Coupling mRNA processing with transcription in time and space

Expansion of the eukaryotic proteome by alternative splicing

Nilsen, T. W., & Graveley, B. R. (2010) · Nature · doi:10.1038/nature08909 · Cited by 2,172 · see citing works

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

Mayr, C., & Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.06.016 · Cited by 1,613 · see citing works

Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution

Cramer, P., Bushnell, D. A., & Kornberg, R. D. (2001) · Science · doi:10.1126/science.1059493 · Cited by 1,247 · see citing works

Regulation of Alternative Splicing by Histone Modifications

Luco, R. F., Pan, Q., Tominaga, K., Blencowe, B. J., Pereira‐Smith, O. M., & Misteli, T. (2010) · Science · doi:10.1126/science.1184208 · Cited by 1,099 · see citing works

Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcriptionPreprint

Komarnitsky, P. B., Cho, E., & Buratowski, S. (2000) · Genes & Development · doi:10.1101/gad.824700 · Cited by 1,098 · see citing works

R Loops: From Transcription Byproducts to Threats to Genome Stability

Aguilera, A., & García‐Muse, T. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.04.009 · Cited by 1,029 · see citing works

DNA sequence required for efficient transcription termination in yeast

Zaret, K. S., & Sherman, F. (1982) · Cell · doi:10.1016/0092-8674(82)90211-2 · Cited by 988 · see citing works

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R., & Oberdoerffer, S. (2011) · Nature · doi:10.1038/nature10442 · Cited by 973 · see citing works

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription

McCracken, S. A., Fong, N., Yankulov, K., Ballantyne, S. M., Pan, G., Greenblatt, J., Patterson, S. D., Wickens, M., & Bentley, D. L. (1997) · Nature · doi:10.1038/385357a0 · Cited by 925 · see citing works

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. (2013) · Science · doi:10.1126/science.1229386 · Cited by 849 · see citing works

Nascent transcript sequencing visualizes transcription at nucleotide resolution

Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823 · see citing works

Progression through the RNA Polymerase II CTD Cycle

Buratowski, S. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.10.019 · Cited by 777 · see citing works

RNA processing and its regulation: global insights into biological networks

Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 760 · see citing works

Mechanisms and Consequences of Alternative Polyadenylation

Di Giammartino, D. C., Nishida, K., & Manley, J. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.017 · Cited by 737 · see citing works

The RNA polymerase II CTD coordinates transcription and RNA processingPreprint

Hsin, J.-P., & Manley, J. L. (2012) · Genes & Development · doi:10.1101/gad.200303.112 · Cited by 696 · see citing works

A Slow RNA Polymerase II Affects Alternative Splicing In Vivo

de la Mata, M., Alonso, C. R., Kadener, S., Fededa, J. P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D., & Kornblihtt, A. R. (2003) · Molecular Cell · doi:10.1016/j.molcel.2003.08.001 · Cited by 683 · see citing works

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

Larson, D. R., Zenklusen, D., Wu, B., Chao, J. A., & Singer, R. H. (2011) · Science · doi:10.1126/science.1202142 · Cited by 680 · see citing works

Differential chromatin marking of introns and expressed exons by H3K36me3

Kolasinska-Zwierz, P., Down, T. A., Latorre, I. J., Liu, T., Liu, X. S., & Ahringer, J. (2009) · Nature Genetics · doi:10.1038/ng.322 · Cited by 671 · see citing works

In vivo dynamics of RNA polymerase II transcription

Darzacq, X., Shav-Tal, Y., de Turris, V., Brody, Y., Shenoy, S. M., Phair, R. D., & Singer, R. H. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1280 · Cited by 665 · see citing works

Chromatin organization marks exon-intron structure

Schwartz, S., Meshorer, E., & Ast, G. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1659 · Cited by 638 · see citing works

Recognition of Trimethylated Histone H3 Lysine 4 Facilitates the Recruitment of Transcription Postinitiation Factors and Pre-mRNA Splicing

Sims, R. J., Millhouse, S., Chen, C.-F., Lewis, B. A., Erdjument‐Bromage, H., Tempst, P., Manley, J. L., & Reinberg, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.11.010 · Cited by 581 · see citing works

AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia

Lin, C., Smith, E. R., Takahashi, H., Lai, K. C., Martin‐Brown, S., Florens, L. A., Washburn, M. P., Conaway, J. W., Conaway, R. C., & Shilatifard, A. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.01.026 · Cited by 574 · see citing works

RNA Polymerase II Elongation Control

Zhou, Q., Li, T., & Price, D. H. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052610-095910 · Cited by 568 · see citing works

The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II

Kim, M., Krogan, N. J., Vasiljeva, L., Rando, O. J., Nedea, E. C., Greenblatt, J., & Buratowski, S. (2004) · Nature · doi:10.1038/nature03041 · Cited by 557 · see citing works

5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase IIPreprint

McCracken, S. A., Fong, N., Rosonina, E., Yankulov, K., Brothers, G. M., Siderovski, D. P., Hessel, A., Foster, S., Program, A. E., Shuman, S., et al. (1997) · Genes & Development · doi:10.1101/gad.11.24.3306 · Cited by 548 · see citing works

Splice site selection, rate of splicing, and alternative splicing on nascent transcripts.Preprint

Beyer, A. L., & Osheim, Y. N. (1988) · Genes & Development · doi:10.1101/gad.2.6.754 · Cited by 541 · see citing works

Phosphorylation of Serine 2 within the RNA Polymerase II C-Terminal Domain Couples Transcription and 3′ End Processing

Ahn, S., Kim, M., & Buratowski, S. (2004) · Molecular Cell · doi:10.1016/s1097-2765(03)00492-1 · Cited by 517 · see citing works

A Novel Domain in Set2 Mediates RNA Polymerase II Interaction and Couples Histone H3 K36 Methylation with Transcript Elongation

Kizer, K. O., Phatnani, H. P., Shibata, Y., Hall, H., Greenleaf, A. L., & Strahl, B. D. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.8.3305-3316.2005 · Cited by 511 · see citing works

Rates of in situ transcription and splicing in large human genes

Singh, J., & Padgett, R. A. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1666 · Cited by 487 · see citing works

mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domainPreprint

Cho, E., Takagi, T., Moore, C. R., & Buratowski, S. (1997) · Genes & Development · doi:10.1101/gad.11.24.3319 · Cited by 478 · see citing works

The human SWI/SNF subunit Brm is a regulator of alternative splicing

Batsché, E., Yaniv, M., & Muchardt, C. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1030 · Cited by 471 · see citing works

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

Berg, M. G., Singh, L. N., Younis, I., Liu, Q., Pinto, A. M., Kaida, D., Zhang, Z., Cho, S., Sherrill-Mix, S. A., Wan, L., et al. (2012) · Cell · doi:10.1016/j.cell.2012.05.029 · Cited by 464 · see citing works

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAsPreprint

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C., Chakrabortty, S. K., Djebali, S., Curado, J., Snyder, M. P., Gingeras, T., & Guigó, R. (2012) · Genome Research · doi:10.1101/gr.134445.111 · Cited by 463 · see citing works

Uniform transitions of the general RNA polymerase II transcription complex

Mayer, A., Lidschreiber, M., Siebert, M., Leike, K., Söding, J., & Cramer, P. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1903 · Cited by 446 · see citing works

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

Bhatt, D. M., Pandya‐Jones, A., Tong, A.-J., Barozzi, I., Lissner, M. M., Natoli, G., Black, D. L., & Smale, S. T. (2012) · Cell · doi:10.1016/j.cell.2012.05.043 · Cited by 442 · see citing works

The MO15 cell cycle kinase is associated with the TFIIH transcription-DNA repair factor

Roy, R., Adamczewski, J. P., Seroz, T., Vermeulen, W., Tassan, J., Schaeffer, L., Nigg, E. A., Hoeijmakers, J. H. J., & Egly, J. (1994) · Cell · doi:10.1016/0092-8674(94)90039-6 · Cited by 439 · see citing works

