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 2,270

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

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

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

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

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

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

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

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

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

Co-transcriptional splicing and the CTD code

Custódio, N., & Carmo‐Fonseca, M. (2016) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2016.1230086 · Cited by 46

Exploring the regulatory roles of circular RNAs in Alzheimer’s disease

Zhang, Y., Zhao, Y., Liu, Y., Wang, M., Yu, W., & Zhang, L. (2020) · Translational Neurodegeneration · doi:10.1186/s40035-020-00216-z · Cited by 47

5′UTR G-quadruplex structure enhances translation in size dependent manner

Lee, C.-Y., Joshi, M., Wang, A. R., & Myong, S. (2024) · Nature Communications · doi:10.1038/s41467-024-48247-8 · Cited by 49

Adenosine to Inosine editing frequency controlled by splicing efficiency

Licht, K., Kapoor, U., Mayrhofer, E., & Jantsch, M. F. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw325 · Cited by 49

Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping

Voong, L. N., Xi, L., Wang, J., & Wang, X. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.007 · Cited by 46

Emerging Properties and Functional Consequences of Noncoding Transcription.

Ard, R., Allshire, R. C., & Marquardt, S. (2017) · Europe PMC (PubMed Central) · doi:10.1534/genetics.117.300095 · Cited by 46

Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes

Speth, C., Szabo, E. X., Martinho, C., Collani, S., Oven‐Krockhaus, S. Z., Richter, S., Droste-Borel, I., Maček, B., Stierhof, Y., Schmid, M., et al. (2018) · eLife · doi:10.7554/elife.37078 · Cited by 49

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt

Habowski, A. N., Flesher, J. L., Bates, J. M., Tsai, C., Martin, K., Zhao, R., Ganesan, A. K., Edwards, R. A., Shi, T., Wiley, H. S., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-01181-z · Cited by 49

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

Goering, R., Engel, K. L., Gillen, A. E., Fong, N., Bentley, D. L., & Taliaferro, J. M. (2021) · BMC Genomics · doi:10.1186/s12864-021-07781-1 · Cited by 45

Mechanisms of mRNA export

Björk, P., & Wieslander, L. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.04.027 · Cited by 48

The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation

Rodor, J., Pan, Q., Blencowe, B. J., Eyras, E., & Cáceres, J. F. (2016) · RNA · doi:10.1261/rna.057158.116 · Cited by 50

Transcription alterations of KCNQ1 associated with imprinted methylation defects in the Beckwith–Wiedemann locus

Valente, F. M., Sparago, A., Freschi, A., Hill-Harfe, K. L., Maas, S. M., Frints, S. G. M., Alders, M. M., Pignata, L., Franzese, M., Angelini, C., et al. (2019) · Genetics in Medicine · doi:10.1038/s41436-018-0416-7 · Cited by 51

Oncogenic dysregulation of pre‐mRNA processing by protein kinases: challenges and therapeutic opportunities

Naro, C., Bielli, P., & Sette, C. (2021) · FEBS Journal · doi:10.1111/febs.16057 · Cited by 49

Enhancers regulate 3′ end processing activity to control expression of alternative 3′UTR isoforms

Kwon, B., Fansler, M. M., Patel, N. D., Lee, J., Ma, W., & Mayr, C. (2022) · Nature Communications · doi:10.1038/s41467-022-30525-y · Cited by 47

Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeastPreprint

Bitton, D. A., Atkinson, S. R., Rallis, C., Smith, G. C., Ellis, D., Chen, Y. Y. C., Małecki, M., Codlin, S., Lemay, J., Cotobal, C., et al. (2015) · Genome Research · doi:10.1101/gr.185371.114 · Cited by 49

CD5 expression is regulated during human T‐cell activation by alternative polyadenylation, PTBP1, and miR‐204

