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  • *Transcription, Genetic  (5)
  • American Association for the Advancement of Science (AAAS)  (5)
  • PANGAEA
  • 2015-2019  (1)
  • 2000-2004  (4)
  • 1
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    Architecture of RNA polymerase II and implications for the transcription mechanism (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-28
    Description: A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Fu, J -- Gnatt, A L -- Maier-Davis, B -- Thompson, N E -- Burgess, R R -- Edwards, A M -- David, P R -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):640-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10784442" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Enzyme Stability ; Escherichia coli/enzymology ; Humans ; *Models, Molecular ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; RNA Polymerase II/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Thermus/enzymology ; Transcription Factors/chemistry/metabolism ; *Transcription Factors, General ; *Transcription, Genetic ; *Transcriptional Elongation Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Empirical analysis of transcriptional activity in the Arabidopsis genome (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-01
    Description: Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamada, Kayoko -- Lim, Jun -- Dale, Joseph M -- Chen, Huaming -- Shinn, Paul -- Palm, Curtis J -- Southwick, Audrey M -- Wu, Hank C -- Kim, Christopher -- Nguyen, Michelle -- Pham, Paul -- Cheuk, Rosa -- Karlin-Newmann, George -- Liu, Shirley X -- Lam, Bao -- Sakano, Hitomi -- Wu, Troy -- Yu, Guixia -- Miranda, Molly -- Quach, Hong L -- Tripp, Matthew -- Chang, Charlie H -- Lee, Jeong M -- Toriumi, Mitsue -- Chan, Marie M H -- Tang, Carolyn C -- Onodera, Courtney S -- Deng, Justine M -- Akiyama, Kenji -- Ansari, Yasser -- Arakawa, Takahiro -- Banh, Jenny -- Banno, Fumika -- Bowser, Leah -- Brooks, Shelise -- Carninci, Piero -- Chao, Qimin -- Choy, Nathan -- Enju, Akiko -- Goldsmith, Andrew D -- Gurjal, Mani -- Hansen, Nancy F -- Hayashizaki, Yoshihide -- Johnson-Hopson, Chanda -- Hsuan, Vickie W -- Iida, Kei -- Karnes, Meagan -- Khan, Shehnaz -- Koesema, Eric -- Ishida, Junko -- Jiang, Paul X -- Jones, Ted -- Kawai, Jun -- Kamiya, Asako -- Meyers, Cristina -- Nakajima, Maiko -- Narusaka, Mari -- Seki, Motoaki -- Sakurai, Tetsuya -- Satou, Masakazu -- Tamse, Racquel -- Vaysberg, Maria -- Wallender, Erika K -- Wong, Cecilia -- Yamamura, Yuki -- Yuan, Shiaulou -- Shinozaki, Kazuo -- Davis, Ronald W -- Theologis, Athanasios -- Ecker, Joseph R -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):842-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Gene Expression Center, Albany, CA 94710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593172" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Cloning, Molecular ; Computational Biology ; DNA, Complementary/genetics ; DNA, Intergenic ; Expressed Sequence Tags ; Gene Expression Profiling ; Genes, Plant ; *Genome, Plant ; Genomics ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; RNA, Messenger/*genetics ; RNA, Plant/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bushnell, David A -- Westover, Kenneth D -- Davis, Ralph E -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):983-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963322" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Hybridization ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/metabolism ; RNA Polymerase II/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA Box ; TATA-Box Binding Protein/chemistry/metabolism ; Templates, Genetic ; Transcription Factor TFIIB/*chemistry/metabolism ; Transcription Factors, TFII/chemistry/metabolism ; *Transcription, Genetic ; Zinc/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Sex-dependent gene expression and evolution of the Drosophila transcriptome (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: Comparison of the gene-expression profiles between adults of Drosophila melanogaster and