Items where Subject is "bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > promoter"

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Number of items at this level: 53.

A

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jorgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Muller, F., Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., FANTOM Consortium, (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836

B

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

Batut, P. J., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R. (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res, 23 (1). pp. 169-180. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Batut, Philippe (2014) Promoter Evolution in Drosophila: Non-Coding Transcription & Transposon-Driven Innovation. PhD thesis, Cold Spring Harbor Laboratory.

Berenstein, D., Olesen, K., Speck, C., Skovgaard, O. (2002) Genetic organization of the Vibrio harveyi dnaA gene region and analysis of the function of the V-harveyi DnaA protein in Escherichia coli. Journal of Bacteriology, 184 (9). 2533-+. ISSN 0021-9193

C

Chen, N., Mah, A., Blacque, O. E., Chu, J., Phgora, K., Bakhoum, M. W., Newbury, C. R. Hunt, Khattra, J., Chan, S. W., Go, A., Efimenko, E., Johnsen, R. C., Phirke, P., Swoboda, P., Marra, M., Moerman, D. G., Leroux, M. R., Baillie, D. L., Stein, L. D. (2006) Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biology, 7 (12). R126. ISSN 1474-760X

Chong, S. S., Hu, P., Hernandez, N. (2001) Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. Journal of Biological Chemistry, 276 (23). pp. 20727-20734. ISSN 0021-9258

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., Lis, J. T. (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet, 46 (12). pp. 1311-20. ISSN 1061-4036

D

Das, G., Hinkley, C., Tanaka, M., Herr, W. (1994) Functional Specificity of Promoter Selective Activation Domains. Journal of Cellular Biochemistry. p. 29. ISSN 0730-2312

Davuluri, R. V., Grosse, I., Zhang, M. Q. (2001) Computational identification of promoters and first exons in the human genome. Nature Genetics, 29 (4). pp. 412-417. ISSN 1061-4036

Denissov, S., Van Driel, M., Voit, R., Hekkelman, M., Hulsen, T., Hernandez, N., Grummt, I., Wehrens, R., Stunnenberg, H. (2007) Identification of novel functional TBP-binding sites and general factor repertoires. Embo Journal, 26 (4). pp. 944-954. ISSN 0261-4189

E

Emran, F., Florens, L., Ma, B., Swanson, S. K., Washburn, M. P., Hernandez, N. (2006) A role for Yin Yang-1 (YY1) in the assembly of snRNA transcription complexes. Gene, 377. pp. 96-108. ISSN 0378-1119 (Print)

F

Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Altschuler, I. A., Albanese, D., Altschule, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J. I., Geijtenbeek, T. B., Gibson, A. P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Sui, S. J. H., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L. (2014) A promoter-level mammalian expression atlas. Nature, 507 (7493). pp. 462-470. ISSN 14764687

Fuda, N. J., Guertin, M. J., Sharma, S., Danko, C. G., Martins, A. L., Siepel, A., Lis, J. T. (2015) GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters. Plos Genetics, 11 (3). e1005108. ISSN 1553-7390

G

Gilbert, M. T., Sun, J. D., Yan, Y., Oddoux, C., Lazarus, A., Tansey, W. P., Lavin, T. N., Catanzaro, D. F. (1994) Renin Gene Promoter Activity in Gc Cells Is Regulated by Camp and Thyroid-Hormone through Pit-1-Dependent Mechanisms. Journal of Biological Chemistry, 269 (45). pp. 28049-28054. ISSN 0021-9258

Gillespie, M., Frendewey, D. (1991) Rna Polymerase Iii Promoter Elements in the Intron of the Fission Yeast U6 Rna Gene. Journal of Cellular Biochemistry, 47 (Suppl ). p. 65.

