.08.002 · Cited by 117

In Vivo Reprogramming Ameliorates Aging Features in Dentate Gyrus Cells and Improves Memory in Mice.

Rodríguez-Matellán, A., Alcazar, N., Hernández, F., Serrano, M., & Ávila, J. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2020.09.010 · Cited by 116

Mammalian hibernation: differential gene expression and novel application of epigenetic controls

Morin, P., & Storey, K. B. (2009) · The International Journal of Developmental Biology · doi:10.1387/ijdb.082643pm · Cited by 116

Histone modifications: Now summoning sumoylation

Nathan, D., Sterner, D. E., & Berger, S. L. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2436173100 · Cited by 116

Chromosomal Protein HMGN1 Modulates Histone H3 Phosphorylation

Lim, J. H., Catez, F., Birger, Y., West, K. L., Prymakowska-Bosak, M., Postnikov, Y. V., & Bustin, M. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.08.006 · Cited by 115

Uteroplacental insufficiency induces site-specific changes in histone H3 covalent modifications and affects DNA-histone H3 positioning in day 0 IUGR rat liver.

Fu, Q., McKnight, R., Yu, X., Wang, L., Callaway, C., & Lane, R. (2004) · Physiological Genomics · doi:10.1152/physiolgenomics.00175.2004 · Cited by 120

Polybromo-1: The chromatin targeting subunit of the PBAF complex

Thompson, M. J. (2008) · Biochimie · doi:10.1016/j.biochi.2008.10.019 · Cited by 113

The effects of repeated social defeat on long-term depressive-like behavior and short-term histone modifications in the hippocampus in male Sprague–Dawley rats

Hollis, F., Wang, H., Dietz, D., Gunjan, A., & Kabbaj, M. (2010) · Psychopharmacology · doi:10.1007/s00213-010-1869-9 · Cited by 115

Involvement of histone acetyltransferase (HAT) in ethanol-induced acetylation of histone H3 in hepatocytes: potential mechanism for gene expression

Park, P., Lim, R. W., & Shukla, S. D. (2005) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00091.2005 · Cited by 112

Integrated kinetics of X chromosome inactivation in differentiating embryonic stem cells

Chaumeil, J., Okamoto, I., Guggiari, M., & Heard, É. (2002) · Cytogenetic and Genome Research · doi:10.1159/000071577 · Cited by 119

Fanconi Anemia Proteins Localize to Chromatin and the Nuclear Matrix in a DNA Damage- and Cell Cycle-regulated Manner

Qiao, F., Moss, A., & Kupfer, G. M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101855200 · Cited by 111

Site-specific Loss of Acetylation upon Phosphorylation of Histone H3

Edmondson, D. G., Davie, J. K., Zhou, J., Mirnikjoo, B., Tatchell, K., & Dent, S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200651200 · Cited by 111

Emerging functions of p21‐activated kinases in human cancer cells

Kumar, R., & Vadlamudi, R. K. (2002) · Journal of Cellular Physiology · doi:10.1002/jcp.10167 · Cited by 111

Multiscale Modeling of Nucleosome Dynamics

Sharma, S. K., Ding, F., & Dokholyan, N. V. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.094805 · Cited by 110

Histone Acetyltransferase Activity of p300 Is Required for Transcriptional Repression by the Promyelocytic Leukemia Zinc Finger Protein

Guidez, F., Howell, L., Isalan, M., Cebrat, M., Alani, R. M., Ivins, S. M., Hormaeche, I., McConnell, M. J., Pierce, S., Cole, P. A., et al. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.13.5552-5566.2005 · Cited by 110

Biological functions of biotinylated histones

Kothapalli, N. R., Camporeale, G., Kueh, A., Chew, Y. C., Oommen, A. M., Griffin, J. B., & Zempleni, J. (2005) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2005.03.025 · Cited by 108

Chromatin Remodeling and Cancer

Davis, P. K., & Brachmann, R. K. (2003) · Cancer Biology & Therapy · doi:10.4161/cbt.189 · Cited by 108