Drosophila simulans has uncovered the evolution of genes that exhibit sex-dependent regulation. Approximately half the genes showed differences in expression between the species, and among these, approximately 83% involved a gain, loss, increase, decrease, or reversal of sex-biased expression. Most of the interspecific differences in messenger RNA abundance affect male-biased genes. Genes that differ in expression between the species showed functional clustering only if they were sex-biased. Our results suggest that sex-dependent selection may drive changes in expression of many of the most rapidly evolving genes in the Drosophila transcriptome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ranz, Jose M -- Castillo-Davis, Cristian I -- Meiklejohn, Colin D -- Hartl, Daniel L -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1742-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805547" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; Drosophila/*genetics ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Female ; *Gene Expression ; Gene Expression Profiling ; Genes, Insect ; *Genome ; Male ; Mutation ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/genetics/metabolism ; Selection, Genetic ; Sex Characteristics ; Species Specificity ; *Transcription, Genetic ; X Chromosome/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-02-14
    Description: Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arner, Erik -- Daub, Carsten O -- Vitting-Seerup, Kristoffer -- Andersson, Robin -- Lilje, Berit -- Drablos, Finn -- Lennartsson, Andreas -- Ronnerblad, Michelle -- Hrydziuszko, Olga -- Vitezic, Morana -- Freeman, Tom C -- Alhendi, Ahmad M N -- Arner, Peter -- Axton, Richard -- Baillie, J Kenneth -- Beckhouse, Anthony -- Bodega, Beatrice -- Briggs, James -- Brombacher, Frank -- Davis, Margaret -- Detmar, Michael -- Ehrlund, Anna -- Endoh, Mitsuhiro -- Eslami, Afsaneh -- Fagiolini, Michela -- Fairbairn, Lynsey -- Faulkner, Geoffrey J -- Ferrai, Carmelo -- Fisher, Malcolm E -- Forrester, Lesley -- Goldowitz, Daniel -- Guler, Reto -- Ha, Thomas -- Hara, Mitsuko -- Herlyn, Meenhard -- Ikawa, Tomokatsu -- Kai, Chieko -- Kawamoto, Hiroshi -- Khachigian, Levon M -- Klinken, S Peter -- Kojima, Soichi -- Koseki, Haruhiko -- Klein, Sarah -- Mejhert, Niklas -- Miyaguchi, Ken -- Mizuno, Yosuke -- Morimoto, Mitsuru -- Morris, Kelly J -- Mummery, Christine -- Nakachi, Yutaka -- Ogishima, Soichi -- Okada-Hatakeyama, Mariko -- Okazaki, Yasushi -- Orlando, Valerio -- Ovchinnikov, Dmitry -- Passier, Robert -- Patrikakis, Margaret -- Pombo, Ana -- Qin, Xian-Yang -- Roy, Sugata -- Sato, Hiroki -- Savvi, Suzana -- Saxena, Alka -- Schwegmann, Anita -- Sugiyama, Daisuke -- Swoboda, Rolf -- Tanaka, Hiroshi -- Tomoiu, Andru -- Winteringham, Louise N -- Wolvetang, Ernst -- Yanagi-Mizuochi, Chiyo -- Yoneda, Misako -- Zabierowski, Susan -- Zhang, Peter -- Abugessaisa, Imad -- Bertin, Nicolas -- Diehl, Alexander D -- Fukuda, Shiro -- Furuno, Masaaki -- Harshbarger, Jayson -- Hasegawa, Akira -- Hori, Fumi -- Ishikawa-Kato, Sachi -- Ishizu, Yuri -- Itoh, Masayoshi -- Kawashima, Tsugumi -- Kojima, Miki -- Kondo, Naoto -- Lizio, Marina -- Meehan, Terrence F -- Mungall, Christopher J -- Murata, Mitsuyoshi -- Nishiyori-Sueki, Hiromi -- Sahin, Serkan -- Nagao-Sato, Sayaka -- Severin, Jessica -- de Hoon, Michiel J L -- Kawai, Jun -- Kasukawa, Takeya -- Lassmann, Timo -- Suzuki, Harukazu -- Kawaji, Hideya -- Summers, Kim M -- Wells, Christine -- FANTOM Consortium -- Hume, David A -- Forrest, Alistair R R -- Sandelin, Albin -- Carninci, Piero -- Hayashizaki, Yoshihide -- P30 CA010815/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678556" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cattle ; Cell Differentiation/*genetics ; Dogs ; *Enhancer Elements, Genetic ; *Gene Expression Regulation, Developmental ; Mice ; RNA, Messenger/genetics/metabolism ; Rats ; Stem Cells/*cytology/metabolism ; Transcription Factors/*metabolism ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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