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Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
Jasmina Ponjavic, Boris Lenhard, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Albin Sandelin
Genome Biol. 2006; 7(8): R78. Published online 2006 August 17. doi: 10.1186/gb-2006-7-8-r78
PMCID:
PMC1779604
Abstract Full Text PDF–1.0M

Is Cited by the Following 22 Articles in this Archive:

Promoter architecture of mouse olfactory receptor genes
Charles Plessy, Giovanni Pascarella, Nicolas Bertin, Altuna Akalin, Claudia Carrieri, Anne Vassalli, Dejan Lazarevic, Jessica Severin, Christina Vlachouli, Roberto Simone, Geoffrey J. Faulkner, Jun Kawai, Carsten O. Daub, Silvia Zucchelli, Yoshihide Hayashizaki, Peter Mombaerts, Boris Lenhard, Stefano Gustincich, Piero Carninci
Genome Res. 2012 March; 22(3): 486–497. doi: 10.1101/gr.126201.111
PMCID:
PMC3290784
Abstract Full Text PDF–1.0M
Transcription factor TFIIF is not required for initiation by RNA polymerase II, but it is essential to stabilize transcription factor TFIIB in early elongation complexes
Pavel Čabart, Andrea Újvári, Mahadeb Pal, Donal S. Luse
Proc Natl Acad Sci U S A. 2011 September 20; 108(38): 15786-15791. Published online 2011 September 6. doi: 10.1073/pnas.1104591108
PMCID:
PMC3179120
Abstract Full Text PDF–813K Supplementary Material
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification
Tadasu Nozaki, Nozomu Yachie, Ryu Ogawa, Anton Kratz, Rintaro Saito, Masaru Tomita
BMC Genomics. 2011; 12: 416. Published online 2011 August 17. doi: 10.1186/1471-2164-12-416
PMCID:
PMC3170308
Abstract Full Text PDF–2.1M Supplementary Material
Novel Core Promoter Elements and a Cognate Transcription Factor in the Divergent Unicellular Eukaryote Trichomonas vaginalis
Alias J. Smith, Lorissa Chudnovsky, Augusto Simoes-Barbosa, Maria G. Delgadillo-Correa, Zophonias O. Jonsson, James A. Wohlschlegel, Patricia J. Johnson
Mol Cell Biol. 2011 April; 31(7): 1444–1458. doi: 10.1128/MCB.00745-10
PMCID:
PMC3135286
Abstract Full Text PDF–2.8M
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
Morana Vitezic, Timo Lassmann, Alistair R. R. Forrest, Masanori Suzuki, Yasuhiro Tomaru, Jun Kawai, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, Carsten O. Daub
Nucleic Acids Res. 2010 December; 38(22): 8141–8148. Published online 2010 August 19. doi: 10.1093/nar/gkq729
PMCID:
PMC3001087
Abstract Full Text PDF–4.0M Supplementary Material
Family-based association analysis of 42 hereditary prostate cancer families identifies the Apolipoprotein L3 region on chromosome 22q12 as a risk locus
Bo Johanneson, Shannon K. McDonnell, Danielle M. Karyadi, Pascale Quignon, Laura McIntosh, Shaun M. Riska, Liesel M. FitzGerald, Gregory Johnson, Kerry Deutsch, Gabrielle Williams, Lori S. Tillmans, Janet L. Stanford, Daniel J. Schaid, Stephen N. Thibodeau, Elaine A. Ostrander
Hum Mol Genet. 2010 October 1; 19(19): 3852–3862. Published online 2010 July 14. doi: 10.1093/hmg/ddq283
PMCID:
PMC2935853
Abstract Full Text PDF–311K
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters
Hans-Jörg Warnatz, Robert Querfurth, Anna Guerasimova, Xi Cheng, Stefan A. Haas, Andrew L. Hufton, Thomas Manke, Dominique Vanhecke, Wilfried Nietfeld, Martin Vingron, Michal Janitz, Hans Lehrach, Marie-Laure Yaspo
Nucleic Acids Res. 2010 October; 38(18): 6112–6123. Published online 2010 May 21. doi: 10.1093/nar/gkq402
PMCID:
PMC2952857
Abstract Full Text PDF–4.0M Supplementary Material
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation
Virginie Bernard, Véronique Brunaud, Alain Lecharny
BMC Genomics. 2010; 11: 166. Published online 2010 March 12. doi: 10.1186/1471-2164-11-166
PMCID:
PMC2842252
Abstract Full Text PDF–764K Supplementary Material
Genetic and Molecular Analyses of PEG10 Reveal New Aspects of Genomic Organization, Transcription and Translation
Heike Lux, Heiko Flammann, Mathias Hafner, Andreas Lux
PLoS One. 2010; 5(1): e8686. Published online 2010 January 13. doi: 10.1371/journal.pone.0008686
PMCID:
PMC2800197
Abstract Full Text PDF–1.2M
Promoting developmental transcription
Uwe Ohler, David A. Wassarman
Development. 2010 January 1; 137(1): 15–26. doi: 10.1242/dev.035493
PMCID:
PMC2796937
Abstract Full Text
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
Rupali P Patwardhan, Choli Lee, Oren Litvin, David L Young, Dana Pe'er, Jay Shendure
Nat Biotechnol. Author manuscript; available in PMC 2010 June 1.