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

Tóth, K. F., Sotirova, V. N., Sachidanandam, R., Gordon, A., Hannon, G. J., Gingeras, T., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., et al. (2009) · Nature · doi:10.1038/nature07759 · Cited by 428 · see citing works

Cracking the RNA polymerase II CTD code

Egloff, S., & Murphy, S. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.03.008 · Cited by 408 · see citing works

CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1Preprint

Bartkowiak, B., Liu, P., Phatnani, H. P., Fuda, N. J., Cooper, J. J., Price, D. H., Adelman, K., Lis, J. T., & Greenleaf, A. L. (2010) · Genes & Development · doi:10.1101/gad.1968210 · Cited by 404 · see citing works

Direct Coupling of Transcription and mRNA Processing through the Thermogenic Coactivator PGC-1

Monsalve, M., Wu, Z., Adelmant, G., Puigserver, P., Fan, M., & Spiegelman, B. M. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)00031-9 · Cited by 395 · see citing works

Primary microRNA transcripts are processed co-transcriptionally

Morlando, M., Ballarino, M., Gromak, N., Pagano, F., Bozzoni, I., & Proudfoot, N. J. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1475 · Cited by 390 · see citing works

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expressionPreprint

Lianoglou, S., Garg, V., Yang, J. L., Leslie, C. S., & Mayr, C. (2013) · Genes & Development · doi:10.1101/gad.229328.113 · Cited by 389 · see citing works

Dynamic association of capping enzymes with transcribing RNA polymerase IIPreprint

Schroeder, S. C., Schwer, B., Shuman, S., & Bentley, D. L. (2000) · Genes & Development · doi:10.1101/gad.836300 · Cited by 387 · see citing works

A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II.Preprint

Connelly, S., & Manley, J. L. (1988) · Genes & Development · doi:10.1101/gad.2.4.440 · Cited by 377 · see citing works

In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes.

Rasmussen, E. B., & Lis, J. T. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.17.7923 · Cited by 369 · see citing works

Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses

Mili, S., & STEITZ, J. A. (2004) · RNA · doi:10.1261/rna.7151404 · Cited by 369 · see citing works

Quality control of mRNA 3′-end processing is linked to the nuclear exosome

Hilleren, P. J., McCarthy, T., Rosbash, M., Parker, R., & Jensen, T. H. (2001) · Nature · doi:10.1038/35097110 · Cited by 364 · see citing works

The splicing factor SC35 has an active role in transcriptional elongation

Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S., & Fu, X. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1461 · Cited by 363 · see citing works

Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA

Aebi, M., Hornig, H., Padgett, R. A., Reiser, J., & Weissmann, C. (1986) · Cell · doi:10.1016/0092-8674(86)90620-3 · Cited by 362 · see citing works

RNA polymerase II is an essential mRNA polyadenylation factor

Hirose, Y., & Manley, J. L. (1998) · Nature · doi:10.1038/25786 · Cited by 359 · see citing works

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

Perales, R., & Bentley, D. L. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.09.018 · Cited by 355 · see citing works

A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II.

Corden, J. L., Cadena, D. L., Ahearn, J. M., & Dahmus, M. E. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.23.7934 · Cited by 354 · see citing works

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

Ji, X., Zhou, Y., Pandit, S., Huang, J. S., Li, H., Lin, C. Y., Xiao, R., Burge, C. B., & Fu, X. (2013) · Cell · doi:10.1016/j.cell.2013.04.028 · Cited by 348 · see citing works

SR Proteins Function in Coupling RNAP II Transcription to Pre-mRNA Splicing

Das, R., Yu, J., Zhang, Z., Gygi, M. P., Krainer, A. R., Gygi, S. P., & Reed, R. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.05.036 · Cited by 346 · see citing works

Functional association between promoter structure and transcript alternative splicing

Cramer, P., Pesce, C. G., Baralle, F. E., & Kornblihtt, A. R. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.21.11456 · Cited by 344 · see citing works

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Glover-Cutter, K. M., Kim, S., Espinosa, J. M., & Bentley, D. L. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1352 · Cited by 343 · see citing works

Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

Pradeepa, M. M., Sutherland, H. G. E., Ule, J., Grimes, G. R., & Bickmore, W. A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002717 · Cited by 342 · see citing works

Cross-Intron Bridging Interactions in the Yeast Commitment Complex Are Conserved in Mammals

Abovich, N., & Rosbash, M. (1997) · Cell · doi:10.1016/s0092-8674(00)80221-4 · Cited by 341 · see citing works

Distinct Roles for CTD Ser-2 and Ser-5 Phosphorylation in the Recruitment and Allosteric Activation of Mammalian mRNA Capping Enzyme

Ho, C. K., & Shuman, S. (1999) · Molecular Cell · doi:10.1016/s1097-2765(00)80468-2 · Cited by 338 · see citing works

The CTD code

Buratowski, S. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb0903-679 · Cited by 334 · see citing works

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., & Kraus, W. L. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.015 · Cited by 333 · see citing works

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

Ameur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L., & Feuk, L. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2143 · Cited by 323 · see citing works

Functional Interaction of Yeast Pre-mRNA 3′ End Processing Factors with RNA Polymerase II

Licatalosi, D. D., Geiger, G., Minet, M., Schroeder, S. C., Cilli, K., McNeil, J. B., & Bentley, D. L. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00518-x · Cited by 316 · see citing works

Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors

Meinhart, A., & Cramer, P. (2004) · Nature · doi:10.1038/nature02679 · Cited by 315 · see citing works

In vitro polyadenylation is stimulated by the presence of an upstream intron.Preprint

Niwa, M., Rose, S. D., & Berget, S. M. (1990) · Genes & Development · doi:10.1101/gad.4.9.1552 · Cited by 314 · see citing works

The mixed-lineage leukemia fusion partner AF4 stimulates RNA polymerase II transcriptional elongation and mediates coordinated chromatin remodeling

Bitoun, E., Oliver, P. L., & Davies, K. E. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl444 · Cited by 311 · see citing works

DNA Damage Regulates Alternative Splicing through Inhibition of RNA Polymerase II Elongation

Muñoz, M. J., Perez-Santángelo, S., Paronetto, M. P., de la Mata, M., Pelisch, F., Boireau, S., Glover-Cutter, K. M., Ben-Dov, C., Blaustein, M., Lozano, J. J., et al. (2009) · Cell · doi:10.1016/j.cell.2009.03.010 · Cited by 310 · see citing works

TFIIH Kinase Places Bivalent Marks on the Carboxy-Terminal Domain of RNA Polymerase II

Akhtar, M. S., Heidemann, M., Tietjen, J. R., Zhang, D. W., Chapman, R. D., Eick, D., & Ansari, A. Z. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.04.016 · Cited by 310 · see citing works

Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells

Listerman, I., Sapra, A. K., & Neugebauer, K. M. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1135 · Cited by 309 · see citing works

Co-transcriptional splicing of constitutive and alternative exons

Pandya‐Jones, A., & Black, D. L. (2009) · RNA · doi:10.1261/rna.1714509 · Cited by 300 · see citing works

Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription

Heidemann, M., Hintermair, C., Voß, K., & Eick, D. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.08.013 · Cited by 300 · see citing works

Identification and analysis of alternative splicing events conserved in human and mouse

Yeo, G. W.-M., Nostrand, E. L. V., Holste, D., Poggio, T., & Burge, C. B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409742102 · Cited by 299 · see citing works

Serine-7 of the RNA Polymerase II CTD Is Specifically Required for snRNA Gene Expression

Egloff, S., O’Reilly, D., Chapman, R. D., Taylor, A., Tanzhaus, K., Pitts, L., Eick, D., & Murphy, S. (2007) · Science · doi:10.1126/science.1145989 · Cited by 294 · see citing works

The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain

Vasiljeva, L., Kim, M., Mutschler, H., Buratowski, S., & Meinhart, A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1468 · Cited by 290 · see citing works

Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion

Girard, C., Will, C. L., Peng, J., Makarov, E. M., Kastner, B., Lemm, I., Urlaub, H., Hartmuth, K., & Lührmann, R. (2012) · Nature Communications · doi:10.1038/ncomms1998 · Cited by 287 · see citing works

Ordered and Dynamic Assembly of Single Spliceosomes

Hoskins, A. A., Friedman, L. J., Gallagher, S. S., Crawford, D. J., Anderson, E. G., Wombacher, R., Ramirez, N., Cornish, V. W., Gelles, J., & Moore, M. J. (2011) · Science · doi:10.1126/science.1198830 · Cited by 279 · see citing works

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

Saint-André, V., Batsché, E., Rachez, C., & Muchardt, C. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1995 · Cited by 278 · see citing works

Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription

Baurén, G., & Wieslander, L. (1994) · Cell · doi:10.1016/0092-8674(94)90182-1 · Cited by 278 · see citing works

Effects of RNA secondary structure on alternative splicing of Pre-mRNA: Is folding limited to a region behind the transcribing RNA polymerase?