Guo, Ya, Xu, Quan, Canzio, Daniele, Shou, Jia, Li, Jinhuan, Gorkin, David U, Jung, Inkyung, Wu, Haiyang, Zhai, Yanan, Tang, Yuanxiao, Lu, Yichao, Wu, Yonghu, Jia, Zhilian, Li, Wei, Zhang, Michael Q, Ren, Bing, Krainer, Adrian R, Maniatis, Tom, Wu, Qiang (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell, 162 (4). pp. 900-910. ISSN 0092-8674

H

Hofmann, J. F., Beach, D. (1994) cdt1 is an essential target of the Cdc10/Sct1 transcription factor: requirement for DNA replication and inhibition of mitosis. Embo J, 13 (2). pp. 425-34. ISSN 0261-4189 (Print)

I

Ioshikhes, I. P., Zhang, M. Q. (2000) Large-scale human promoter mapping using CpG islands. Nature Genetics, 26 (1). pp. 61-63. ISSN 1061-4036

K

Kessler, M., Mathews, M. B. (1991) Tat transactivation of the human immunodeficiency virus type 1 promoter is influenced by basal promoter activity and the simian virus 40 origin of DNA replication. Proc Natl Acad Sci U S A, 88 (22). pp. 10018-22. ISSN 0027-8424 (Print)0027-8424 (Linking)

Kraus, V. B., Inostroza, J. A., Reinberg, D., Moran, E., Nevins, J. R. (1993) The Activation of the Hsp70-Promoter by E1a Coincides with a Release of Tbp from an Interaction with the Inhibitory Factor Dr1. Journal of Cellular Biochemistry, 53 (17B). p. 226. ISSN 0730-2312

Kraus, V. B., Moran, E., Nevins, J. R. (1992) Promoter-Specific Transactivation by the Adenovirus-E1a12s Product Involves Separate E1a Domains. Molecular and Cellular Biology, 12 (10). pp. 4391-4399. ISSN 0270-7306

Kumari, S., Ware, D. (2013) Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots. PLoS ONE, 8 (10). Art no. e79011. ISSN 1932-6203

L

Labrie, C., Morris, G. F., Mathews, M. B. (1993) A complex promoter element mediates transactivation of the human proliferating cell nuclear antigen promoter by the 243-residue adenovirus E1A oncoprotein. Mol Cell Biol, 13 (3). pp. 1697-707. ISSN 0270-7306 (Print)

Laspia, M. F., Wendel, P., Mathews, M. B. (1993) HIV-1 Tat overcomes inefficient transcriptional elongation in vitro. J Mol Biol, 232 (3). pp. 732-46. ISSN 0022-2836 (Print)

Lees-Miller, J. P., Goodwin, L. O., Helfman, D. M. (1990) Three novel brain tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene through the use of alternative promoters and alternative RNA processing. Mol Cell Biol, 10 (4). pp. 1729-42. ISSN 0270-7306 (Print)0270-7306 (Linking)

M

Mills, A. A. (2005) p53: link to the past, bridge to the future. Genes Dev, 19 (18). pp. 2091-9. ISSN 0890-9369 (Print)

Morris, G. F., Mathews, M. B. (1990) Analysis of the proliferating cell nuclear antigen promoter and its response to adenovirus early region 1. J Biol Chem, 265 (27). pp. 16116-25. ISSN 0021-9258 (Print)0021-9258 (Linking)

N

Nelson, K. K., Subbaram, S., Connor, K. M., Dasgupta, J., Ha, X. F., Meng, T. C., Tonks, N. K., Melendez, J. A. (2006) Redox-dependent matrix metalloproteinase-1 expression is regulated by JNK through Ets and AP-1 promoter motifs. Journal of Biological Chemistry, 281 (20). pp. 14100-14110. ISSN 00219258

P

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

Revyakin, A., Ebright, R. H., Strick, T. R. (2004) Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation. Proceedings of the National Academy of Sciences of the United States of America, 101 (14). pp. 4776-4780. ISSN 0027-8424

Revyakin, A. G., Strick, T. R., Ebright, R. H. (2002) Promoter melting by RNA polymerase: Detection and analysis by single-molecule DNA nanomanipulation. Biophysical Journal, 82 (1). 115A-115A. ISSN 0006-3495