Published in final edited form as: Nat Biotechnol. 2009 December; 27(12): 1173–1175. doi: 10.1038/nbt.1589
PMCID:
PMC2849652
Abstract Full Text PDF–485K Supplementary Material
Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain
Jasmina Ponjavic, Peter L. Oliver, Gerton Lunter, Chris P. Ponting
PLoS Genet. 2009 August; 5(8): e1000617. Published online 2009 August 21. doi: 10.1371/journal.pgen.1000617
PMCID:
PMC2722021
Abstract Full Text PDF–746K Supplementary Material
Computational Design and Application of Endogenous Promoters for Transcriptionally Targeted Gene Therapy for Rheumatoid Arthritis
Jeroen Geurts, Leo AB Joosten, Nozomi Takahashi, Onno J Arntz, Anton Glück, Miranda B Bennink, Wim B van den Berg, Fons AJ van de Loo
Mol Ther. 2009 November; 17(11): 1877–1887. Published online 2009 August 18. doi: 10.1038/mt.2009.182
PMCID:
PMC2835043
Abstract Full Text PDF–397K Supplementary Material
Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery
Tamar Juven-Gershon, James T. Kadonaga
Dev Biol. Author manuscript; available in PMC 2010 March 15.
Published in final edited form as: Dev Biol. 2010 March 15; 339(2): 225–229. Published online 2009 August 13. doi: 10.1016/j.ydbio.2009.08.009
PMCID:
PMC2830304
Abstract Full Text PDF–1.0M
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler
Genome Biol. 2009; 10(7): R73. Published online 2009 July 9. doi: 10.1186/gb-2009-10-7-r73
PMCID:
PMC2728527
Abstract Full Text PDF–1.6M Supplementary Material
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
Ken Daigoro Yokoyama, Uwe Ohler, Gregory A. Wray
Nucleic Acids Res. 2009 July; 37(13): e92. Published online 2009 July. doi: 10.1093/nar/gkp423
PMCID:
PMC2715254
Abstract Full Text PDF–4.4M Supplementary Material
A transcription factor affinity-based code for mammalian transcription initiation
Molly Megraw, Fernando Pereira, Shane T. Jensen, Uwe Ohler, Artemis G. Hatzigeorgiou
Genome Res. 2009 April; 19(4): 644–656. doi: 10.1101/gr.085449.108
PMCID:
PMC2665783
Abstract Full Text PDF–1.1M
The RNA Polymerase II Core Promoter – the Gateway to Transcription
Tamar Juven-Gershon, Jer-Yuan Hsu, Joshua W. M. Theisen, James T. Kadonaga
Curr Opin Cell Biol. Author manuscript; available in PMC 2008 November 24.
Published in final edited form as: Curr Opin Cell Biol. 2008 June; 20(3): 253–259. Published online 2008 April 22. doi: 10.1016/j.ceb.2008.03.003
PMCID:
PMC2586601
Abstract Full Text PDF–148K
A code for transcription initiation in mammalian genomes
Martin C. Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci, Albin Sandelin
Genome Res. 2008 January; 18(1): 1–12. doi: 10.1101/gr.6831208
PMCID:
PMC2134772
Abstract Full Text PDF–740K
Noncanonical TATA Sequence in the UL44 Late Promoter of Human Cytomegalovirus Is Required for the Accumulation of Late Viral Transcripts
Hiroki Isomura, Mark F. Stinski, Ayumi Kudoh, Takayuki Murata, Sanae Nakayama, Yoshitaka Sato, Satoko Iwahori, Tatsuya Tsurumi
J Virol. 2008 February; 82(4): 1638–1646. Published online 2007 December 5. doi: 10.1128/JVI.01917-07
PMCID:
PMC2258720
Abstract Full Text PDF–561K
The ets-Related Transcription Factor GABP Directs Bidirectional Transcription
Patrick J Collins, Yuya Kobayashi, Loan Nguyen, Nathan D Trinklein, Richard M Myers
PLoS Genet. 2007 November; 3(11): e208. Published online 2007 November 16. doi: 10.1371/journal.pgen.0030208
PMCID:
PMC2077898
Abstract Full Text PDF–377K Supplementary Material
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
Jasmina Ponjavic, Chris P. Ponting, Gerton Lunter
Genome Res. 2007 May; 17(5): 556–565. doi: 10.1101/gr.6036807
PMCID:
PMC1855172
Abstract Full Text PDF–351K
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