Items where Subject is "bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > histone"

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Number of items at this level: 63.

B

Bergmann, J. H., Jakubsche, J. N., Martins, N. M., Kagansky, A., Nakano, M., Kimura, H., Kelly, D. A., Turner, B. M., Masumoto, H., Larionov, V., Earnshaw, W. C. (2012) Epigenetic engineering: Histone H3K9 acetylation is compatible with kinetochore structure and function. Journal of Cell Science, 125 (2). pp. 411-421. ISSN 00219533 (ISSN)

Bernstein, Bradley E., Kamal, Michael, Lindblad-Toh, Kerstin, Bekiranov, Stefan, Bailey, Dione K., Huebert, Dana J., McMahon, Scott, Karlsson, Elinor K., Kulbokas Iii, Edward J., Gingeras, Thomas R., Schreiber, Stuart L., Lander, Eric S. (2005) Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse. Cell, 120 (2). pp. 169-181. ISSN 0092-8674

C

Calarco, Joseph P. (2013) Chromatin Dynamics during Germline Development. PhD thesis, Cold Spring Harbor Laboratory.

Chandra, T., Kirschner, K., Thuret, J., Pope, B. D., Ryba, T., Newman, S., Ahmed, K., Samarajiwa, S. A., Salama, R., Carroll, T., Stark, R., Janky, R., Narita, M., Xue, L., Chicas, A., Nũnez, S., Janknecht, Ralf, Hayashi-Takanaka, Y., Wilson, M. D., Marshall, A., Odom, D. T, Babu, M.  M., Bazett-Jones, D. P., Tavaré, S., Edwards, P. A. W., Lowe, S. W., Kimura, H., Gilbert, D. M., Narita, M. (2012) Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation. Molecular Cell, 47 (2). pp. 203-214. ISSN 1097-2765

Croston, G. E., Kerrigan, L. A., Lira, L. M., Marshak, D. R., Kadonaga, J. T. (1991) Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science, 251 (4994). pp. 643-9. ISSN 0036-8075 (Print)0036-8075 (Linking)

D

Das, G., Herr, W. (1993) Enhanced activation of the human histone H2B promoter by an Oct-1 variant generated by alternative splicing. J Biol Chem, 268 (33). pp. 25026-32. ISSN 0021-9258 (Print)

E

Eckersley-Maslin, M. A., Thybert, D., Bergmann, J. H., Marioni, J. C., Flicek, P., Spector, D. L. (2014) Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation. Developmental Cell, 28 (4). pp. 351-65. ISSN 1534-5807

G

Gingeras, T. R. (2012) Important lessons from a complex genome. In: 22nd IUBMB & 37th FEBS Congress, Sept 4th-9th 2012, Seville, Spain.

Giordano, A., Lee, J. H., Scheppler, J. A., Herrmann, C., Harlow, E., Deuschle, U., Beach, D., Franza, B. R. (1991) Cell cycle regulation of histone H1 kinase activity associated with the adenoviral protein E1A. Science, 253 (5025). pp. 1271-5. ISSN 0036-8075 (Print)0036-8075 (Linking)

Giordano, A., Scheppler, J., Lee, J., Ross, J., Mak, G., Franza, B. R. Jr (1991) Cell-Cycle Dependent Modulation of an E1a-Immune Complex Histone H1 Specific Kinase Activity. Journal of Cellular Biochemistry , 47 (Suppl ). p. 68.

Guertin, M. J., Martins, A. L., Siepel, A., Lis, J. T. (2012) Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet, 8 (3). e1002610. ISSN 1553-7390

H

Hansen, K. R., Burns, G., Mata, J., Volpe, T. A., Martienssen, R. A., Bahler, J., Thon, G. (2005) Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Molecular and Cellular Biology, 25 (2). pp. 590-601. ISSN 0270-7306

Hansen, K. R., Hazan, I., Shanker, S., Watt, S., Verhein-Hansen, J., Bahler, J., Martienssen, R. A., Partridge, J. F., Cohen, A., Thon, G. (2011) H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases. Plos Genetics, 7 (1). ISSN 1553-7390

Hoek, M., Myers, M. P., Stillman, B. (2011) An analysis of CAF-1 interacting proteins reveals dynamic and direct interactions with the ku complex and 14-3-3 proteins. Journal of Biological Chemistry, 286 (12). pp. 10876-10887. ISSN 0021-9258