Domingues, R. G., Lago‐Baldaia, I., Pereira‐Castro, I., Fachini, J. M., Oliveira, L., Drpic, D., Lopes, N., Henriques, T., Neilson, J. R., Carmo, A. M., et al. (2016) · European Journal of Immunology · doi:10.1002/eji.201545663 · Cited by 46

Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control

Justice, S. A. P., Hughes, K. D., Victorino, J. F., & Mosley, A. L. (2019) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1529 · Cited by 49

Prolyl Isomerase Pin1 in Human Cancer: Function, Mechanism, and Significance

Pu, W., Zheng, Y., & Peng, Y. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00168 · Cited by 49

Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore

Li, Y., Aksenova, V., Tingey, M., Yu, J., Ma, P., Arnaoutov, A., Chen, S., Dasso, M., & Yang, W. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2015621118 · Cited by 47

The transcriptional elongation rate regulates alternative polyadenylation in yeast

Geisberg, J. V., Moqtaderi, Z., & Struhl, K. (2020) · eLife · doi:10.7554/elife.59810 · Cited by 45

Roles of RNA-binding Proteins and Post-transcriptional Regulation in Driving Male Germ Cell Development in the Mouse

Licatalosi, D. D. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-29073-7_6 · Cited by 46

The contribution of alternative splicing to genetic risk for psychiatric disorders

Reble, E., Dineen, A., & Barr, C. L. (2017) · Genes Brain & Behavior · doi:10.1111/gbb.12430 · Cited by 47

Promoter-proximal pausing mediated by the exon junction complex regulates splicing

Akhtar, J., Kreim, N., Marini, F., Mohana, G., Brüne, D., Binder, H., & Roignant, J. (2019) · Nature Communications · doi:10.1038/s41467-019-08381-0 · Cited by 45

The reciprocal regulation between splicing and 3′‐end processing

Kaida, D. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1348 · Cited by 47

Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response

Pai, A. A., & Luca, F. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1503 · Cited by 48

A genome-wide perspective of the maternal mRNA translation program during oocyte development

Conti, M., & Kunitomi, C. (2023) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2023.03.003 · Cited by 43

Cdk12 Is A Gene-Selective RNA Polymerase II Kinase That Regulates a Subset of the Transcriptome, Including Nrf2 Target Genes

Li, X., Chatterjee, N., Spirohn, K., Boutros, M., & Bohmann, D. (2016) · Scientific Reports · doi:10.1038/srep21455 · Cited by 44

Intron retention in viruses and cellular genes: Detention, border controls and passports

Rekosh, D. M., & Hammarskjöld, M. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1470 · Cited by 43

SOX9 has distinct regulatory roles in alternative splicing and transcription

Girardot, M., Bayet, E., Maurin, J., Fort, P., Roux, P., & Raynaud, P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky553 · Cited by 43

The dynamic landscape of fission yeast meiosis alternative-splice isoformsPreprint

Kuang, Z., Boeke, J. D., & Canzar, S. (2016) · Genome Research · doi:10.1101/gr.208041.116 · Cited by 42

The THO Complex as a Paradigm for the Prevention of Cotranscriptional R-LoopsPreprint

Luna, R., Rondón, A. G., Calero, C. P., Salas‐Armenteros, I., & Aguilera, A. (2019) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2019.84.039594 · Cited by 43

Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome

Swindell, W. R., Xing, X., Voorhees, J. J., Elder, J. T., Johnston, A., & Gudjonsson, J. E. (2014) · Physiological Genomics · doi:10.1152/physiolgenomics.00022.2014 · Cited by 42

miRNA Editing: New Insights into the Fast Control of Gene Expression in Health and Disease

Mingardi, J., Musazzi, L., Petro, G. D., & Barbon, A. (2018) · Molecular Neurobiology · doi:10.1007/s12035-018-0951-x · Cited by 44

Availability of splicing factors in the nucleoplasm can regulate the release of mRNA from the gene after transcription

