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Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
Alexander S Brodsky, Clifford A Meyer, Ian A Swinburne, Giles Hall, Benjamin J Keenan, Xiaole S Liu, Edward A Fox, Pamela A Silver
Genome Biol. 2005; 6(8): R64. Published online 2005 July 15. doi: 10.1186/gb-2005-6-8-r64
PMCID:
PMC1273631
Abstract Full Text PDF–1.4M Supplementary Material

Is Cited by the Following 22 Articles in this Archive:

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Satish Sati, Vinay Singh Tanwar, K. Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, S. Umakar Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
PLoS One. 2012; 7(2): e31621. Published online 2012 February 15. doi: 10.1371/journal.pone.0031621
PMCID:
PMC3280313
Abstract Full Text PDF–688K Supplementary Material
Depolarization-Mediated Regulation of Alternative Splicing
Alok Sharma, Hua Lou
Front Neurosci. 2011; 5: 141. Prepublished online 2011 November 23. Published online 2011 December 27. doi: 10.3389/fnins.2011.00141
PMCID:
PMC3246316
Abstract Full Text PDF–405K
RNA Polymerase II Elongation at the Crossroads of Transcription and Alternative Splicing
Manuel de la Mata, Manuel J. Muñoz, Mariano Alló, Juan Pablo Fededa, Ignacio E. Schor, Alberto R. Kornblihtt
Genet Res Int. 2011; 2011: 309865. Published online 2011 September 20. doi: 10.4061/2011/309865
PMCID:
PMC3335476
Abstract Full Text PDF–1.3M
Splicing-Dependent RNA Polymerase Pausing in Yeast
Ross D. Alexander, Steven A. Innocente, J. David Barrass, Jean D. Beggs
Mol Cell. 2010 November 24; 40(4): 582–593. doi: 10.1016/j.molcel.2010.11.005
PMCID:
PMC3000496
Abstract Full Text Supplementary Material
Noncanonical transcript forms in yeast and their regulation during environmental stress
Oh Kyu Yoon, Rachel B. Brem
RNA. 2010 June; 16(6): 1256–1267. doi: 10.1261/rna.2038810
PMCID:
PMC2874177
Abstract Full Text PDF–927K
Widespread transcription at neuronal activity-regulated enhancers
Tae-Kyung Kim, Martin Hemberg, Jesse M. Gray, Allen M. Costa, Daniel M. Bear, Jing Wu, David A. Harmin, Mike Laptewicz, Kellie Barbara-Haley, Scott Kuersten, Eirene Markenscoff-Papadimitriou, Dietmar Kuhl, Haruhiko Bito, Paul F. Worley, Gabriel Kreiman, Michael E. Greenberg
Nature. Author manuscript; available in PMC 2011 January 12.
Published in final edited form as: Nature. 2010 May 13; 465(7295): 182–187. Published online 2010 April 14. doi: 10.1038/nature09033
PMCID:
PMC3020079
Abstract Full Text PDF–1.6M Supplementary Material
PPS, a Large Multidomain Protein, Functions with Sex-Lethal to Regulate Alternative Splicing in Drosophila
Matthew L. Johnson, Alexis A. Nagengast, Helen K. Salz
PLoS Genet. 2010 March; 6(3): e1000872. Published online 2010 March 5. doi: 10.1371/journal.pgen.1000872
PMCID:
PMC2832672
Abstract Full Text PDF–508K
The organization of nucleosomes around splice sites
Wei Chen, Liaofu Luo, Lirong Zhang
Nucleic Acids Res. 2010 May; 38(9): 2788–2798. Published online 2010 January 21. doi: 10.1093/nar/gkq007
PMCID:
PMC2875036
Abstract Full Text PDF–2.1M Supplementary Material
Chromatin Architecture and Transcription Factor Binding Regulate Expression of Erythrocyte Membrane Protein Genes
Laurie A. Steiner, Yelena Maksimova, Vincent Schulz, Clara Wong, Debasish Raha, Milind C. Mahajan, Sherman M. Weissman, Patrick G. Gallagher
Mol Cell Biol. 2009 October; 29(20): 5399–5412. Published online 2009 August 17. doi: 10.1128/MCB.00777-09
PMCID:
PMC2756878
Abstract Full Text PDF–1.0M Supplementary Material
A biological function for the neuronal activity-dependent component of Bdnf transcription in the development of cortical inhibition
Elizabeth J. Hong, Alejandra E. McCord, Michael E. Greenberg
Neuron. Author manuscript; available in PMC 2010 May 19.
