Nova Fong, Hyunmin Kim, Yu Zhou, Xiong Ji, Jinsong Qiu, Tassa Saldi, Katrina Diener, Ken Jones, Xiang-Dong Fu, David L Bentley. Genes Dev 2014
Times Cited: 170
Times Cited: 170
Times Cited
Times Co-cited
Similarity
A slow RNA polymerase II affects alternative splicing in vivo.
Manuel de la Mata, Claudio R Alonso, Sebastián Kadener, Juan P Fededa, Matías Blaustein, Federico Pelisch, Paula Cramer, David Bentley, Alberto R Kornblihtt. Mol Cell 2003
Manuel de la Mata, Claudio R Alonso, Sebastián Kadener, Juan P Fededa, Matías Blaustein, Federico Pelisch, Paula Cramer, David Bentley, Alberto R Kornblihtt. Mol Cell 2003
46
How slow RNA polymerase II elongation favors alternative exon skipping.
Gwendal Dujardin, Celina Lafaille, Manuel de la Mata, Luciano E Marasco, Manuel J Muñoz, Catherine Le Jossic-Corcos, Laurent Corcos, Alberto R Kornblihtt. Mol Cell 2014
Gwendal Dujardin, Celina Lafaille, Manuel de la Mata, Luciano E Marasco, Manuel J Muñoz, Catherine Le Jossic-Corcos, Laurent Corcos, Alberto R Kornblihtt. Mol Cell 2014
37
33
Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing.
Takayuki Nojima, Tomás Gomes, Ana Rita Fialho Grosso, Hiroshi Kimura, Michael J Dye, Somdutta Dhir, Maria Carmo-Fonseca, Nicholas J Proudfoot. Cell 2015
Takayuki Nojima, Tomás Gomes, Ana Rita Fialho Grosso, Hiroshi Kimura, Michael J Dye, Somdutta Dhir, Maria Carmo-Fonseca, Nicholas J Proudfoot. Cell 2015
26
Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing.
Tassa Saldi, Michael A Cortazar, Ryan M Sheridan, David L Bentley. J Mol Biol 2016
Tassa Saldi, Michael A Cortazar, Ryan M Sheridan, David L Bentley. J Mol Biol 2016
25
STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
24
Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Vahid Aslanzadeh, Yuanhua Huang, Guido Sanguinetti, Jean D Beggs. Genome Res 2018
Vahid Aslanzadeh, Yuanhua Huang, Guido Sanguinetti, Jean D Beggs. Genome Res 2018
43
Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.
Fernando Carrillo Oesterreich, Lydia Herzel, Korinna Straube, Katja Hujer, Jonathon Howard, Karla M Neugebauer. Cell 2016
Fernando Carrillo Oesterreich, Lydia Herzel, Korinna Straube, Katja Hujer, Jonathon Howard, Karla M Neugebauer. Cell 2016
23
Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons.
Iris Jonkers, Hojoong Kwak, John T Lis. Elife 2014
Iris Jonkers, Hojoong Kwak, John T Lis. Elife 2014
23
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
20
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation.
Joanna Y Ip, Dominic Schmidt, Qun Pan, Arun K Ramani, Andrew G Fraser, Duncan T Odom, Benjamin J Blencowe. Genome Res 2011
Joanna Y Ip, Dominic Schmidt, Qun Pan, Arun K Ramani, Andrew G Fraser, Duncan T Odom, Benjamin J Blencowe. Genome Res 2011
19
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.
Gene Yeo, Christopher B Burge. J Comput Biol 2004
Gene Yeo, Christopher B Burge. J Comput Biol 2004
19
Alternative isoform regulation in human tissue transcriptomes.
Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, Christopher B Burge. Nature 2008
Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, Christopher B Burge. Nature 2008
19
Splice site selection, rate of splicing, and alternative splicing on nascent transcripts.
A L Beyer, Y N Osheim. Genes Dev 1988
A L Beyer, Y N Osheim. Genes Dev 1988
18
Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications.