Individual differences in the effect of social defeat on anhedonia and histone acetylation in the rat hippocampus

Hollis, F., Duclot, F., Gunjan, A., & Kabbaj, M. (2010) · Hormones and Behavior · doi:10.1016/j.yhbeh.2010.09.005 · Cited by 111

The Activation Domains, the Proline-rich Domain, and the C-terminal Basic Domain in p53 Are Necessary for Acetylation of Histones on the Proximal p21 Promoter and Interaction with p300/CREB-binding Protein

Liu, G., Xia, T., & Chen, X. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m210696200 · Cited by 108

ATF3-Mediated Epigenetic Regulation Protects against Acute Kidney Injury

Li, H., Cheng, C., Liao, W., Lin, H., & Yang, R. (2010) · Journal of the American Society of Nephrology · doi:10.1681/asn.2009070690 · Cited by 107

Chromatin remodeling by nuclear receptors

Hebbar, P. B., & Archer, T. (2003) · Chromosoma · doi:10.1007/s00412-003-0232-x · Cited by 106

Quantification of Histone Acetyltransferase and Histone Deacetylase Transcripts During Early Bovine Embryo Development1

McGraw, S., Robert, C., Massicotte, L., & Sirard, M. (2003) · Biology of Reproduction · doi:10.1095/biolreprod.102.005991 · Cited by 109

HP1 promotes tumor suppressor BRCA1 functions during the DNA damage response

Lee, Y.-H., Kuo, C., Stark, J. M., Shih, H., & Ann, D. K. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt231 · Cited by 116

Inhibition of Histone Deacetylases Preserves Myocardial Performance and Prevents Cardiac Remodeling through Stimulation of Endogenous Angiomyogenesis

Zhang, L., Qin, X., Zhao, Y., Fast, L. D., Zhuang, S., Liu, P. Y., Cheng, G., & Zhao, T. C. (2012) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.111.189910 · Cited by 105

Mitotic phosphorylation of histone H3 at threonine 3

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Glucose Regulates Insulin Gene Transcription by Hyperacetylation of Histone H4

Mosley, A. L., & Özcan, S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m212375200 · Cited by 103

Structures of protein domains that create or recognize histone modifications

Bottomley, M. J. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400146 · Cited by 110

Transcriptional profiling of epigenetic regulators in somatic embryos during temperature induced formation of an epigenetic memory in Norway spruce

Yakovlev, I., Carneros, E., Lee, Y., Olsen, J. E., & Fossdal, C. G. (2016) · Planta · doi:10.1007/s00425-016-2484-8 · Cited by 102

Histone Modifications in Cancer Biology and Prognosis

Kurdistani, S. K. (2010) · Springer eBooks · doi:10.1007/978-3-7643-8989-5_5 · Cited by 106

Arsenic Trioxide Promotes Histone H3 Phosphoacetylation at the Chromatin of CASPASE-10 in Acute Promyelocytic Leukemia Cells

Li, J., Chen, P., Sinogeeva, N. I., Gorospe, M., Wersto, R. P., Chrest, F. J., Barnes, J., & Liu, Y. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207836200 · Cited by 102

Temporal and Spatial Changes in Transcription Factor Binding and Histone Modifications at the Steroidogenic Acute Regulatory Protein (StAR) Locus Associated withStARTranscription

Hiroi, H., Christenson, L. K., Chang, L., Sammel, M. D., Berger, S. L., & Strauss, J. F. (2004) · Molecular Endocrinology · doi:10.1210/me.2003-0305 · Cited by 103

Selective Requirements for Histone H3 and H4 N Termini in p300-Dependent Transcriptional Activation from Chromatin

An, W., Palhan, V. B., Karymov, M. A., Leuba, S. H., & Roeder, R. G. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00497-5 · Cited by 100