Eperon, L. P., Graham, I. R., Griffiths, A. D., & Eperon, I. C. (1988) · Cell · doi:10.1016/0092-8674(88)90202-4 · Cited by 275 · see citing works

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

Schor, I. E., Rascovan, N., Pelisch, F., Alló, M., & Kornblihtt, A. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810666106 · Cited by 270 · see citing works

A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene.

Logan, J., Falck-Pedersen, E., Darnell, J. E., & Shenk, T. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.23.8306 · Cited by 261 · see citing works

CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II

Mayer, A., Heidemann, M., Lidschreiber, M., Schreieck, A., Sun, M., Hintermair, C., Kremmer, E., Eick, D., & Cramer, P. (2012) · Science · doi:10.1126/science.1219651 · Cited by 257 · see citing works

Splicing-Dependent RNA Polymerase Pausing in Yeast

Alexander, R. D., Innocente, S. A., Barrass, J. D., & Beggs, J. D. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.11.005 · Cited by 251 · see citing works

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in <i>Drosophila</i>

Khodor, Y. L., Rodriguez, J., Abruzzi, K. C., Tang, C.-H. A., Marr, M. T., & Rosbash, M. (2011) · Genes &amp; Development · doi:10.1101/gad.178962.111 · Cited by 250 · see citing works

RNA FOLDING DURING TRANSCRIPTION

Pan, T., & Sosnick, T. R. (2006) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.35.040405.102053 · Cited by 244 · see citing works

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

Oesterreich, F. C., Preibisch, S., & Neugebauer, K. M. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.11.004 · Cited by 244 · see citing works

Phosphorylated RNA polymerase II stimulates pre-mRNA splicingPreprint

Hirose, Y., Tacke, R., & Manley, J. L. (1999) · Genes & Development · doi:10.1101/gad.13.10.1234 · Cited by 241 · see citing works

The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIa

Payne, J., Laybourn, P. J., & Dahmus, M. E. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)47159-7 · Cited by 240 · see citing works

FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2Preprint

Schwartz, J. C., Ebmeier, C. C., Podell, E. R., Heimiller, J., Taatjes, D. J., & Cech, T. R. (2012) · Genes & Development · doi:10.1101/gad.204602.112 · Cited by 240 · see citing works

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

de Almeida, S. F., Grosso, A. R., Koch, F., Fenouil, R., Carvalho, S., Andrade, J., Levezinho, H. I. D. S. P., Gut, M., Eick, D., Gut, I. G., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2123 · Cited by 239 · see citing works

Alpha‐thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3′ end processing in the human alpha 2 globin gene.

Whitelaw, E., & Proudfoot, N. J. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04587.x · Cited by 237 · see citing works

Gene-specific RNA polymerase II phosphorylation and the CTD code

Kim, H., Erickson, B., Luo, W., Seward, D. J., Graber, J. H., Pollock, D. D., Megee, P. C., & Bentley, D. L. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1913 · Cited by 235 · see citing works

Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing.

Wuarin, J., & Schibler, U. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.11.7219 · Cited by 233 · see citing works

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargas, D. Y., Shah, K. N., Batish, M., Levandoski, M., Sinha, S., Marras, S. A. E., Schedl, P. D., & Tyagi, S. (2011) · Cell · doi:10.1016/j.cell.2011.10.024 · Cited by 226 · see citing works

Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognitionPreprint

Venkataraman, K., Brown, K. M., & Gilmartin, G. M. (2005) · Genes & Development · doi:10.1101/gad.1298605 · Cited by 223 · see citing works

Phosphorylated Pol II CTD Recruits Multiple HDACs, Including Rpd3C(S), for Methylation-Dependent Deacetylation of ORF Nucleosomes

Govind, C. K., Qiu, H., Ginsburg, D. S., Ruan, C., Hofmeyer, K., Hu, C., Venkatesh, S., Workman, J. L., Li, B., & Hinnebusch, A. G. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.07.003 · Cited by 216 · see citing works

Transcription elongation factor hSPT5 stimulates mRNA cappingPreprint

Wen, Y., & Shatkin, A. J. (1999) · Genes & Development · doi:10.1101/gad.13.14.1774 · Cited by 210 · see citing works

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

Brody, Y., Neufeld, N., Bieberstein, N. I., Causse, S., Böhnlein, E.-M., Neugebauer, K. M., Darzacq, X., & Shav‐Tal, Y. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000573 · Cited by 205 · see citing works

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

Brannan, K. W., Kim, H., Erickson, B., Glover-Cutter, K. M., Kim, S., Fong, N., Kiemele, L., Hansen, K. C., Davis, R. E., Lykke‐Andersen, J., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.03.006 · Cited by 205 · see citing works

Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns.Preprint

Niwa, M., & Berget, S. M. (1991) · Genes & Development · doi:10.1101/gad.5.11.2086 · Cited by 205 · see citing works

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

Bintu, L., Ishibashi, T., Dangkulwanich, M., Wu, Y.-Y., Lubkowska, L., Kashlev, M., & Bustamante, C. (2012) · Cell · doi:10.1016/j.cell.2012.10.009 · Cited by 192 · see citing works

Pre-mRNA splicing is a determinant of histone H3K36 methylation

Kim, S., Kim, H., Fong, N., Erickson, B., & Bentley, D. L. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109475108 · Cited by 192 · see citing works

The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65–Prp19 complexPreprint

David, C. J., Boyne, A. R., Millhouse, S., & Manley, J. L. (2011) · Genes & Development · doi:10.1101/gad.2038011 · Cited by 191 · see citing works

Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition

Czudnochowski, N., Bösken, C. A., & Geyer, M. (2012) · Nature Communications · doi:10.1038/ncomms1846 · Cited by 191 · see citing works

Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II

Mandal, S. S., Chu, C., Wada, T., Handa, H., Shatkin, A. J., & Reinberg, D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401493101 · Cited by 191 · see citing works

The transcriptional cycle of HIV-1 in real-time and live cells

Boireau, S., Maiuri, P., Basyuk, E., de la Mata, M., Knezevich, A., Pradet-Balade, B., Bäcker, V., Kornblihtt, A., Marcello, A., & Bertrand, E. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200706018 · Cited by 191 · see citing works

First Exon Length Controls Active Chromatin Signatures and Transcription

Bieberstein, N. I., Oesterreich, F. C., Straube, K., & Neugebauer, K. M. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.05.019 · Cited by 187 · see citing works

Intronic delay is essential for oscillatory expression in the segmentation clock

Takashima, Y., Ohtsuka, T., González, A., Miyachi, H., & Kageyama, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014418108 · Cited by 182 · see citing works

Updating the RNA polymerase CTD code: adding gene-specific layers

Egloff, S., Dienstbier, M., & Murphy, S. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.03.007 · Cited by 177 · see citing works

Identification of a quality-control mechanism for mRNA 5′-end capping

Jiao, X., Xiang, S., Oh, C., Martin, C. E., Tong, L., & Kiledjian, M. (2010) · Nature · doi:10.1038/nature09338 · Cited by 176 · see citing works

CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae.