S

Saxena, A., Ma, B. C., Schramm, L., Hernandez, N. (2005) Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription. Molecular and Cellular Biology, 25 (21). pp. 9406-9418. ISSN 0270-7306

Schramm, L., Hernandez, N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes & Development, 16 (20). pp. 2593-2620. ISSN 0890-9369

Schramm, L., Pendergrast, P. S., Sun, Y. L., Hernandez, N. (2000) Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters. Genes & Development, 14 (20). pp. 2650-2663. ISSN 0890-9369

Skowronski, J. (1991) Expression of a human immunodeficiency virus type 1 long terminal repeat/simian virus 40 early region fusion gene in transgenic mice. J Virol, 65 (2). pp. 754-62. ISSN 0022-538X (Print)0022-538X (Linking)

Smith, A. D., Sumazin, P., Xuan, Z., Zhang, M. Q. (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A, 103 (16). pp. 6275-80. ISSN 0027-8424 (Print)

Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)

T

Tanaka, M., Lai, J. S., Herr, W. (1992) Promoter-selective activation domains in Oct-1 and Oct-2 direct differential activation of an snRNA and mRNA promoter. Cell, 68 (4). pp. 755-67. ISSN 0092-8674 (Print)0092-8674 (Linking)

Tansey, W. P., Schaufele, F., Heslewood, M., Handford, C., Reudelhuber, T. L., Catanzaro, D. F. (1993) Distance-dependent interactions between basal, cyclic AMP, and thyroid hormone response elements in the rat growth hormone promoter. J Biol Chem, 268 (20). pp. 14906-11. ISSN 1067-8816

W

Weinmann, A. S., Bartley, S. M., Zhang, T., Zhang, M. Q., Farnham, P. J. (2001) Use of chromatin immunoprecipitation to clone novel E2F target promoters. Molecular and Cellular Biology, 21 (20). pp. 6820-6832. ISSN 0270-7306

Weinstein, I. B., Wigler, M. H. (1977) Cell culture studies provide new information on tumour promoters. Nature, 270 (5639). pp. 659-550.

Wigler, M. H., DeFeo, D., Weinstein, I. B. (1978) Induction of Plasminogen Activator in Cultured Cells by Macrocyclic Plant Diterpene Esters and Other Agents Related to Tumor Promotion. Cancer Res, 38 (5). pp. 1434-1437.

Wigler, M. H., Weinstein, I. B. (1976) Tumor Promotor Induces Plasminogen Activator. Nature, 259 (5540). pp. 232-233. ISSN 0028-0836

X

Xuan, Z. Y., Zhao, F., Wang, J., Chen, G., Zhang, M. Q. (2005) Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology, 6 (8). R72. ISSN 1465-6906

Y

Yang, W., Jefferson, R. A., Huttner, E., Moore, J. M., Gagliano, W. B., Grossniklaus, U. (2005) An egg apparatus-specific enhancer of Arabidopsis, identified by enhancer detection. Plant Physiology, 139 (3). pp. 1421-1432. ISSN 0032-0889

Z

Zhang, C., Xuan, Z., Otto, S., Hover, J. R., McCorkle, S. R., Mandel, G., Zhang, M. Q. (2006) A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res, 34 (8). pp. 2238-46. ISSN 1362-4962 (Electronic)

Zhang, M. Q. (2003) Prediction, annotation, and analysis of human promoters. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 217-25. ISSN 0091-7451 (Print)

Zhang, M. Q. (2005) Using CorePromoter to find human core promoters. Curr Protoc Bioinformatics, Chapte. Unit 2.9. ISSN 1934-340X (Electronic)

Zhang, T., Zhang, M. (2001) Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinformatics, 17 (12). pp. 1232-1233. ISSN 1367-4803

Zhao, X. Y., Pendergrast, P. S., Hernandez, N. (2001) A positioned nucleosome on the human U6 promoter allows recruitment of SNAP(c) by the Oct-1 POU domain. Molecular Cell, 7 (3). pp. 539-549. ISSN 1097-2765

Zhu, J., Zhang, M. Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15 (7-8). pp. 607-11. ISSN 1367-4803 (Print)

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