Hochberg-Laufer, H., Neufeld, N., Brody, Y., Nadav-Eliyahu, S., Ben-Yishay, R., & Shav‐Tal, Y. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008459 · Cited by 42

CDK12: cellular functions and therapeutic potential of versatile player in cancer

Pilařová, K., Herudek, J., & Blažek, D. (2020) · NAR Cancer · doi:10.1093/narcan/zcaa003 · Cited by 43

Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylationPreprint

Yague‐Sanz, C., Vanrobaeys, Y. S., Fernandez, R., Duval, M., Larochelle, M., Beaudoin, J., Berro, J., Labbé, S., Jacques, P., & Bachand, F. (2020) · Genes & Development · doi:10.1101/gad.337212.120 · Cited by 46

Origins and Impacts of New Mammalian Exons

Merkin, J. J., Chen, P., Alexis, M. S., Hautaniemi, S., & Burge, C. B. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.058 · Cited by 42

FUS ‐mediated regulation of alternative RNA processing in neurons: insights from global transcriptome analysis

Masuda, A., Takeda, J., & Ohno, K. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1338 · Cited by 42

A direct interaction between CPF and RNA Pol II links RNA 3′ end processing to transcription

Carminati, M., Rodríguez‐Molina, J. B., Manav, M. C., Bellini, D., & Passmore, L. A. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.11.004 · Cited by 41

The RNA polymerase II CTD “orphan” residues: Emerging insights into the functions of Tyr-1, Thr-4, and Ser-7

Yurko, N., & Manley, J. L. (2017) · Transcription · doi:10.1080/21541264.2017.1338176 · Cited by 41

An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response

Chang, J.-W., Zhang, W., Yeh, H.-S., Park, M., Yao, C., Shi, Y., Kuang, R., & Yong, J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky340 · Cited by 41

Conserved long-range base pairings are associated with pre-mRNA processing of human genes

Kalmykova, S., Kalinina, M., Denisov, S., Mironov, A., Skvortsov, D. A., Guigó, R., & Pervouchine, D. D. (2021) · Nature Communications · doi:10.1038/s41467-021-22549-7 · Cited by 39

Nuclear m6A reader YTHDC1 suppresses proximal alternative polyadenylation sites by interfering with the 3′ processing machinery

Chen, L., Fu, Y., Hu, Z., Deng, K., Song, Z., Liu, S., Li, M., Ou, X., Wu, R., Liu, M., et al. (2022) · EMBO Reports · doi:10.15252/embr.202254686 · Cited by 38

Depletion of REF/Aly alters gene expression and reduces RNA polymerase II occupancy

Stubbs, S. H., & Conrad, N. K. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1278 · Cited by 39

Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells

Dias, J. D., Rito, T., Triglia, E. T., Kukalev, A., Ferrai, C., Chotalia, M., Brookes, E., Kimurâ, H., & Pombo, A. (2015) · eLife · doi:10.7554/elife.11215 · Cited by 39

HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing

Liu, H., Liang, C., Kollipara, R. K., Matsui, M., Ke, X., Jeong, B., Wang, Z., Yoo, K. S., Yadav, G. P., Kinch, L. N., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.014 · Cited by 39

Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway

Shelton, S. B., Reinsborough, C. W., & Xhemalçe, B. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006139 · Cited by 40

AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors

Hu, J., Khodadadi‐Jamayran, A., Mao, M., Shah, K. K., Yang, Z., Nasim, T., Wang, Z., & Jiang, H. (2016) · Nature Communications · doi:10.1038/ncomms13347 · Cited by 37

Fluctuation Analysis

Coulon, A., & Larson, D. R. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.03.017 · Cited by 38

The nuts and bolts of the endogenous spliceosome

Sperling, R. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1377 · Cited by 40

The Chromatin Remodeler ISW1 Is a Quality Control Factor that Surveys Nuclear mRNP Biogenesis