Lee, J. M., & Greenleaf, A. L. (1991) · PubMed · Cited by 176 · see citing works

Crystal structure of the human symplekin–Ssu72–CTD phosphopeptide complex

Xiang, K., Nagaike, T., Xiang, S., Kilic, T., Beh, M. M., Manley, J. L., & Tong, L. (2010) · Nature · doi:10.1038/nature09391 · Cited by 171 · see citing works

Interactions between Fission Yeast mRNA Capping Enzymes and Elongation Factor Spt5

Pei, Y., & Shuman, S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200015200 · Cited by 168 · see citing works

Evidence of the Involvement of O-GlcNAc-modified Human RNA Polymerase II CTD in Transcription in Vitro and in Vivo

Ranuncolo, S. M., Ghosh, S. K., Hanover, J. A., Hart, G. W., & Lewis, B. A. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.330910 · Cited by 164 · see citing works

A Mammalian Pre-mRNA 5′ End Capping Quality Control Mechanism and an Unexpected Link of Capping to Pre-mRNA Processing

Jiao, X., Chang, J. H., Kilic, T., Tong, L., & Kiledjian, M. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.017 · Cited by 164 · see citing works

Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells

Lu, S., & Cullen, B. R. (2003) · RNA · doi:10.1261/rna.5260303 · Cited by 163 · see citing works

Mediator Complex Regulates Alternative mRNA Processing via the MED23 Subunit

Huang, Y., Li, W., Xiao, Y., Lin, Q.-J., Yin, J., Liang, Y., Heiner, M., Tian, B., Hui, J., & Wang, G. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.022 · Cited by 160 · see citing works

Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain

Lunde, B. M., Reichow, S., Kim, M., Suh, H., Leeper, T. C., Yang, F., Mutschler, H., Buratowski, S., Meinhart, A., & Varani, G. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1893 · Cited by 160 · see citing works

In Vivo Kinetics of mRNA Splicing and Transport in Mammalian Cells

Audibert, A., Weil, D., & Dautry, F. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.19.6706-6718.2002 · Cited by 149 · see citing works

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolutionPreprint

Windhager, L., Bonfert, T., Burger, K., Ruzsics, Z., Krebs, S., Kaufmann, S., Malterer, G., L’Hernault, A., Schilhabel, M. B., Schreiber, S., et al. (2012) · Genome Research · doi:10.1101/gr.131847.111 · Cited by 147 · see citing works

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

Braberg, H., Jin, H., Moehle, E. A., Chan, Y. A., Wang, S., Shales, M., Benschop, J. J., Morris, J. H., Qiu, C., Hu, F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.033 · Cited by 143 · see citing works

Functional interactions between the transcription and mRNA 3′ end processing machineries mediated by Ssu72 and Sub1Preprint

He, X., Khan, A. U., Cheng, H.-L. M., Pappas, D. L., Hampsey, M., & Moore, C. L. (2003) · Genes & Development · doi:10.1101/gad.1075203 · Cited by 143 · see citing works

Tat Stimulates Cotranscriptional Capping of HIV mRNA

Chiu, Y., Ho, C. K., Saha, N., Schwer, B., Shuman, S., & Rana, T. M. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00630-5 · Cited by 140 · see citing works

Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner

Zhou, H.-L., Hinman, M. N., Barron, V. A., Geng, C., Zhou, G., Luo, G., Siegel, R. E., & Lou, H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103344108 · Cited by 136 · see citing works

RNA polymerase II kinetics in polo polyadenylation signal selection

Pinto, P. A. B., Henriques, T., Freitas, M. O., Martins, T., Domingues, R. G., Wyrzykowska, P. S., Coelho, P. A., Carmo, A. M., Sunkel, C. E., Proudfoot, N. J., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.156 · Cited by 136 · see citing works

Deciphering the RNA Polymerase II CTD Code in Fission Yeast

Schwer, B., & Shuman, S. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.05.024 · Cited by 135 · see citing works

Transcription of herpes simplex virus tk sequences under the control of wild-type and mutant human RNA polymerase I promoters.

Smale, S. T., & Tjian, R. (1985) · Molecular and Cellular Biology · doi:10.1128/mcb.5.2.352 · Cited by 134 · see citing works

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

Hazelbaker, D. Z., Marquardt, S., Wlotzka, W., & Buratowski, S. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.10.014 · Cited by 128 · see citing works

RNA Polymerase II Carboxy-Terminal Domain Phosphorylation Is Required for Cotranscriptional Pre-mRNA Splicing and 3′-End Formation

Bird, G. A., Zorio, D. A. R., & Bentley, D. L. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.20.8963-8969.2004 · Cited by 126 · see citing works

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

Khodor, Y. L., Menet, J. S., Tolan, M., & Rosbash, M. (2012) · RNA · doi:10.1261/rna.034090.112 · Cited by 126 · see citing works

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

Ehrensberger, A. H., Kelly, G. P., & Svejstrup, J. Q. (2013) · Cell · doi:10.1016/j.cell.2013.07.032 · Cited by 125 · see citing works

Expanding the Functional Repertoire of CTD Kinase I and RNA Polymerase II: Novel PhosphoCTD-Associating Proteins in the Yeast Proteome

Phatnani, H. P., Jones, J. C., & Greenleaf, A. L. (2004) · Biochemistry · doi:10.1021/bi048364h · Cited by 123 · see citing works

Identification of a Cytoplasmic Complex That Adds a Cap onto 5′-Monophosphate RNA

Otsuka, Y., Kedersha, N., & Schoenberg, D. R. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01325-08 · Cited by 121 · see citing works

Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation

Schmidt, U., Basyuk, E. I., Robert, M.-C., Yoshida, M., Villemin, J.-P., Auboeuf, D., Aitken, S., & Bertrand, É. (2011) · The Journal of Cell Biology · doi:10.1083/jcb.201009012 · Cited by 119 · see citing works

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

Rodriguez, J., Menet, J. S., & Rosbash, M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.002 · Cited by 119 · see citing works

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

Close, P., East, P., Dirac-Svejstrup, A. B., Hartmann, H., Heron, M., Maslen, S., Chariot, A., Söding, J., Skehel, M., & Svejstrup, J. Q. (2012) · Nature · doi:10.1038/nature10925 · Cited by 119 · see citing works

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

Zamft, B., Bintu, L., Ishibashi, T., & Bustamante, C. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205063109 · Cited by 117 · see citing works

Transcriptional Activators Enhance Polyadenylation of mRNA Precursors

Nagaike, T., Logan, C. J., Hotta, I., Rozenblatt–Rosen, O., Meyerson, M. M., & Manley, J. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.01.022 · Cited by 116 · see citing works

Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation.

Sisodia, S. S., Sollner-Webb, B., & Cleveland, D. W. (1987) · Molecular and Cellular Biology · doi:10.1128/mcb.7.10.3602 · Cited by 115 · see citing works

Positive patches and negative noodles: linking RNA processing to transcription?