TOP2B: The First Thirty Years

Austin, C. A., Lee, K. C., Swan, R. L., Khazeem, M. M., Manville, C. M., Cridland, P., Treumann, A., Porter, A., Morris, N. J., & Cowell, I. G. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092765 · Cited by 100

Regulation of the p53 transcriptional activity

Liu, G., & Chen, X. (2005) · Journal of Cellular Biochemistry · doi:10.1002/jcb.20700 · Cited by 100

Cell Growth Inhibition and Gene Expression Induced by the Histone Deacetylase Inhibitor, Trichostatin A, on Human Hepatoma Cells

Chiba, T., Yokosuka, O., Fukai, K., Kojima, H., Tada, M., Arai, M., Imazeki, F., & Saisho, H. (2004) · Oncology · doi:10.1159/000079503 · Cited by 100

Tumor Promoter Arsenite Stimulates Histone H3 Phosphoacetylation of Proto-oncogenes c-fos and c-jun Chromatin in Human Diploid Fibroblasts

Li, J., Gorospe, M., Barnes, J., & Liu, Y. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300269200 · Cited by 99

Control of gene expression in Plasmodium falciparum – Ten years on

Horrocks, P., Wong, E., Russell, K. L., & Emes, R. D. (2008) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2008.11.010 · Cited by 99

Influenza A virus-encoded NS1 virulence factor protein inhibits innate immune response by targeting IKK

Gao, S., Song, L., Li, J., Zhang, Z., Peng, H., Jiang, W., Wang, Q., Kang, T., Chen, S., & Huang, W. (2012) · Cellular Microbiology · doi:10.1111/cmi.12005 · Cited by 105

m-Bop, a Repressor Protein Essential for Cardiogenesis, Interacts with skNAC, a Heart- and Muscle-specific Transcription Factor

Sims, R. J., Weihe, E., Zhu, L., O'Malley, S. W., Harriss, J. V., & Gottlieb, P. D. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204121200 · Cited by 101

Phosphorylation of LSD1 by PKCα Is Crucial for Circadian Rhythmicity and Phase Resetting

Nam, H. J., Boo, K.-J., Kim, D., Han, D.-H., Choe, H. K., Kim, C. R., Sun, W., Kim, H., Kim, K., Lee, H., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.01.028 · Cited by 103

Smooth Muscle Cell Differentiation: Model Systems, Regulatory Mechanisms, and Vascular Diseases

Shi, N., & Chen, S. (2015) · Journal of Cellular Physiology · doi:10.1002/jcp.25208 · Cited by 99

p16INK4a Suppression by Glucose Restriction Contributes to Human Cellular Lifespan Extension through SIRT1-Mediated Epigenetic and Genetic Mechanisms

Li, Y., & Tollefsbol, T. O. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017421 · Cited by 99

14-3-3 Interaction with Histone H3 Involves a Dual Modification Pattern of Phosphoacetylation

Walter, W., Clynes, D., Tang, Y., Marmorstein, R., Mellor, J., & Berger, S. L. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01457-07 · Cited by 97

Mitogen- and Stress-Activated Kinase 1–Mediated Histone H3 Phosphorylation Is Crucial for Cell Transformation

Kim, H.-G., Lee, K. W., Cho, Y., Kang, N. J., Oh, S., Bode, A. M., & Dong, Z. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-6597 · Cited by 100

KDM2B is a histone H3K79 demethylase and induces transcriptional repression via sirtuin‐1‐mediated chromatin silencing

Kang, J., Kim, J., Kim, K., Park, J. W., Cho, H., Hahm, J. Y., Chae, Y., Kim, D., Kook, H. Y., Rhee, S., et al. (2018) · The FASEB Journal · doi:10.1096/fj.201800242r · Cited by 103

Methylation-Mediated Proviral Silencing Is Associated with MeCP2 Recruitment and Localized Histone H3 Deacetylation

Lorincz, M. C., Schübeler, D., & Groudine, M. T. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.23.7913-7922.2001 · Cited by 98