Artur Veloso, Killeen S Kirkconnell, Brian Magnuson, Benjamin Biewen, Michelle T Paulsen, Thomas E Wilson, Mats Ljungman. Genome Res 2014
Artur Veloso, Killeen S Kirkconnell, Brian Magnuson, Benjamin Biewen, Michelle T Paulsen, Thomas E Wilson, Mats Ljungman. Genome Res 2014
18
Splicing and transcription touch base: co-transcriptional spliceosome assembly and function.
Lydia Herzel, Diana S M Ottoz, Tara Alpert, Karla M Neugebauer. Nat Rev Mol Cell Biol 2017
Lydia Herzel, Diana S M Ottoz, Tara Alpert, Karla M Neugebauer. Nat Rev Mol Cell Biol 2017
17
Splicing-dependent RNA polymerase pausing in yeast.
Ross D Alexander, Steven A Innocente, J David Barrass, Jean D Beggs. Mol Cell 2010
Ross D Alexander, Steven A Innocente, J David Barrass, Jean D Beggs. Mol Cell 2010
17
Nascent transcript sequencing visualizes transcription at nucleotide resolution.
L Stirling Churchman, Jonathan S Weissman. Nature 2011
L Stirling Churchman, Jonathan S Weissman. Nature 2011
17
Regulation of alternative splicing through coupling with transcription and chromatin structure.
Shiran Naftelberg, Ignacio E Schor, Gil Ast, Alberto R Kornblihtt. Annu Rev Biochem 2015
Shiran Naftelberg, Ignacio E Schor, Gil Ast, Alberto R Kornblihtt. Annu Rev Biochem 2015
16
Chromatin organization marks exon-intron structure.
Schraga Schwartz, Eran Meshorer, Gil Ast. Nat Struct Mol Biol 2009
Schraga Schwartz, Eran Meshorer, Gil Ast. Nat Struct Mol Biol 2009
16
Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution.
Andreas Mayer, Julia di Iulio, Seth Maleri, Umut Eser, Jeff Vierstra, Alex Reynolds, Richard Sandstrom, John A Stamatoyannopoulos, L Stirling Churchman. Cell 2015
Andreas Mayer, Julia di Iulio, Seth Maleri, Umut Eser, Jeff Vierstra, Alex Reynolds, Richard Sandstrom, John A Stamatoyannopoulos, L Stirling Churchman. Cell 2015
16
Getting up to speed with transcription elongation by RNA polymerase II.
Iris Jonkers, John T Lis. Nat Rev Mol Cell Biol 2015
Iris Jonkers, John T Lis. Nat Rev Mol Cell Biol 2015
15
Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila.
Yevgenia L Khodor, Joseph Rodriguez, Katharine C Abruzzi, Chih-Hang Anthony Tang, Michael T Marr, Michael Rosbash. Genes Dev 2011
Yevgenia L Khodor, Joseph Rodriguez, Katharine C Abruzzi, Chih-Hang Anthony Tang, Michael T Marr, Michael Rosbash. Genes Dev 2011
15
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
Qun Pan, Ofer Shai, Leo J Lee, Brendan J Frey, Benjamin J Blencowe. Nat Genet 2008
Qun Pan, Ofer Shai, Leo J Lee, Brendan J Frey, Benjamin J Blencowe. Nat Genet 2008
15
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Sanjeev Shukla, Ersen Kavak, Melissa Gregory, Masahiko Imashimizu, Bojan Shutinoski, Mikhail Kashlev, Philipp Oberdoerffer, Rickard Sandberg, Shalini Oberdoerffer. Nature 2011
Sanjeev Shukla, Ersen Kavak, Melissa Gregory, Masahiko Imashimizu, Bojan Shutinoski, Mikhail Kashlev, Philipp Oberdoerffer, Rickard Sandberg, Shalini Oberdoerffer. Nature 2011
14
Spliceosome structure and function.
Cindy L Will, Reinhard Lührmann. Cold Spring Harb Perspect Biol 2011
Cindy L Will, Reinhard Lührmann. Cold Spring Harb Perspect Biol 2011
14
From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
Hannes Braberg, Huiyan Jin, Erica A Moehle, Yujia A Chan, Shuyi Wang, Michael Shales, Joris J Benschop, John H Morris, Chenxi Qiu, Fuqu Hu,[...]. Cell 2013
Hannes Braberg, Huiyan Jin, Erica A Moehle, Yujia A Chan, Shuyi Wang, Michael Shales, Joris J Benschop, John H Morris, Chenxi Qiu, Fuqu Hu,[...]. Cell 2013
14
13
The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
13
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.