Greenleaf, A. L. (1993) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(93)90016-g · Cited by 115 · see citing works

First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal

de la Mata, M., Lafaille, C., & Kornblihtt, A. R. (2010) · RNA · doi:10.1261/rna.1993510 · Cited by 115 · see citing works

CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo

Gu, B., Eick, D., & Bensaude, O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1327 · Cited by 114 · see citing works

A Genome-Wide Analysis Indicates that Yeast Pre-mRNA Splicing Is Predominantly Posttranscriptional

Tardiff, D. F., Lacadie, S. A., & Rosbash, M. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.12.002 · Cited by 114 · see citing works

Deciphering 3′ss Selection in the Yeast Genome Reveals an RNA Thermosensor that Mediates Alternative Splicing

Meyer, M., Plass, M., Pérez‐Valle, J., Eyras, E., & Vilardell, J. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.07.030 · Cited by 113 · see citing works

Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1Preprint

Kubíček, K., Cerná, H., Holub, P., Pasulka, J., Hroššová, D., Loehr, F., Hofr, C., Vaňáčová, Š., & Štefl, R. (2012) · Genes & Development · doi:10.1101/gad.192781.112 · Cited by 109 · see citing works

Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture

Darnell, J. E., Jr. (2013) · RNA · doi:10.1261/rna.038596.113 · Cited by 109 · see citing works

Counting on co-transcriptional splicing

Brugiolo, M., Herzel, L., & Neugebauer, K. M. (2013) · F1000Prime Reports · doi:10.12703/p5-9 · Cited by 108 · see citing works

Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression

Pandya‐Jones, A., Bhatt, D. M., Lin, C.-H., Tong, A.-J., Smale, S. T., & Black, D. L. (2013) · RNA · doi:10.1261/rna.039081.113 · Cited by 106 · see citing works

A pause site for RNA polymerase II is associated with termination of transcription.

Enriquez-Harris, P., Levitt, N. C., Briggs, D., & Proudfoot, N. J. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07709.x · Cited by 105 · see citing works

Dxo1 is a new type of eukaryotic enzyme with both decapping and 5′-3′ exoribonuclease activity

Chang, J. H., Jiao, X., Chiba, K., Oh, C., Martin, C. E., Kiledjian, M., & Tong, L. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2381 · Cited by 105 · see citing works

The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells

Huranová, M., Ivani, I., Benda, A., Poser, I., Brody, Y., Hof, M., Shav‐Tal, Y., Neugebauer, K. M., & Staněk, D. (2010) · The Journal of Cell Biology · doi:10.1083/jcb.201004030 · Cited by 103 · see citing works

Structural Insights to How Mammalian Capping Enzyme Reads the CTD Code

Ghosh, A., Shuman, S., & Lima, C. D. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.001 · Cited by 99 · see citing works

Conformational dynamics of single pre-mRNA molecules during in vitro splicing

Abelson, J. N., Blanco, M. R., Ditzler, M. A., Fuller, F. D., Aravamudhan, P., Wood, M. L., Villa, T., Ryan, D. E., Pleiss, J. A., Maeder, C., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1767 · Cited by 97 · see citing works

Co‐transcriptional degradation of aberrant pre‐mRNA by Xrn2

Davidson, L., Kerr, A. R. W., & West, S. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.101 · Cited by 93 · see citing works

RNA splicing regulates the temporal order of TNF-induced gene expression

Hao, S., & Baltimore, D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309990110 · Cited by 91 · see citing works

Transcriptional elongation and alternative splicing

Dujardin, G., Lafaille, C., Petrillo, E., Buggiano, V., Acuña, L. I. G., Fiszbein, A., Herz, M. A. G., Moreno, N. N., Muñoz, M. J., Alló, M., et al. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.08.005 · Cited by 91 · see citing works

Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3′-end formation and excision of the 3′-terminal intronPreprint

Baurén, G., Belikov, S. V., & Wieslander, L. (1998) · Genes & Development · doi:10.1101/gad.12.17.2759 · Cited by 88 · see citing works

Cap-binding Protein Complex Links Pre-mRNA Capping to Transcription Elongation and Alternative Splicing through Positive Transcription Elongation Factor b (P-TEFb)

Lenasi, T., Peterlin, B. M., & Barborič, M. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.235077 · Cited by 87 · see citing works

Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4–Spt5/DSIF promotes mRNA localization to the yeast budPreprint

Shen, Z., St‐Denis, A., & Chartrand, P. (2010) · Genes & Development · doi:10.1101/gad.1937510 · Cited by 86 · see citing works

The export factor Yra1 modulates mRNA 3′ end processing

Johnson, S. A., Kim, H., Erickson, B., & Bentley, D. L. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2126 · Cited by 84 · see citing works

Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes

Martins, S., Rino, J., Carvalho, T., Carvalho, C., Yoshida, M., Klose, J. M., de Almeida, S. F., & Carmo‐Fonseca, M. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2124 · Cited by 80 · see citing works

The CTD code of RNA polymerase II: a structural view

Jasnovidova, O., & Štefl, R. (2012) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1138 · Cited by 78 · see citing works

Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements

Gunderson, F. Q., Merkhofer, E., & Johnson, T. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011982108 · Cited by 75 · see citing works

Transcription goes digital

Lionnet, T., & Singer, R. H. (2012) · EMBO Reports · doi:10.1038/embor.2012.31 · Cited by 73 · see citing works

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center

Batada, N. N., Westover, K. D., Bushnell, D. A., Levitt, M., & Kornberg, R. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408168101 · Cited by 72 · see citing works

An active role for splicing in 3′‐end formation

Martinson, H. G. (2010) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.68 · Cited by 68 · see citing works

Functional roles of protein splicing factors

Chen, H.-C., & Cheng, S.-C. (2012) · Bioscience Reports · doi:10.1042/bsr20120007 · Cited by 67 · see citing works

A Function of Yeast mRNA Cap Methyltransferase, Abd1, in Transcription by RNA Polymerase II

Schroeder, S. C., Zorio, D. A. R., Schwer, B., Shuman, S., & Bentley, D. L. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00007-3 · Cited by 67 · see citing works

Transcriptional Activators Control Splicing and 3′-End Cleavage Levels

Rosonina, E., Bakowski, M. A., McCracken, S. A., & Blencowe, B. J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m307289200 · Cited by 66 · see citing works

Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells

Spiluttini, B., Gu, B., Belagal, P., Henriques, A. S., Nguyen, V. T., Hébert, C., Schmidt, U., Bertrand, É., Darzacq, X., & Bensaude, O. (2010) · Journal of Cell Science · doi:10.1242/jcs.061358 · Cited by 63 · see citing works

A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination

de Almeida, S. F., García-Sacristán, A., Custódio, N., & Carmo‐Fonseca, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq703 · Cited by 62 · see citing works

S-Adenosyl Homocysteine Hydrolase Is Required for Myc-Induced mRNA Cap Methylation, Protein Synthesis, and Cell Proliferation

Fernández-Sánchez, M. E., Gonatopoulos-Pournatzis, T., Preston, G., Lawlor, M. A., & Cowling, V. H. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00973-09 · Cited by 62 · see citing works

Connections between chromatin signatures and splicing

Acuña, L. I. G., Fiszbein, A., Alló, M., Schor, I. E., & Kornblihtt, A. R. (2012) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1142 · Cited by 54 · see citing works

Newly Initiated RNA Encounters a Factor Involved in Splicing Immediately upon Emerging from within RNA Polymerase II

Újvári, A., & Luse, D. S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409087200 · Cited by 52 · see citing works

Cotranscriptional folding kinetics of ribonucleic acid secondary structures

Zhao, P., Zhang, W., & Chen, S. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3671644 · Cited by 52 · see citing works

Ribozyme Cleavage Reveals Connections between mRNA Release from the Site of Transcription and Pre-mRNA Processing

Bird, G. A., Fong, N., Gatlin, J. C., Farabaugh, S., & Bentley, D. L. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.11.009 · Cited by 52 · see citing works

The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript

Ryman, K., Fong, N., Bratt, E., Bentley, D. L., & Öhman, M. (2007) · RNA · doi:10.1261/rna.404407 · Cited by 50 · see citing works

Punctuation and syntax of the RNA polymerase II CTD code in fission yeast

Schwer, B., Sánchez, A. M., & Shuman, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208995109 · Cited by 49 · see citing works

fus/TLS orchestrates splicing of developmental regulators during gastrulationPreprint

Dichmann, D. S., & Harland, R. M. (2012) · Genes & Development · doi:10.1101/gad.187278.112 · Cited by 45 · see citing works

Splice-Site Mutations Cause Rrp6-Mediated Nuclear Retention of the Unspliced RNAs and Transcriptional Down-Regulation of the Splicing-Defective Genes