Remembrance of Things Past: Chromatin Remodeling in Plant Development

Goodrich, J., & Tweedie, S. (2002) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.18.040202.114836 · Cited by 98

The Histone Modification Code in the Pathogenesis of Autoimmune Diseases

Araki, Y., & Mimura, T. (2017) · Mediators of Inflammation · doi:10.1155/2017/2608605 · Cited by 100

Intracellular Bacteria Differentially Regulated Endothelial Cytokine Release by MAPK-Dependent Histone Modification

Schmeck, B., Beermann, W., van Laak, V., Zahlten, J., Opitz, B., Witzenrath, M., Hocke, A. C., Chakraborty, T., Kracht, M., Rosseau, S., et al. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.175.5.2843 · Cited by 96

A Signaling Role of Histone-binding Proteins and INHAT Subunits pp32 and Set/TAF-Iβ in Integrating Chromatin Hypoacetylation and Transcriptional Repression

Kutney, S. N., Hong, R., Macfarlan, T. S., & Chakravarti, D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m404969200 · Cited by 97

Promoter Activation by Enhancer-Dependent and -Independent Loading of Activator and Coactivator Complexes

Spicuglia, S., Kumar, S., Yeh, J.-H., Vachez, E., Chasson, L., Gorbatch, S., Cautres, J., & Ferrier, P. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00791-8 · Cited by 95

Glucocorticoid receptor-mediated chromatin remodeling in vivo

Deroo, B. J., & Archer, T. (2001) · Oncogene · doi:10.1038/sj.onc.1204328 · Cited by 95

Importance of a deficiency in S-adenosyl-l-methionine synthesis in the pathogenesis of liver injury,,,

Martínez‐Chantar, M. L., García–Trevijano, E. R., Latasa, M. U., Pérez-Mato, I., del Pino, M. M. S., Corrales, F. J., Avila, M. A., & Mato, J. M. (2002) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/76.5.1177s · Cited by 95

Mesenchymal stem cells and vascular regeneration

Gu, W., Hong, X., Potter, C. M. F., Qu, A., & Xu, Q. (2016) · Microcirculation · doi:10.1111/micc.12324 · Cited by 94

Inhibition of Aurora-B kinase activity by poly(ADP-ribosyl)ation in response to DNA damage

Monaco, L., Kolthur‐Seetharam, U., Loury, R., Murcia, J. M., de MURCIA, G., & Sassone‐Corsi, P. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506252102 · Cited by 97

Chromosomal protein HMGN1 enhances the acetylation of lysine 14 in histone H3

Lim, J., West, K. L., Rubinstein, Y., Bergel, M., Postnikov, Y. V., & Bustin, M. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600768 · Cited by 93

The Characterization of Protein Post-Translational Modifications by Mass Spectrometry

Schweppe, R. E., Haydon, C. E., Lewis, T. S., Resing, K. A., & Ahn, N. G. (2003) · Accounts of Chemical Research · doi:10.1021/ar020143l · Cited by 92

Competitive Cofactor Recruitment by Orphan Receptor Hepatocyte Nuclear Factor 4α1: Modulation by the F Domain

Ruse, M. D., Privalsky, M. L., & Sladek, F. M. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.6.1626-1638.2002 · Cited by 93

The N‐terminus of histone H2B, but not that of histone H3 or its phosphorylation, is essential for chromosome condensation

de la Barre, A.-E., Angelov, D., Molla, A., & Dimitrov, S. I. (2001) · The EMBO Journal · doi:10.1093/emboj/20.22.6383 · Cited by 92

Structure-specific binding of the proto-oncogene protein DEK to DNA

Waldmann, T. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg864 · Cited by 91

Selective Interactions between Vertebrate Polycomb Homologs and the SUV39H1 Histone Lysine Methyltransferase Suggest that Histone H3-K9 Methylation Contributes to Chromosomal Targeting of Polycomb Group Proteins

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