Hoek, M., Stillman, B. (2003) Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication in vivo. Proceedings of the National Academy of Sciences of the United States of America, 100 (21). pp. 12183-12188. ISSN 0027-8424

I

Iizuka, M., Stillman, B. (1999) Histone acetyltransferase HBO1 interacts with the ORC1 subunit of the human initiator protein. Journal of Biological Chemistry, 274 (33). pp. 23027-34. ISSN 0021-9258

J

Jacob, Y., Bergamin, E., Donoghue, M. T., Mongeon, V., LeBlanc, C., Voigt, P., Underwood, C. J., Brunzelle, J. S., Michaels, S. D., Reinberg, D., Couture, J. F., Martienssen, R. A. (2014) Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science, 343 (6176). pp. 1249-53. ISSN 0036-8075

Janicki, S. M., Tsukamoto, T., Salghetti, S. E., Tansey, W. P., Sachidanandam, R., Prasanth, K. V. , Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R. H., Spector, D. L. (2004) From silencing to gene expression: real-time analysis in single cells. Cell, 116 (5). pp. 683-98. ISSN 0092-8674 (Print)

K

Kimura, H., Takizawa, N., Allemand, E., Hori, T., Iborra, F. J., Nozaki, N., Muraki, M., Hagiwara, M., Krainer, A. R., Fukagawa, T., Okawa, K. (2006) A novel histone exchange factor, protein phosphatase 2Cgamma, mediates the exchange and dephosphorylation of H2A-H2B. Journal of Cell Biology, 175 (3). pp. 389-400. ISSN 00219525

Kininis, M., Chen, B. S., Diehl, A. G., Isaacs, G. D., Zhang, T., Siepel, A. C., Clark, A. G., Kraus, W. L. (2007) Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol, 27 (14). pp. 5090-104. ISSN 0270-7306 (Print)0270-7306

Krishnan, N., Jeong, D. G., Jung, S.-k., Ryu, S. E., Xiao, A., Allis, C. D., Kim, S. J., Tonks, N. K. (2009) Dephosphorylation of the C-terminal tyrosyl residue of the DNA damage-related histone H2A.X is mediated by the protein phosphatase eyes absent. Journal of Biological Chemistry, 284 (24). pp. 16066-16070.

L

Landry, J., Sutton, A., Hesman, T., Min, J. R., Xu, R. M., Johnston, M., Sternglanz, R. (2003) Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in Saccharomyces cerevisiae. Molecular and Cellular Biology, 23 (17). pp. 5972-5978. ISSN 0270-7306

Lee, S., Horn, V., Julien, E., Liu, Y., Wysocka, J., Bowerman, B., Hengartner, M. O., Herr, W. (2007) Epigenetic Regulation of Histone H3 Serine 10 Phosphorylation Status by HCF-1 Proteins in C. elegans and Mammalian Cells. PLoS ONE, 2 (11). e1213. ISSN 1932-6203 (Electronic)

Leung, A. (2010) Regulation of Chromatin by Histone H2B Ubiquitylation. PhD thesis, Cold Spring Harbor Laboratory.

Leung, A., Cajigas, I., Jia, P., Ezhkova, E., Brickner, J. H., Zhao, Z., Geng, F., Tansey, W. P. (2011) Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol Biol Cell, 22 (15). pp. 2741-2753. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

Li, F., Huarte, M., Zaratiegui, M., Vaughn, M. W., Shi, Y., Martienssen, R., Cande, W. Z. (2008) Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin. Cell, 135 (2). pp. 272-83. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Lu, X. W., Wontakal, S. N., Kavi, H., Kim, B. J., Guzzardo, P. M., Emelyanov, A. V., Xu, N., Hannon, G. J., Zavadil, J., Fyodorov, D. V., Skoultchi, A. I. (2013) Drosophila H1 Regulates the Genetic Activity of Heterochromatin by Recruitment of Su(var)3-9. Science, 340 (6128). pp. 78-81. ISSN 0036-8075

M

Min, J. R., Xu, R. M. (2004) Structural analysis of histone methyltransferases. Faseb Journal, 18 (8). C114-C114. ISSN 0892-6638