Eberle, A. B., Hessle, V., Helbig, R., Dantoft, W., Gimber, N., & Visa, N. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011540 · Cited by 44 · see citing works

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

Benson, M. J., Äijö, T., Chang, X., Gagnon, J. D., Pape, U. J., Anantharaman, V., Aravind, L., Pursiheimo, J., Oberdoerffer, S., Liu, X. S., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1214414109 · Cited by 42 · see citing works

An RNA Polymerase Pause Site Is Associated with the Immunoglobulin μs Poly(A) Site

Peterson, M. L., Bertolino, S., & Davis, F. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.15.5606-5615.2002 · Cited by 40 · see citing works

The RNA Tether from the Poly(A) Signal to the Polymerase Mediates Coupling of Transcription to Cleavage and Polyadenylation

Rigo, F., Kazerouninia, A., Nag, A., & Martinson, H. G. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.09.026 · Cited by 34 · see citing works

A Dual Interface Determines the Recognition of RNA Polymerase II by RNA Capping Enzyme*

Suh, M.-H., Meyer, P. A., Gu, M., Ye, P., Zhang, M., Kaplan, C. D., Lima, C. D., & Fu, J. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.145110 · Cited by 33 · see citing works

Definition of RNA Polymerase II CoTC Terminator Elements in the Human Genome

Nojima, T., Dienstbier, M., Murphy, S., Proudfoot, N. J., & Dye, M. J. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.03.012 · Cited by 32 · see citing works

Promoter-proximal polyadenylation sites reduce transcription activityPreprint

Andersen, P. K., Lykke‐Andersen, S., & Jensen, T. H. (2012) · Genes & Development · doi:10.1101/gad.189126.112 · Cited by 32 · see citing works

RNA Polymerase II C-Terminal Domain Phosphorylation Patterns in Caenorhabditis elegans Operons, Polycistronic Gene Clusters with Only One Promoter

Garrido‐Lecca, A., & Blumenthal, T. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00325-10 · Cited by 17 · see citing works

The biogenesis, biology and characterization of circular RNAs

Kristensen, L. S., Andersen, M. S., Stagsted, L. V. W., Ebbesen, K. K., Hansen, T. B., & Kjems, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0158-7 · Cited by 4,823 · see citing works

circRNA biogenesis competes with pre-mRNA splicing

Ashwal-Fluss, R., Meyer, M., Pamudurti, N. R., Ivanov, A., Bartok, O., Hanan, M., Evantal, N., Memczak, S., Rajewsky, N., & Kadener, S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.019 · Cited by 3,083 · see citing works

The Biogenesis, Functions, and Challenges of Circular RNAs

Li, X., Yang, L. C., & Chen, L. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.034 · Cited by 2,043 · see citing works

The biogenesis and emerging roles of circular RNAs

Chen, L.-L. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.32 · Cited by 1,743 · see citing works

mRNAs, proteins and the emerging principles of gene expression control

Buccitelli, C., & Selbach, M. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0258-4 · Cited by 1,243 · see citing works

Context-dependent control of alternative splicing by RNA-binding proteins

Fu, X.-D., & Ares, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3778 · Cited by 1,044 · see citing works

mRNA-based therapeutics: powerful and versatile tools to combat diseases

Qin, S., Tang, X., Chen, Y., Chen, K., Fan, N., Xiao, W., Zheng, Q., Li, G., Teng, Y., Wu, M., et al. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01007-w · Cited by 801 · see citing works

Organization and regulation of gene transcription

Cramer, P. (2019) · Nature · doi:10.1038/s41586-019-1517-4 · Cited by 732 · see citing works

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

Li, W., Notani, D., & Rosenfeld, M. G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.4 · Cited by 710 · see citing works

The Biogenesis of Nascent Circular RNAs

Zhang, Y., Xue, W., Li, X., Zhang, J., Chen, S., Zhang, J.-L., Yang, L., & Chen, L.-L. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.03.058 · Cited by 643 · see citing works

Transcription regulation by the Mediator complex

Soutourina, J. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.115 · Cited by 591 · see citing works

A survey of the sorghum transcriptome using single-molecule long reads

Abdel‐Ghany, S. E., Hamilton, M., Jacobi, J. L., Ngam, P. B., Devitt, N. P., Schilkey, F., Ben‐Hur, A., & Reddy, A. S. N. (2016) · Nature Communications · doi:10.1038/ncomms11706 · Cited by 595 · see citing works

Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA lossPreprint

Arun, G., Diermeier, S. D., Akerman, M., Chang, K.-C., Wilkinson, J. E., Hearn, S., Kim, Y., MacLeod, A. R., Krainer, A. R., Norton, L., et al. (2015) · Genes & Development · doi:10.1101/gad.270959.115 · Cited by 586 · see citing works

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

Harlen, K. M., & Churchman, L. S. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.10 · Cited by 499 · see citing works

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

Weirather, J. L., de Cesare, M., Wang, Y., Piazza, P., Sebastiano, V., Wang, X., Buck, D., & Au, K. F. (2017) · F1000Research · doi:10.12688/f1000research.10571.2 · Cited by 483 · see citing works

Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis

Velthuis, A. J. W. T., & Fodor, E. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.87 · Cited by 479 · see citing works

Insights into circular RNA biology

Ebbesen, K. K., Hansen, T. B., & Kjems, J. (2016) · RNA Biology · doi:10.1080/15476286.2016.1271524 · Cited by 454 · see citing works

Born to run: control of transcription elongation by RNA polymerase II

Chen, F. X., Smith, E. R., & Shilatifard, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0010-5 · Cited by 447 · see citing works

The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting

Liang, D., Tatomer, D. C., Luo, Z., Wu, H., Yang, L. C., Chen, L., Cherry, S. R., & Wilusz, J. E. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.034 · Cited by 435 · see citing works

Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

Nojima, T., & Proudfoot, N. J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00447-6 · Cited by 424 · see citing works

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

Xiao, R., Chen, J., Liang, Z., Luo, D., Chen, G., Lu, Z. J., Chen, Y., Zhou, B., Li, H., Du, X., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.001 · Cited by 378 · see citing works

RNA promotes the formation of spatial compartments in the nucleus

Quinodoz, S. A., Jachowicz, J. W., Bhat, P., Ollikainen, N., Banerjee, A. K., Goronzy, I. N., Blanco, M. R., Chovanec, P., Chow, A. Y., Markaki, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.10.014 · Cited by 384 · see citing works

Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG

Zhou, K. I., Shi, H., Lyu, R., Wylder, A. C., Matuszek, Ż., Pan, J. N., He, C., Parisien, M., & Pan, T. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.005 · Cited by 385 · see citing works

The Diversity of Long Noncoding RNAs and Their Generation

Wu, H., Yang, L. C., & Chen, L. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.004 · Cited by 378 · see citing works

Polyglutamine spinocerebellar ataxias — from genes to potential treatments

Paulson, H. L., Shakkottai, V. G., Clark, H. B., & Orr, H. T. (2017) · Nature reviews. Neuroscience · doi:10.1038/nrn.2017.92 · Cited by 376 · see citing works

Enhancer RNAs are an important regulatory layer of the epigenome

Sartorelli, V., & Lauberth, S. M. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0446-0 · Cited by 367 · see citing works

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., Sandstrom, R., Stamatoyannopoulos, J. A., & Churchman, L. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.010 · Cited by 367 · see citing works

MYC protein interactors in gene transcription and cancer

Lourenco, C., Resetca, D., Redel, C., Lin, P., MacDonald, A. S., Ciaccio, R., Kenney, T. M. G., Wei, Y., Andrews, D. W., Sunnerhagen, M., et al. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00367-9 · Cited by 341 · see citing works

Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

de Klerk, E., & ‘t Hoen, P. A. C. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.01.001 · Cited by 350 · see citing works

The FLC Locus: A Platform for Discoveries in Epigenetics and Adaptation

Whittaker, C., & Dean, C. (2017) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100616-060546 · Cited by 344 · see citing works

