Items where Subject is "promoter"

Paper

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 (March 2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836

Balinth, Seamus, Fisher, Matthew L, Hwangbo, Yon, Wu, Caizhi, Ballon, Carlos, Sun, Xueqin, Mills, Alea A (July 2022) EZH2 regulates a SETDB1/ΔNp63α axis via RUNX3 to drive a cancer stem cell phenotype in squamous cell carcinoma. Oncogene. ISSN 0950-9232 (Public Dataset)

Barnes, S. L., Belliveau, N. M., Ireland, W. T., Kinney, J. B., Phillips, R. (February 2019) Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comput Biol, 15 (2). e1006226. ISSN 1553-734x

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)

Baumruker, T., Sturm, R., Herr, W. (November 1988) OBP100 binds remarkably degenerate octamer motifs through specific interactions with flanking sequences. Genes Dev, 2 (11). pp. 1400-13. ISSN 0890-9369

Belliveau, N. M., Barnes, S. L., Ireland, W. T., Jones, D. L., Sweredoski, M. J., Moradian, A., Hess, S., Kinney, J. B., Phillips, R. (May 2018) Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A, 115 (21). E4796-e4805. ISSN 0027-8424

Berenstein, D., Olesen, K., Speck, C., Skovgaard, O. (May 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

Bitter, Grant A, Chang, Kenneth KH, Egan, Kevin M (December 1991) A multi-component upstream activation sequence of the Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase gene promoter. Molecular Genetics and Genomics: an international journal, 231 (1). pp. 22-32. ISSN 0026-8925

Cao, Zhendong, Budinich, Krista A, Huang, Hua, Ren, Diqiu, Lu, Bin, Zhang, Zhen, Chen, Qingzhou, Zhou, Yeqiao, Huang, Yu-Han, Alikarami‬, Fatemeh, Kingsley, Molly C, Lenard, Alexandra K, Wakabayashi, Aoi, Khandros, Eugene, Bailis, Will, Qi, Jun, Carroll, Martin P, Blobel, Gerd A, Faryabi, Robert B, Bernt, Kathrin M, Berger, Shelley L, Shi, Junwei (August 2021) ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Molecular Cell. ISSN 1097-2765

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. (December 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. (June 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. (December 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

Das, G., Hinkley, C., Tanaka, M., Herr, W. (February 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. (December 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. (February 2007) Identification of novel functional TBP-binding sites and general factor repertoires. Embo Journal, 26 (4). pp. 944-954. ISSN 0261-4189

Dergai, O., Cousin, P., Gouge, J., Satia, K., Praz, V., Kuhlman, T., Lhote, P., Vannini, A., Hernandez, N. (May 2018) Mechanism of selective recruitment of RNA polymerases II and III to snRNA gene promoters. Genes Dev, 32 (9-10). pp. 711-722. ISSN 0890-9369

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

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. (March 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. (March 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

Gilbert, M. T., Sun, J. D., Yan, Y., Oddoux, C., Lazarus, A., Tansey, W. P., Lavin, T. N., Catanzaro, D. F. (November 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

Hendelman, Anat, Zebell, Sophia, Rodriguez-Leal, Daniel, Dukler, Noah, Robitaille, Gina, Wu, Xuelin, Kostyun, Jamie, Tal, Lior, Wang, Peipei, Bartlett, Madelaine E, Eshed, Yuval, Efroni, Idan, Lippman, Zachary B (April 2021) Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell, 184 (7). 1724-1739.e16. ISSN 0092-8674

Hofmann, J. F., Beach, D. (January 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)

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

Kessler, M., Mathews, M. B. (November 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. (January 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. (October 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. (October 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

Labrie, C., Morris, G. F., Mathews, M. B. (March 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. (August 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. (April 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)

Liu, Lei, Gallagher, Joseph, Arevalo, Edgar Demesa, Chen, Richelle, Skopelitis, Tara, Wu, Qingyu, Bartlett, Madelaine, Jackson, David (March 2021) Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes. Nature Plants, 7 (3). pp. 287-294. ISSN 2055-026X