Min, J. R., Zhang, X., Cheng, X. D., Grewal, S. I. S., Xu, R. M. (2002) Structure of the SET domain histone lysine methyltransferase Clr4. Nature Structural Biology, 9 (11). pp. 828-832. ISSN 1072-8368

Min, J. R., Zhang, Y., Xu, R. M. (2003) Structural basis for specific binding of polycomb chromodomain to histone H3 methylated at Lys 27. Genes & Development, 17 (15). pp. 1823-1828. ISSN 0890-9369

N

Nakagawa, H., Lee, J. K., Hurwitz, J., Allshire, R. C., Nakayama, J., Grewal, S. I. S., Tanaka, K., Murakami, Y. (2002) Fission yeast CENP-B homologs nucleate centromeric heterochromatin by promoting heterochromatin-specific histone tail modifications. Genes & Development, 16 (14). pp. 1766-1778. ISSN 0890-9369

Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D., Grewal, S. I. S. (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science, 292 (5514). pp. 110-113. ISSN 0036-8075

Ng, H. H., Xu, R. M., Zhang, Y., Struhl, K. (2002) Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. Journal of Biological Chemistry, 277 (38). pp. 34655-34657. ISSN 0021-9258

Noma, K., Allis, C. D., Grewal, S. I. S. (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science, 293 (5532). pp. 1150-1155. ISSN 0036-8075

P

Paul, S., Kuo, A., Schalch, T., Vogel, H., Joshua-Tor, L., McCombie, W. R., Gozani, O., Hammell, M., Mills, A. A. (2013) Chd5 Requires PHD-Mediated Histone 3 Binding for Tumor Suppression. Cell Reports, 3 (1). pp. 92-102. ISSN 2211-1247

Perales, R., Erickson, B., Zhang, L., Kim, H., Valiquett, E., Bentley, D. (2013) Gene promoters dictate histone occupancy within genes. Embo Journal, 32 (19). pp. 2645-2656. ISSN 02614189 (ISSN)

R

Rajagopal, N., Ernst, J., Ray, P., Wu, J., Zhang, M., Kellis, M., Ren, B. (2014) Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3: Genes, Genomes, Genetics, 4 (11). pp. 2051-63. ISSN 21601836

Rangan, P., Malone, Colin D. , Navarro, C., Newbold, S. P, Hayes, P. S, Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) piRNA Production Requires Heterochromatin Formation in Drosophila. Current Biology, 21 (16). pp. 1373-1379. ISSN 0960-9822

Rao, S. G., Janiszewski, M. M., Duca, E., Nelson, B., Abhinav, K., Panagakou, I., Vass, S., Heck, M. M. S. (2015) Invadolysin acts genetically via the SAGA complex to modulate chromosome structure. Nucleic Acids Research, 43 (7). pp. 3546-3562.

Rosenfeld, J. A., Wang, Z., Schones, D. E., Zhao, K., DeSalle, R., Zhang, M. Q. (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics, 10 (1). p. 143. ISSN 1471-2164

Rosenfeld, J. A., Xuan, Z., Desalle, R. (2009) Investigating repetitively matching short sequencing reads: The enigmatic nature of H3K9me3. Epigenetics, 4 (7).

Rossmann, M. P., Stillman, B. (2013) Immunoblotting histones from yeast whole-cell protein extracts. Cold Spring Harbor Protocols, 2013 (7). ISSN 1559-6095

Roth, S. Y., Collini, M. P., Draetta, G., Beach, D., Allis, C. D. (1991) A cdc2-like kinase phosphorylates histone H1 in the amitotic macronucleus of Tetrahymena. EMBO J, 10 (8). pp. 2069-75. ISSN 0261-4189 (Print)0261-4189 (Linking)

S

Scheppler, J., Lee, J. H., Ross, J., Mak, G., Franza, B. R. (1991) Modulation of an E1a-Immune Complex Histone H1 Kinase Activity Throughout the Cell-Division Cycle. Proceedings American Association for Cancer Research Annual Meeting. p. 285.