Evolution and Biological Roles of Alternative 3′UTRs

Mayr, C. (2015) · Trends in Cell Biology · doi:10.1016/j.tcb.2015.10.012 · Cited by 329 · see citing works

CDK12 regulates DNA repair genes by suppressing intronic polyadenylation

Dubbury, S. J., Boutz, P. L., & Sharp, P. A. (2018) · Nature · doi:10.1038/s41586-018-0758-y · Cited by 318 · see citing works

The role of alternative splicing in cancer: From oncogenesis to drug resistance

Sciarrillo, R., Wojtuszkiewicz, A., Assaraf, Y. G., Jansen, G., Kaspers, G. J. L., Giovannetti, E., & Cloos, J. J. (2020) · Drug Resistance Updates · doi:10.1016/j.drup.2020.100728 · Cited by 311 · see citing works

Biogenesis and Regulatory Roles of Circular RNAs

Yang, L. C., Wilusz, J. E., & Chen, L. (2022) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-125117 · Cited by 303 · see citing works

Proteomic and interactomic insights into the molecular basis of cell functional diversity

Bludau, I., & Aebersold, R. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0231-2 · Cited by 297 · see citing works

The multiple functions of RNA helicases as drivers and regulators of gene expression

Bourgeois, C. F., Mortreux, F., & Auboeuf, D. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.50 · Cited by 284 · see citing works

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

Fong, N., Kim, H., Zhou, Y., Ji, X., Qiu, J., Saldi, T., Diener, K., Jones, K., Fu, X.-D., & Bentley, D. L. (2014) · Genes &amp; Development · doi:10.1101/gad.252106.114 · Cited by 287 · see citing works

SR Proteins: Binders, Regulators, and Connectors of RNA

Jeong-Yu, S. (2017) · Molecules and Cells · doi:10.14348/molcells.2017.2319 · Cited by 270 · see citing works

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

Leung, M. K. K., Delong, A., Alipanahi, B., & Frey, B. J. (2015) · Proceedings of the IEEE · doi:10.1109/jproc.2015.2494198 · Cited by 276 · see citing works

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

Krajewska, M., Dries, R., Grassetti, A. V., Dust, S., Gao, Y., Huang, H., Sharma, B., Day, D. S., Kwiatkowski, N., Pomaville, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09703-y · Cited by 281 · see citing works

Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects

Rogalska, M. E., Vivori, C., & Valcárcel, J. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00556-8 · Cited by 269 · see citing works

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

Saldi, T. K., Cortázar, M. A., Sheridan, R. M., & Bentley, D. L. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.04.017 · Cited by 246 · see citing works

Going circular: history, present, and future of circRNAs in cancer

Pisignano, G., Michael, D. C., Visal, T. H., Pîrlog, R., Ladomery, M., & Călin, G. A. (2023) · Oncogene · doi:10.1038/s41388-023-02780-w · Cited by 258 · see citing works

Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency

Louloupi, A., Ntini, E., Conrad, T., & Ørom, U. A. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.077 · Cited by 233 · see citing works

Control of mammalian gene expression by selective mRNA export

Wickramasinghe, V. O., & Laskey, R. A. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4010 · Cited by 230 · see citing works

Chromatin-associated RNAs as facilitators of functional genomic interactions

Li, X., & Fu, X. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0135-1 · Cited by 229 · see citing works

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

Drexler, H. L., Choquet, K., & Churchman, L. S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.11.017 · Cited by 234 · see citing works

Nanopore Technology and Its Applications in Gene Sequencing

Lin, B., Hui, J., & Mao, H. (2021) · Biosensors · doi:10.3390/bios11070214 · Cited by 230 · see citing works

BS69/ZMYND11 Reads and Connects Histone H3.3 Lysine 36 Trimethylation-Decorated Chromatin to Regulated Pre-mRNA Processing

Guo, R., Zheng, L., Park, J. W., Lyu, R., Chen, H., Jiao, F., Xu, W., Mu, S.-R., Wen, H., Qiu, J., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.022 · Cited by 229 · see citing works

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon, A., Ferguson, M., de Turris, V., Palangat, M., Chow, C. C., & Larson, D. R. (2014) · eLife · doi:10.7554/elife.03939 · Cited by 228 · see citing works

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

Cortazar, M. A., Sheridan, R. M., Erickson, B., Fong, N., Glover-Cutter, K., Brannan, K., & Bentley, D. L. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.031 · Cited by 227 · see citing works

Transcription-mediated replication hindrance: a major driver of genome instabilityPreprint

Gómez‐González, B., & Aguilera, A. (2019) · Genes & Development · doi:10.1101/gad.324517.119 · Cited by 225 · see citing works

Transcription in Living Cells: Molecular Mechanisms of Bursting

Rodriguez, J., & Larson, D. R. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011520-105250 · Cited by 224 · see citing works

Roles of circular RNAs in immune regulation and autoimmune diseases

Zhou, Z. G., Sun, B., Huang, S., & Zhao, L. (2019) · Cell Death and Disease · doi:10.1038/s41419-019-1744-5 · Cited by 223 · see citing works

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

Bogard, N., Linder, J., Rosenberg, A. B., & Seelig, G. (2019) · Cell · doi:10.1016/j.cell.2019.04.046 · Cited by 215 · see citing works

Defective control of pre–messenger RNA splicing in human disease

Chabot, B., & Shkreta, L. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201510032 · Cited by 209 · see citing works

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

Voong, L. N., Xi, L., Sebeson, A. C., Xiong, B., Wang, J., & Wang, X. (2016) · Cell · doi:10.1016/j.cell.2016.10.049 · Cited by 203 · see citing works

Ageing-associated changes in transcriptional elongation influence longevity

Debès, C., Papadakis, A., Grönke, S., Karalay, Ö., Tain, L. S., Mizi, A., Nakamura, S., Hahn, O., Weigelt, C. M., Josipović, N., et al. (2023) · Nature · doi:10.1038/s41586-023-05922-y · Cited by 209 · see citing works

RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

Muniz, L., Nicolas, E., & Trouche, D. (2021) · The EMBO Journal · doi:10.15252/embj.2020105740 · Cited by 203 · see citing works

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

Hage, A. E., Webb, S., Kerr, A. R. W., & Tollervey, D. W. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004716 · Cited by 203 · see citing works

Functions and clinical significance of circular RNAs in glioma

Sun, J., Li, B., Shu, C., Ma, Q., & Wang, J. (2020) · Molecular Cancer · doi:10.1186/s12943-019-1121-0 · Cited by 196 · see citing works

Transcription Dynamics in Living Cells

Lenstra, T. L., Rodriguez, J., Chen, H., & Larson, D. R. (2016) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010838 · Cited by 179 · see citing works

Targeting mRNA processing as an anticancer strategy

Desterro, J. M. P., Bak‐Gordon, P., & Carmo‐Fonseca, M. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0042-3 · Cited by 180 · see citing works

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

Reimer, K. A., Mimoso, C. A., Adelman, K., & Neugebauer, K. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.018 · Cited by 180 · see citing works

Noncoding RNA and its associated proteins as regulatory elements of the immune system

Turner, M., Galloway, A., & Vigorito, E. (2014) · Nature Immunology · doi:10.1038/ni.2887 · Cited by 172 · see citing works

THZ1 Reveals Roles for Cdk7 in Co-transcriptional Capping and Pausing

Nilson, K. A., Guo, J., Turek, M. E., Brogie, J. E., Delaney, E., Luse, D. S., & Price, D. H. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.032 · Cited by 170 · see citing works

RNA editing in nascent RNA affects pre-mRNA splicingPreprint

Hsiao, Y.-H. E., Bahn, J. H., Yang, Y., Lin, X., Tran, S. S., Yang, E.-W., Quinones-Valdez, G., & Xiao, X. G. (2018) · Genome Research · doi:10.1101/gr.231209.117 · Cited by 166 · see citing works