Babour, A., Shen, Q., Julien, D.-S., Murray, S. C., Gay, A., Challal, D., Fasken, M. B., Palancade, B., Corbett, A. H., Libri, D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.048 · Cited by 41

Subgenic Pol II interactomes identify region‐specific transcription elongation regulators

Harlen, K. M., & Churchman, L. S. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167279 · Cited by 38

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses

Davari, K., Lichti, J., Gallus, C., Greulich, F., Uhlenhaut, N. H., Heinig, M., Friedel, C. C., & Glasmacher, E. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.03.069 · Cited by 36

The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5‘ and 3‘ gene regions

Fischer, J. D., Song, Y. S., Yosef, N., di Iulio, J., Churchman, L. S., & Choder, M. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.013426 · Cited by 36

Novel Nuclear Functions of Arabidopsis ARGONAUTE1: Beyond RNA Interference

Bajczyk, M., Bhat, S. S., Szewc, Ł., Szweykowska-Kulińska, Z., Jarmołowski, A., & Dolata, J. (2019) · PLANT PHYSIOLOGY · doi:10.1104/pp.18.01351 · Cited by 39

P-TEFb goes viral

Zaborowska, J., Isa, N. F., & Murphy, S. (2015) · Inside the Cell · doi:10.1002/icl3.1037 · Cited by 36

Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max

Iñiguez, L., Ramı́rez, M., Barbazuk, W. B., & Hernández, G. (2017) · BMC Genomics · doi:10.1186/s12864-017-4054-2 · Cited by 36

The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex

Pfab, A., Bruckmann, A., Nazet, J., Merkl, R., & Grasser, K. D. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.03.018 · Cited by 36

The biogenesis, biological functions and modification of Circular RNAs

Liu, S., Guo, X., Shang, Q. J., & Gao, P. (2023) · Experimental and Molecular Pathology · doi:10.1016/j.yexmp.2023.104861 · Cited by 37

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner

Nemec, C. M., Yang, F., Gilmore, J. M., Hintermair, C., Ho, Y., Tseng, S. C., Heidemann, M., Zhang, Y., Florens, L. A., Gasch, A. P., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700128114 · Cited by 36

Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence

Han, X., Xing, L., Hong, Y., Zhang, X., Hao, B., Lu, J. Y., Huang, M., Wang, Z., Ma, S., Zhan, G., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.03.015 · Cited by 36

Role of circular RNAs in cancer therapy resistance

Liu, W., Niu, J., Huo, Y., Zhang, L., Han, L., Zhang, N., & Yang, M. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02254-5 · Cited by 41

IntergenicAluexonisation facilitates the evolution of tissue-specific transcript ends

Tajnik, M., Vigilante, A., Braun, S., Hänel, H., Luscombe, N. M., Ule, J., Zarnack, K., & König, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv956 · Cited by 36

Alternative Splicing of STAT3 Is Affected by RNA Editing

Goldberg, L., Abutbul‐Amitai, M., Paret, G., & Nevo‐Caspi, Y. (2017) · DNA and Cell Biology · doi:10.1089/dna.2016.3575 · Cited by 37

How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes

Dergai, O., & Hernandez, N. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.04.001 · Cited by 35

Dynamics and Functional Roles of Splicing Factor Autoregulation

Ding, F., Su, C. J., Edmonds, K. K., Liang, G., & Elowitz, M. B. (2021) · Cell Reports · doi:10.1016/j.celrep.2022.110985 · Cited by 36

Looping out of control: R-loops in transcription-replication conflict

Kumar, C., & Remus, D. (2023) · Chromosoma · doi:10.1007/s00412-023-00804-8 · Cited by 34

P‐TEFb goes viral

Zaborowska, J., Isa, N. F., & Murphy, S. (2016) · BioEssays · doi:10.1002/bies.201670912 · Cited by 34