Hagen Tilgner, David G Knowles, Rory Johnson, Carrie A Davis, Sudipto Chakrabortty, Sarah Djebali, João Curado, Michael Snyder, Thomas R Gingeras, Roderic Guigó. Genome Res 2012
Hagen Tilgner, David G Knowles, Rory Johnson, Carrie A Davis, Sudipto Chakrabortty, Sarah Djebali, João Curado, Michael Snyder, Thomas R Gingeras, Roderic Guigó. Genome Res 2012
13
The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain.
Kevin M Harlen, L Stirling Churchman. Nat Rev Mol Cell Biol 2017
Kevin M Harlen, L Stirling Churchman. Nat Rev Mol Cell Biol 2017
13
Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae.
Kenneth James Howe, Caroline M Kane, Manuel Ares. RNA 2003
Kenneth James Howe, Caroline M Kane, Manuel Ares. RNA 2003
13
The RNA polymerase II CTD coordinates transcription and RNA processing.
Jing-Ping Hsin, James L Manley. Genes Dev 2012
Jing-Ping Hsin, James L Manley. Genes Dev 2012
13
Rates of in situ transcription and splicing in large human genes.
Jarnail Singh, Richard A Padgett. Nat Struct Mol Biol 2009
Jarnail Singh, Richard A Padgett. Nat Struct Mol Biol 2009
12
Nucleosome positioning as a determinant of exon recognition.
Hagen Tilgner, Christoforos Nikolaou, Sonja Althammer, Michael Sammeth, Miguel Beato, Juan Valcárcel, Roderic Guigó. Nat Struct Mol Biol 2009
Hagen Tilgner, Christoforos Nikolaou, Sonja Althammer, Michael Sammeth, Miguel Beato, Juan Valcárcel, Roderic Guigó. Nat Struct Mol Biol 2009
12
Regulation of alternative splicing by histone modifications.
Reini F Luco, Qun Pan, Kaoru Tominaga, Benjamin J Blencowe, Olivia M Pereira-Smith, Tom Misteli. Science 2010
Reini F Luco, Qun Pan, Kaoru Tominaga, Benjamin J Blencowe, Olivia M Pereira-Smith, Tom Misteli. Science 2010
12
Epigenetics in alternative pre-mRNA splicing.
Reini F Luco, Mariano Allo, Ignacio E Schor, Alberto R Kornblihtt, Tom Misteli. Cell 2011
Reini F Luco, Mariano Allo, Ignacio E Schor, Alberto R Kornblihtt, Tom Misteli. Cell 2011
12
RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing.
Takayuki Nojima, Kenny Rebelo, Tomás Gomes, Ana Rita Grosso, Nicholas J Proudfoot, Maria Carmo-Fonseca. Mol Cell 2018
Takayuki Nojima, Kenny Rebelo, Tomás Gomes, Ana Rita Grosso, Nicholas J Proudfoot, Maria Carmo-Fonseca. Mol Cell 2018
17
A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes.
Magdalena M Maslon, Ulrich Braunschweig, Stuart Aitken, Abigail R Mann, Fiona Kilanowski, Chris J Hunter, Benjamin J Blencowe, Alberto R Kornblihtt, Ian R Adams, Javier F Cáceres. EMBO J 2019
Magdalena M Maslon, Ulrich Braunschweig, Stuart Aitken, Abigail R Mann, Fiona Kilanowski, Chris J Hunter, Benjamin J Blencowe, Alberto R Kornblihtt, Ian R Adams, Javier F Cáceres. EMBO J 2019
44
DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation.
Manuel J Muñoz, M Soledad Pérez Santangelo, Maria P Paronetto, Manuel de la Mata, Federico Pelisch, Stéphanie Boireau, Kira Glover-Cutter, Claudia Ben-Dov, Matías Blaustein, Juan J Lozano,[...]. Cell 2009
Manuel J Muñoz, M Soledad Pérez Santangelo, Maria P Paronetto, Manuel de la Mata, Federico Pelisch, Stéphanie Boireau, Kira Glover-Cutter, Claudia Ben-Dov, Matías Blaustein, Juan J Lozano,[...]. Cell 2009
11
Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing.