The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3′ processing

Abe, K., Yamamoto, R., Franke, V., Cao, M., Suzuki, Y., Suzuki, M. G., Vlahoviček, K., Svoboda, P., Schultz, R. M., & Aoki, F. (2015) · The EMBO Journal · doi:10.15252/embj.201490648 · Cited by 166 · see citing works

The core promoter: At the heart of gene expression

Danino, Y. M., Even, D. Y., Ideses, D., & Juven‐Gershon, T. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.04.003 · Cited by 161 · see citing works

The RNA Splicing Response to DNA Damage

Shkreta, L., & Chabot, B. (2015) · Biomolecules · doi:10.3390/biom5042935 · Cited by 154 · see citing works

Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

Licht, K., & Jantsch, M. F. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201511041 · Cited by 153 · see citing works

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

Harlen, K. M., Trotta, K. L., Smith, E. E., Mosaheb, M. M., Fuchs, S. M., & Churchman, L. S. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.05.010 · Cited by 150 · see citing works

Heptad-Specific Phosphorylation of RNA Polymerase II CTD

Schüller, R., Forné, I., Straub, T., Schreieck, A., Texier, Y., Shah, N., Decker, T.-M., Cramer, P., Imhof, A., & Eick, D. (2016) · Molecular Cell · doi:10.1016/j.molcel.2015.12.003 · Cited by 150 · see citing works

Transcriptional Signatures of Aging

Stegeman, R., & Weake, V. M. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.06.019 · Cited by 146 · see citing works

Regulation of RNA editing by RNA-binding proteins in human cells

Quinones-Valdez, G., Tran, S. S., Jun, H.-I., Bahn, J. H., Yang, E.-W., Zhan, L., Brümmer, A., Wei, X., Nostrand, E. L. V., Pratt, H., et al. (2019) · Communications Biology · doi:10.1038/s42003-018-0271-8 · Cited by 142 · see citing works

The RNAs of RNA-directed DNA methylation

Wendte, J. M., & Pikaard, C. S. (2017) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.08.004 · Cited by 140 · see citing works

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins

Gregersen, L. H., Mitter, R., Ugalde, A. P., Nojima, T., Proudfoot, N. J., Agami, R., Stewart, A., & Svejstrup, J. Q. (2019) · Cell · doi:10.1016/j.cell.2019.04.038 · Cited by 140 · see citing works

Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants

Jia, J., Long, Y., Zhang, H., Li, Z., Liu, Z., Zhao, Y., Lu, D., Jin, X., Deng, X. M., Xia, R., et al. (2020) · Nature Plants · doi:10.1038/s41477-020-0688-1 · Cited by 140 · see citing works

Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle

Kinouchi, K., Magnan, C., Ceglia, N., Liu, Y., Cervantes, M., Pastore, N., Huynh, T., Ballabio, A., Baldi, P., Masri, S., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.077 · Cited by 130 · see citing works

The RNA Polymerase II CTD: The Increasing Complexity of a Low-Complexity Protein Domain

Jerónimo, C., Collin, P., & Robert, F. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.02.006 · Cited by 136 · see citing works

Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation

Gehring, N. H., & Roignant, J. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.10.008 · Cited by 134 · see citing works

Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development

Tang, S. J., Shen, H., An, Ö., Hong, H., Li, J., Song, Y., Han, J., Tay, D. J. T., Ng, V. H. E., Molías, F. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14621-5 · Cited by 134 · see citing works

Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb

Quaresma, A. J. C., Bugai, A., & Barborič, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw585 · Cited by 131 · see citing works

FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP

Yu, Y., & Reed, R. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1506282112 · Cited by 127 · see citing works

Deciphering the mRNP Code: RNA-Bound Determinants of Post-Transcriptional Gene Regulation

Gehring, N. H., Wahle, E., & Fischer, U. (2017) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2017.02.004 · Cited by 127 · see citing works

An oomycete plant pathogen reprograms host pre-mRNA splicing to subvert immunity

Huang, J., Gu, L., Zhang, Y., Yan, T., Kong, G., Kong, L., Guo, B., Qiu, M., Wang, Y., Jing, M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-02233-5 · Cited by 125 · see citing works

DNA methylation directs microRNA biogenesis in mammalian cells

Glaich, O., Parikh, S., Bell, R. E., Mekahel, K., Donyo, M., Leader, Y., Shayevitch, R., Sheinboim, D., Yannai, S., Hollander, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13527-1 · Cited by 124 · see citing works

The life and times of a tRNA

Phizicky, E. M., & Hopper, A. K. (2023) · RNA · doi:10.1261/rna.079620.123 · Cited by 120 · see citing works

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

Sheridan, R. M., Fong, N., D’Alessandro, A., & Bentley, D. L. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.10.031 · Cited by 123 · see citing works

Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination

Lai, F., Damle, S. S., Ling, K., & Rigo, F. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.029 · Cited by 122 · see citing works

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Anvar, S. Y., Allard, G., Tseng, E., Sheynkman, G. M., de Klerk, E., Vermaat, M., Yin, R. H., Johansson, H. E., Ariyurek, Y., den Dunnen, J. T., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1418-0 · Cited by 118 · see citing works

Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences

Heyn, P. C., Kalinka, A. T., Tomančák, P., & Neugebauer, K. M. (2014) · BioEssays · doi:10.1002/bies.201400138 · Cited by 115 · see citing works

Circular RNAs: Unexpected outputs of many protein-coding genes

Wilusz, J. E. (2016) · RNA Biology · doi:10.1080/15476286.2016.1227905 · Cited by 112 · see citing works

Mechanisms by which HPV Induces a Replication Competent Environment in Differentiating Keratinocytes

Moody, C. A. (2017) · Viruses · doi:10.3390/v9090261 · Cited by 114 · see citing works

Long-read sequencing of nascent RNA reveals coupling among RNA processing eventsPreprint

Herzel, L., Straube, K., & Neugebauer, K. M. (2018) · Genome Research · doi:10.1101/gr.232025.117 · Cited by 107 · see citing works

The DDX5/Dbp2 subfamily of DEAD‐box RNA helicases

Xing, Z., Ma, W. K., & Tran, E. J. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1519 · Cited by 108 · see citing works

RNA Processing and Genome Stability: Cause and Consequence

Wickramasinghe, V. O., & Venkitaraman, A. R. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.001 · Cited by 107 · see citing works

A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences

Linder, J., Bogard, N., Rosenberg, A. B., & Seelig, G. (2020) · Cell Systems · doi:10.1016/j.cels.2020.05.007 · Cited by 107 · see citing works

Keratinocyte Differentiation-Dependent Human Papillomavirus Gene Regulation

Graham, S. V. (2017) · Viruses · doi:10.3390/v9090245 · Cited by 106 · see citing works

Exon-Mediated Activation of Transcription Starts

Fiszbein, A., Krick, K. S., Begg, B. E., & Burge, C. B. (2019) · Cell · doi:10.1016/j.cell.2019.11.002 · Cited by 104 · see citing works

Integrating mRNA Processing with Transcription

Proudfoot, N. J., Furger, A., & Dye, M. J. (2002) · Cell · doi:10.1016/s0092-8674(02)00617-7 · Cited by 1,084 · see citing works

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

Saldi, T. K., Cortázar, M. A., Sheridan, R. M., & Bentley, D. L. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.04.017 · Cited by 246 · see citing works

Coupling of Transcription with mRNA Processing in time and Space

Bentley, D. L., Fong, N., Kim, H., Zhou, Y., & Fu, X.-D. (2015) · The FASEB Journal · doi:10.1096/fasebj.29.1_supplement.238.1

Coupling RNA polymerase II transcription with pre-mRNA processing

Bentley, D. L. (1999) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(99)80048-9 · Cited by 228 · see citing works

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription

McCracken, S. A., Fong, N., Yankulov, K., Ballantyne, S. M., Pan, G., Greenblatt, J., Patterson, S. D., Wickens, M., & Bentley, D. L. (1997) · Nature · doi:10.1038/385357a0 · Cited by 925 · see citing works