Lu, B., Klingbeil, O., Tarumoto, Y., Somerville, T. D. D., Huang, Y. H., Wei, Y., Wai, D. C., Low, J. K. K., Milazzo, J. P., Wu, X. S., Cao, Z., Yan, X., Demerdash, O. E., Huang, G., Mackay, J. P., Kinney, J. B., Shi, J., Vakoc, C. R. (November 2018) A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell, 34 (6). pp. 970-981. ISSN 1535-6108

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

Mirbahai, Leda, Williams, Timothy D, Zhan, Huiqing, Gong, Zhiyuan, Chipman, J Kevin (January 2011) Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis. BMC Genomics, 12 (1). p. 3. ISSN 1471-2164

Morris, G. F., Mathews, M. B. (September 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)

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

Pan, Xiufang, Zhan, Huiqing, Gong, Zhiyuan (2008) Ornamental expression of red fluorescent protein in transgenic founders of white skirt tetra (Gymnocorymbus ternetzi). Marine Biotechnology, 10 (5). pp. 497-501. ISSN 1436-2228

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

Rajagopal, N., Ernst, J., Ray, P., Wu, J., Zhang, M., Kellis, M., Ren, B. (August 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. (April 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. (January 2002) Promoter melting by RNA polymerase: Detection and analysis by single-molecule DNA nanomanipulation. Biophysical Journal, 82 (1). 115A-115A. ISSN 0006-3495

Saxena, A., Ma, B. C., Schramm, L., Hernandez, N. (November 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. (October 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. (October 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

Sheu, Yi-Jun, Kawaguchi, Risa Karakida, Gillis, Jesse, Stillman, Bruce (May 2021) Prevalent and Dynamic Binding of the Cell Cycle Checkpoint Kinase Rad53 to Gene Promoters. bioRxiv. (Unpublished)

Sheu, Yi-Jun, Kawaguchi, Risa Karakida, Gillis, Jesse, Stillman, Bruce (December 2022) Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters. eLife, 11. e84320. ISSN 2050-084X (Public Dataset)

Skowronski, J. (February 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. (April 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)

Stefanski, Heather E, Xing, Yan, Nicholls, Jemma, Jonart, Leslie, Goren, Emily, Taylor, Patricia A, Mills, Alea A, Riddle, Megan, McGrath, John, Tolar, Jakub, Hollander, Georg A, Blazar, Bruce R (January 2022) P63 targeted deletion under the FOXN1 promoter disrupts pre-and post-natal thymus development, function and maintenance as well as induces severe hair loss. PLoS One, 17 (1). ISSN 1932-6203

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

Tanaka, M., Lai, J. S., Herr, W. (February 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. (July 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

Wang, Xingang, Aguirre, Lyndsey, Rodríguez-Leal, Daniel, Hendelman, Anat, Benoit, Matthias, Lippman, Zachary B (April 2021) Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nature Plants, 7 (4). pp. 419-427. ISSN 2055-026X

Weinmann, A. S., Bartley, S. M., Zhang, T., Zhang, M. Q., Farnham, P. J. (October 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. (December 1977) Cell culture studies provide new information on tumour promoters. Nature, 270 (5639). pp. 659-550.

Wigler, M. H., DeFeo, D., Weinstein, I. B. (May 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

Xiao, Yutong, Yee, Callista, Zhao, Chris Z, Martinez, Michael AQ, Zhang, Wan, Shen, Kang, Matus, David Q, Hammell, Christopher (February 2023) An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in Caenorhabditis elegans. Genetics: a periodical record of investigations bearing on heredity and variation. iyad013. ISSN 0016-6731

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

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

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

Zhang, T., Zhang, M. (December 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, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam (October 2023) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Research. ISSN 0305-1048

Zhao, Yixin, Liu, Lingjie, Siepel, Adam (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. bioRxiv. (Submitted)

Zhao, X. Y., Pendergrast, P. S., Hernandez, N. (March 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. (July 1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15 (7-8). pp. 607-11. ISSN 1367-4803 (Print)

Thesis

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