Published in final edited form as: Neuron. 2008 November 26; 60(4): 610–624. doi: 10.1016/j.neuron.2008.09.024
PMCID:
PMC2873221
Abstract Full Text PDF–5.2M Supplementary Material
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
Zheng Lian, Alexander Karpikov, Jin Lian, Milind C. Mahajan, Stephen Hartman, Mark Gerstein, Michael Snyder, Sherman M. Weissman
Genome Res. 2008 August; 18(8): 1224–1237. doi: 10.1101/gr.075804.107
PMCID:
PMC2493437
Abstract Full Text PDF–991K
Cotranscriptional Splicing Potentiates the mRNA Production from a Subset of Estradiol-Stimulated Genes
Danielle Bittencourt, Martin Dutertre, Gabriel Sanchez, Jérôme Barbier, Lise Gratadou, Didier Auboeuf
Mol Cell Biol. 2008 September; 28(18): 5811–5824. Published online 2008 July 21. doi: 10.1128/MCB.02231-07
PMCID:
PMC2546936
Abstract Full Text PDF–1.2M
Mapping of Small RNAs in the Human ENCODE Regions
Christelle Borel, Maryline Gagnebin, Corinne Gehrig, Evgenia V. Kriventseva, Evgeny M. Zdobnov, Stylianos E. Antonarakis
Am J Hum Genet. 2008 April 11; 82(4): 971–981. Published online 2008 April 4. doi: 10.1016/j.ajhg.2008.02.016
PMCID:
PMC2427294
Abstract Full Text PDF–1.2M Supplementary Material
Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes
Christopher R. Brown, Caleb J. Kennedy, Valerie A. Delmar, Douglass J. Forbes, Pamela A. Silver
Genes Dev. 2008 March 1; 22(5): 627–639. doi: 10.1101/gad.1632708
PMCID:
PMC2259032
Abstract Full Text PDF–704K
Intron Delays and Transcriptional Timing during Development
Ian A. Swinburne, Pamela A. Silver
Dev Cell. Author manuscript; available in PMC 2010 February 19.
Published in final edited form as: Dev Cell. 2008 March; 14(3): 324–330. doi: 10.1016/j.devcel.2008.02.002
PMCID:
PMC2825037
Abstract Full Text PDF–243K
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
Zhuo Du, Yiqiang Zhao, Ning Li
Genome Res. 2008 February; 18(2): 233–241. doi: 10.1101/gr.6905408
Correction in:
Genome Res. 2008 March; 18(3): 516.
PMCID:
PMC2203621
Abstract Full Text PDF–607K Correction
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Leah O. Barrera, Zirong Li, Andrew D. Smith, Karen C. Arden, Webster K. Cavenee, Michael Q. Zhang, Roland D. Green, Bing Ren
Genome Res. 2008 January; 18(1): 46–59. doi: 10.1101/gr.6654808
PMCID:
PMC2134779
Abstract Full Text PDF–1.2M
Transcription of Hepatitis Delta Virus RNA by RNA Polymerase II
Jinhong Chang, Xingcao Nie, Ho Eun Chang, Ziying Han, John Taylor
J Virol. 2008 February; 82(3): 1118–1127. Published online 2007 November 21. doi: 10.1128/JVI.01758-07
PMCID:
PMC2224410
Abstract Full Text PDF–351K
Identifying synergistic regulation involving c-Myc and sp1 in human tissues
Fabio Parisi, Pratyaksha Wirapati, Felix Naef
Nucleic Acids Res. 2007 February; 35(4): 1098–1107. Published online 2007 January 30. doi: 10.1093/nar/gkl1157
PMCID:
PMC1851645
Abstract Full Text PDF–4.2M
Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors
Margarida Gama-Carvalho, Nuno L Barbosa-Morais, Alexander S Brodsky, Pamela A Silver, Maria Carmo-Fonseca
Genome Biol. 2006; 7(11): R113. Published online 2006 November 30. doi: 10.1186/gb-2006-7-11-r113
PMCID:
PMC1794580
Abstract Full Text PDF–566K Supplementary Material
In vivo binding of NF-κB to the IκBβ promoter is insufficient for transcriptional activation
Bryan D. Griffin, Paul N. Moynagh
Biochem J. 2006 November 15; 400(Pt 1): 115–125. Prepublished online 2006 June 23. Published online 2006 October 27. doi: 10.1042/BJ20060786
PMCID:
PMC1635438
Abstract Full Text PDF–572K
Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription
Ian A. Swinburne, Clifford A. Meyer, X. Shirley Liu, Pamela A. Silver, Alexander S. Brodsky
Genome Res. 2006 July; 16(7): 912–921. doi: 10.1101/gr.5211806
PMCID:
PMC1484458
Abstract Full Text PDF–708K
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