A saga of cancer epigenetics: linking epigenetics to alternative splicing

Narayanan, S. P., Singh, S., & Shukla, S. (2017) · Biochemical Journal · doi:10.1042/bcj20161047 · Cited by 36

Cholesterol signaling in single cells: lessons from STAR and sm-FISH

Jefcoate, C. R. E., & Lee, J. (2018) · Journal of Molecular Endocrinology · doi:10.1530/jme-17-0281 · Cited by 33

NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing

Fasina, O. O., Dong, Y., & Pintel, D. J. (2015) · Journal of Virology · doi:10.1128/jvi.02618-15 · Cited by 33

Ovule identity mediated by pre-mRNA processing in Arabidopsis

Rodríguez‐Cazorla, E., Ortuño‐Miquel, S., Candela, H., Bailey-Steinitz, L. J., Yanofsky, M. F., Martínez‐Laborda, A., Ripoll, J. J., & Vera, A. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007182 · Cited by 33

RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications

Pelea, O., Fulga, T. A., & Sauka‐Spengler, T. (2022) · The CRISPR Journal · doi:10.1089/crispr.2022.0052 · Cited by 35

A Neuronal Activity-Dependent Dual Function Chromatin-Modifying Complex RegulatesArcExpression

Oey, N. E., Leung, H.-W., Rajaram, E., Zhou, L., Beuerman, R. W., VanDongen, H. M. A., & VanDongen, A. M. J. (2015) · eNeuro · doi:10.1523/eneuro.0020-14.2015 · Cited by 32

SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus

Ma, J., Xiang, Y., Xiong, Y., Lin, Z. Y., Xue, Y., Mao, M., Sun, L., Zhou, Y., Li, X., & Huang, Z. (2019) · PeerJ · doi:10.7717/peerj.7062 · Cited by 32

Intranucleus Single-Molecule Imaging in Living Cells

Shao, S., Xue, B., & Sun, Y. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2018.05.017 · Cited by 30

STARD1 Functions in Mitochondrial Cholesterol Metabolism and Nascent HDL Formation. Gene Expression and Molecular mRNA Imaging Show Novel Splicing and a 1:1 Mitochondrial Association

Larsen, M. C., Lee, J., Jorgensen, J. S., & Jefcoate, C. R. E. (2020) · Frontiers in Endocrinology · doi:10.3389/fendo.2020.559674 · Cited by 31

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

Ren, Y., Huo, Y., Li, W., He, M., Liu, S., Yang, J., Zhao, H., Xu, L., Guo, Y., Si, Y., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02508-7 · Cited by 32

Structural insights into human co-transcriptional capping

Garg, G., Dienemann, C., Farnung, L., Schwarz, J., Linden, A., Urlaub, H., & Cramer, P. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.002 · Cited by 33

Gene expression and protein abundance: Just how associated are these molecular traits?

Samih, A., Ferreira, M. A. D. M., & Nikoloski, Z. (2025) · Biotechnology Advances · doi:10.1016/j.biotechadv.2025.108720 · Cited by 35

Nascent RNA kinetics: Transient and steady state behavior of models of transcription

Choubey, S. (2018) · Physical review. E · doi:10.1103/physreve.97.022402 · Cited by 31

Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo

Malik, I., Qiu, C., Snavely, T. C., & Kaplan, C. D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx037 · Cited by 31

The Role of Circular RNAs in Pancreatic Ductal Adenocarcinoma and Biliary-Tract Cancers

Limb, C., Liu, D., Venø, M. T., Rees, E., Krell, J., Bagwan, I., Giovannetti, E., Pandha, H., Strobel, O., Rockall, T., et al. (2020) · Cancers · doi:10.3390/cancers12113250 · Cited by 31

Cotranscriptional RNA processing and modification in plants

Marquardt, S., Petrillo, E., & Manavella, P. A. (2022) · The Plant Cell · doi:10.1093/plcell/koac309 · Cited by 32