Ignacio E Schor, Nicolás Rascovan, Federico Pelisch, Mariano Alló, Alberto R Kornblihtt. Proc Natl Acad Sci U S A 2009
Ignacio E Schor, Nicolás Rascovan, Federico Pelisch, Mariano Alló, Alberto R Kornblihtt. Proc Natl Acad Sci U S A 2009
11
A splicing-dependent transcriptional checkpoint associated with prespliceosome formation.
Keerthi T Chathoth, J David Barrass, Shaun Webb, Jean D Beggs. Mol Cell 2014
Keerthi T Chathoth, J David Barrass, Shaun Webb, Jean D Beggs. Mol Cell 2014
16
TT-seq maps the human transient transcriptome.
Björn Schwalb, Margaux Michel, Benedikt Zacher, Katja Frühauf, Carina Demel, Achim Tresch, Julien Gagneur, Patrick Cramer. Science 2016
Björn Schwalb, Margaux Michel, Benedikt Zacher, Katja Frühauf, Carina Demel, Achim Tresch, Julien Gagneur, Patrick Cramer. Science 2016
11
Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation.
Micaela A Godoy Herz, M Guillermina Kubaczka, Grzegorz Brzyżek, Lucas Servi, Michal Krzyszton, Craig Simpson, John Brown, Szymon Swiezewski, Ezequiel Petrillo, Alberto R Kornblihtt. Mol Cell 2019
Micaela A Godoy Herz, M Guillermina Kubaczka, Grzegorz Brzyżek, Lucas Servi, Michal Krzyszton, Craig Simpson, John Brown, Szymon Swiezewski, Ezequiel Petrillo, Alberto R Kornblihtt. Mol Cell 2019
21
The spliceosome: design principles of a dynamic RNP machine.
Markus C Wahl, Cindy L Will, Reinhard Lührmann. Cell 2009
Markus C Wahl, Cindy L Will, Reinhard Lührmann. Cell 2009
11
The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing.
Yehuda Brody, Noa Neufeld, Nicole Bieberstein, Sebastien Z Causse, Eva-Maria Böhnlein, Karla M Neugebauer, Xavier Darzacq, Yaron Shav-Tal. PLoS Biol 2011
Yehuda Brody, Noa Neufeld, Nicole Bieberstein, Sebastien Z Causse, Eva-Maria Böhnlein, Karla M Neugebauer, Xavier Darzacq, Yaron Shav-Tal. PLoS Biol 2011
11
Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Fernando Carrillo Oesterreich, Stephan Preibisch, Karla M Neugebauer. Mol Cell 2010
Fernando Carrillo Oesterreich, Stephan Preibisch, Karla M Neugebauer. Mol Cell 2010
11
The C-terminal domain of RNA polymerase II couples mRNA processing to transcription.
S McCracken, N Fong, K Yankulov, S Ballantyne, G Pan, J Greenblatt, S D Patterson, M Wickens, D L Bentley. Nature 1997
S McCracken, N Fong, K Yankulov, S Ballantyne, G Pan, J Greenblatt, S D Patterson, M Wickens, D L Bentley. Nature 1997
11
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.
Adam Ameur, Ammar Zaghlool, Jonatan Halvardson, Anna Wetterbom, Ulf Gyllensten, Lucia Cavelier, Lars Feuk. Nat Struct Mol Biol 2011
Adam Ameur, Ammar Zaghlool, Jonatan Halvardson, Anna Wetterbom, Ulf Gyllensten, Lucia Cavelier, Lars Feuk. Nat Struct Mol Biol 2011
11
Born to run: control of transcription elongation by RNA polymerase II.
Fei Xavier Chen, Edwin R Smith, Ali Shilatifard. Nat Rev Mol Cell Biol 2018
Fei Xavier Chen, Edwin R Smith, Ali Shilatifard. Nat Rev Mol Cell Biol 2018
11
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