Shankaranarayana, G. D., Motamedi, M. R., Moazed, D., Grewal, S. I. (2003) Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast. Current Biology, 13 (14). pp. 1240-6. ISSN 0960-9822

Steger, D. J., Lefterova, M. I., Ying, L., Stonestrom, A. J., Schupp, M., Zhuo, D., Vakoc, A. L., Kim, J. E., Chen, J., Lazar, M. A., Blobel, G. A., Vakoc, C. R. (2008) DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Molecular and Cellular Biology, 28 (8). pp. 2825-2839. ISSN 02707306 (ISSN)

Sturm, R. A., Cassady, J. L., Das, G., Romo, A., Evans, G. A. (1993) Chromosomal Structure and Expression of the Human Otf1 Locus Encoding the Oct-1 Protein. Genomics, 16 (2). pp. 333-341. ISSN 0888-7543

Swedlow, J. R., Hirano, T. (2003) The making of the mitotic chromosome: Modern insights into classical questions. Molecular Cell, 11 (3). pp. 557-569. ISSN 1097-2765

T

Tamaru, H., Zhang, X., McMillen, D., Singh, P. B., Nakayama, J., Grewal, S. I., Allis, C. D., Cheng, X. D., Selker, E. U. (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nature Genetics, 34 (1). pp. 75-79. ISSN 1061-4036

Tramantano, M., Sun, L., Au, C., Labuz, D., Liu, Z., Chou, M., Shen, C., Luk, E. (2016) Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking)

Trotman, L. C., Mosberger, N., Fornerod, M., Stidwill, R. P., Greber, U. F. (2001) Import of adenovirus DNA involves the nuclear pore complex receptor CAN/Nup214 and histone H1. Nature Cell Biology, 3 (12). pp. 1092-1100. ISSN 14657392 (ISSN)

Tscherner, M., Zwolanek, F., Jenull, S., Sedlazeck, F. J., Petryshyn, A., Frohner, I. E., Mavrianos, J., Chauhan, N., von Haeseler, A., Kuchler, K. (2015) The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog, 11 (10). e1005218. ISSN 1553-7374 (Electronic)1553-7366 (Linking)

Tyler, J. K., Collins, K. A., Prasad-Sinha, J., Amiott, E., Bulger, M., Harte, P. J., Kobayashi, R., Kadonaga, J. T. (2001) Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Molecular and Cellular Biology, 21 (19). pp. 6574-6584. ISSN 0270-7306

V

Vakoc, C. R., Mandat, S. A., Olenchock, B. A., Blobel, G. A. (2005) Histone H3 lysine 9 methylation and HP1γ are associated with transcription elongation through mammalian chromatin. Molecular Cell, 19 (3). pp. 381-391. ISSN 10972765 (ISSN)

Vakoc, C. R., Mandat, S. A., Olenschock, B. A., Blobel, G. A. (2005) Histone H3 lysine 9 methylation and HP1 gamma are associated with transcription elongation through mammalian chromatin. Blood, 106 (11). 493A-493A. ISSN 0006-4971

Verreault, A., Kaufman, P. D., Kobayashi, R., Stillman, B. (1998) Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Current Biology, 8 (2). pp. 96-108. ISSN 0960-9822

Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., Martienssen, R. A. (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297 (5588). pp. 1833-7. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

W

Wang, E., Kawaoka, S., Yu, M., Shi, J., Ni, T., Yang, W., Zhu, J., Roeder, R. G., Vakoc, C. R. (2013) Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proceedings of the National Academy of Sciences of the United States of America, 110 (10). pp. 3901-6. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Peng, W., Zhang, M. Q., Zhao, K. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet, 40 (7). pp. 897-903.

Wysocka, J., Myers, M. P., Laherty, C. D., Eisenman, R. N., Herr, W. (2003) Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes and Development, 17 (7). pp. 896-911. ISSN 08909369 (ISSN)

X

Xing, H., Mo, Y., Liao, W., Zhang, M. Q. (2012) Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data. PLoS Comput Biol, 8 (7). e1002613. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Z

Zegerman, P., Canas, B., Pappin, D., Kouzarides, T. (2002) Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J Biol Chem, 277 (14). pp. 11621-4. ISSN 0021-9258 (Print)0021-9258 (Linking)

Zhang, M. Q. (1999) Promoter analysis of co-regulated genes in the yeast genome. Computers & Chemistry, 23 (3-4). pp. 233-50. ISSN 0097-8485 (Print)

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