A code for transcription elongation speed

Cohen, E., Zafrir, Z., & Tuller, T. (2018) · RNA Biology · doi:10.1080/15476286.2017.1384118 · Cited by 29

tRIP‐seq reveals repression of premature polyadenylation by co‐transcriptional FUS‐U1 snRNP assembly

Masuda, A., Kawachi, T., Takeda, J., Ohkawara, B., Ito, M., & Ohno, K. (2020) · EMBO Reports · doi:10.15252/embr.201949890 · Cited by 31

Coordination of transcription and processing of tRNA

Jarrous, N., Mani, D., & Ramanathan, A. S. K. (2021) · FEBS Journal · doi:10.1111/febs.15904 · Cited by 31

A data‐independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus

Root, L., Campo, A., MacNiven, L. M., Con, P., Cnaani, A., & Kültz, D. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13445 · Cited by 31

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane, D. L., Chowdhury, T. A., & Kleene, K. C. (2014) · Reproduction · doi:10.1530/rep-14-0394 · Cited by 31

Purifying Selection on Exonic Splice Enhancers in Intronless Genes

Savisaar, R., & Hurst, L. D. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw018 · Cited by 30

Multifaceted Regulation of Gene Expression by the Apoptosis- and Splicing-Associated Protein Complex and Its Components

Deka, B., & Singh, K. K. (2017) · International Journal of Biological Sciences · doi:10.7150/ijbs.18649 · Cited by 26

CirGRDB: a database for the genome-wide deciphering circadian genes and regulators

Li, X., Shi, L., Zhang, K., Wei, W., Liu, Q., Mao, F., Li, J., Cai, W., Chen, H., Teng, H., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx944 · Cited by 35

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcriptionPreprint

Russo, M., Piccolo, V., Polizzese, D., Prosperini, E., Borriero, C., Polletti, S., Bedin, F., Marenda, M., Michieletto, D., Mandana, G. M., et al. (2023) · Genes & Development · doi:10.1101/gad.351057.123 · Cited by 31

Cotranscriptional splicing efficiencies differ within genes and between cell types

Bedi, K., Magnuson, B., Narayanan, I. V., Paulsen, M. T., Wilson, T. E., & Ljungman, M. E. (2021) · RNA · doi:10.1261/rna.078662.120 · Cited by 28

Cytoplasmic mRNA decay represses RNA polymerase II transcription during early apoptosis

Duncan-Lewis, C., Hartenian, E., King, V. M., & Glaunsinger, B. A. (2021) · eLife · doi:10.7554/elife.58342 · Cited by 29

Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover

Root, L., Campo, A., MacNiven, L. M., Con, P., Cnaani, A., & Kültz, D. (2021) · Genomics · doi:10.1016/j.ygeno.2021.07.016 · Cited by 29

It’s a DoG-eat-DoG world—altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production

Morgan, M. A., Shiekhattar, R., Shilatifard, A., & Lauberth, S. M. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.04.008 · Cited by 32

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

Patrick, K. L., Ryan, C. J., Xu, J., Lipp, J., Nissen, K. E., Roguev, A., Shales, M., Krogan, N. J., & Guthrie, C. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005074 · Cited by 28

Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II

Voß, K., Forné, I., Descostes, N., Hintermair, C., Schüller, R., Maqbool, M. A., Heidemann, M., Flatley, A., Imhof, A., Gut, M., et al. (2015) · Transcription · doi:10.1080/21541264.2015.1114983 · Cited by 28

Novel roles of Drosophila FUS and Aub responsible for piRNA biogenesis in neuronal disorders

Wakisaka, K. T., Tanaka, R., Hirashima, T., Muraoka, Y., Azuma, Y., Yoshida, H., Tokuda, T., Asada, S., Suda, K., Ichiyanagi, K., et al. (2018) · Brain Research · doi:10.1016/j.brainres.2018.12.028 · Cited by 30

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

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 266

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

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