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

The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing

Sánchez-Hernández, N., Boireau, S., Schmidt, U., Muñoz-Cobo, J. P., Hernández-Munaín, C., Bertrand, É., & Suñé, C. (2016) · RNA · doi:10.1261/rna.052795.115 · Cited by 16

Transcriptional regulation of metabolism in disease: From transcription factors to epigenetics

Hawkins, L. J., Al-attar, R., & Storey, K. B. (2018) · PeerJ · doi:10.7717/peerj.5062 · Cited by 17

Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity

Kinyamu, H. K., Bennett, B. D., Bushel, P. R., & Archer, T. (2020) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)49885-1 · Cited by 16

Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment

Lambert, C. A., Garbacki, N., & Colige, A. (2017) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2017.04.006 · Cited by 15

Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1st and 2nd chemical steps

Gildea, M. A., Dwyer, Z. W., & Pleiss, J. A. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.06.020 · Cited by 15

Plant immunity suppressor SKRP encodes a novel RNA ‐binding protein that targets exon 3′ end of unspliced RNA

Chen, L., Xu, Z., Huang, J., Shu, H., Hui, Y., Zhu, D., Wu, Y., Dong, S., & Wu, Z. (2023) · New Phytologist · doi:10.1111/nph.19236 · Cited by 15

Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription

Cameron, D. P., Grosser, J., Ladigan, S., Kuzin, V., Iliopoulou, E., Wiegard, A., Benredjem, H., Jackson, K., Liffers, S. T., Lueong, S., et al. (2023) · Science Advances · doi:10.1126/sciadv.adg5109 · Cited by 16

Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5

Yan, Y., Luo, H., Qin, Y., Yan, T., Jia, J., Hou, Y., Liu, Z., Zhai, J., Long, Y., Deng, X. M., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2317408121 · Cited by 15

The Function of Circular RNAs in Myocardial Ischemia–Reperfusion Injury: Underlying Mechanisms and Therapeutic Advancement

Chen, K., Liu, Z., Lu, J., Yang, S., Hu, X., & Liang, G. (2024) · Cardiovascular Drugs and Therapy · doi:10.1007/s10557-024-07557-1 · Cited by 16

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Lin, G., Barnes, C. O., Weiss, S. C., Dutagaci, B., Qiu, C., Feig, M., Song, J., Lyubimov, A. Y., Cohen, A. E., Kaplan, C. D., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2318527121 · Cited by 15

RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease

Kuldell, J. C., & Kaplan, C. D. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168770 · Cited by 16

Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex

Yanagisawa, T., Murayama, Y., Ehara, H., Goto, M., Aoki, M., & Sekine, S.-I. (2024) · Nature Communications · doi:10.1038/s41467-024-52157-0 · Cited by 15

The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster

Fear, J. M., Arbeitman, M. N., Salomon, M. P., Dalton, J. E., Tower, J., Nuzhdin, S. V., & McIntyre, L. M. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0200-0 · Cited by 15

Genome stability versus transcript diversity

Magnuson, B., Bedi, K., & Ljungman, M. E. (2016) · DNA repair · doi:10.1016/j.dnarep.2016.05.010 · Cited by 16

Emerging Roles of the Nuclear Cap-Binding Complex in Abiotic Stress Responses

Daszkowska‐Golec, A. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01017 · Cited by 15

Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies

Balestra, D., & Branchini, A. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20123036 · Cited by 15

The RNA-dependent RNA polymerase of enterovirus A71 associates with ribosomal proteins and positively regulates protein translation

Lee, K.-M., Wu, C., Wu, S.-E., Lin, Y.-H., Wang, L., Chang, C.-R., Huang, P.-N., Shih, S., & Kuo, R. (2020) · RNA Biology · doi:10.1080/15476286.2020.1722448 · Cited by 15

Mediator and TREX-2: Emerging links between transcription initiation and mRNA export

Schubert, T., & Köhler, A. (2016) · Nucleus · doi:10.1080/19491034.2016.1169352 · Cited by 15

Structure of a transcribing RNA polymerase II–U1 snRNP complexPreprint

Zhang, S., Aibara, S., Vos, S. M., Agafonov, D. E., Lührmann, R., & Cramer, P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.19.344200 · Cited by 15

Imaging Organization of RNA Processing within the NucleusPreprint

Biswas, J., Li, W., Singer, R. H., & Coleman, R. A. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039453 · Cited by 15

Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide

Kopczyńska, M., Saha, U., Romanenko, A., Nojima, T., Gdula, M. R., & Kamieniarz-Gdula, K. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1240 · Cited by 14

hnRNPA1 SUMOylation promotes cold hypersensitivity in chronic inflammatory pain by stabilizing TRPA1 mRNA

Zhang, Q., Weng, W., Gu, X., Xiang, J., Yang, Y., Zhu, M. X., Gu, W., He, Z., & Li, Y. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113401 · Cited by 14

Pause Patrol: Negative Elongation Factor’s Role in Promoter-Proximal Pausing and Beyond

Diao, A. J., Su, B. G., & Vos, S. M. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168779 · Cited by 14

Cytoplasmic deadenylase Ccr4 is required for translational repression of LRG1 mRNA in the stationary phase

Duy, D. L., Suda, Y., & Irie, K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172476 · Cited by 16

Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions

Qi, F., & Frishman, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx161 · Cited by 16

Alternative mRNA processing sites decrease genetic variability while increasing functional diversity

Auboeuf, D. (2017) · Transcription · doi:10.1080/21541264.2017.1373891 · Cited by 13

Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon–Intron Split Analysis (EISA)

Pillman, K. A., Scheer, K. G., Hackett-Jones, E., Saunders, K., Bert, A. G., Toubia, J., Whitfield, H. J., Sapkota, S., Sourdin, L., Pham, V., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz664 · Cited by 14

Targeting Aberrant Splicing in Myelodysplastic Syndromes

Brunner, A. M., & Steensma, D. P. (2019) · Hematology/Oncology Clinics of North America · doi:10.1016/j.hoc.2019.10.003 · Cited by 14

CircRNAs as Novel Biomarkers and Therapeutic Targets in Renal Cell Carcinoma

Zhou, Y., Li, C., Wang, Z., Tan, S., Liu, Y., Zhang, H., & Li, X. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.833079 · Cited by 14

Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance

Palumbo, R. J., McKean, N., Leatherman, E., Namitz, K. E. W., Connell, L. B., Wolfe, A. J., Moody, K. J., Gostinčar, C., Gunde‐Cimerman, N., Bah, A., et al. (2022) · Science Advances · doi:10.1126/sciadv.abq3235 · Cited by 14

Alternative Splicing in the Regulatory Circuit of Plant Temperature Response

Xue, R., Mo, R., Cui, D., Cheng, W., Wang, H., Qin, J., & Liu, Z. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043878 · Cited by 13

An unnatural enzyme with endonuclease activity towards small non-coding RNAs

Ahmed, N. T., Ahmed, N., Bilodeau, D. A., & Pezacki, J. P. (2023) · Nature Communications · doi:10.1038/s41467-023-39105-0 · Cited by 14

Nineteen complex–related factor Prp45 is required for the early stages of cotranscriptional spliceosome assembly

Hálová, M., Gahura, O., Převorovský, M., Cit, Z., Novotný, M., Valentová, A., Abrhámová, K., Půta, F., & Folk, P. (2017) · RNA · doi:10.1261/rna.061986.117 · Cited by 13

Suboptimal RNA–RNA interaction limits U1 snRNP inhibition of canonical mRNA 3’ processing

Shi, J., Deng, Y., Huang, S., Huang, C., Wang, J., Xiang, A. P., & Yao, C. (2019) · RNA Biology · doi:10.1080/15476286.2019.1636596 · Cited by 14

Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity

Kinyamu, H. K., Bennett, B. D., Bushel, P. R., & Archer, T. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.011174 · Cited by 15

Never a dull enzyme, RNA polymerase II

Huang, J. S., & Ji, X. (2023) · Transcription · doi:10.1080/21541264.2023.2208023 · Cited by 13

Consolidating multiple evolutionary theories of ageing suggests a need for new approaches to study genetic contributions to ageing decline

Slade, L., Etheridge, T., & Szewczyk, N. J. (2024) · Ageing Research Reviews · doi:10.1016/j.arr.2024.102456 · Cited by 15

Condensation of ZFP207 and U1 snRNP promotes spliceosome assembly

Zhou, Y., Tong, C., Shi, Z., Zhang, Y., Xiong, X., Shen, X., Li, X., & Yin, Y. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01501-z · Cited by 15

Conformational Dynamics of mRNA in Gene Expression as New Pharmaceutical Target

Endoh, T., & Sugimoto, N. (2017) · The Chemical Record · doi:10.1002/tcr.201700016 · Cited by 13

Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing

Davis‐Turak, J., Johnson, T., & Hoffmann, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky870 · Cited by 13

Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis

Zhou, J., Liu, L., Li, Q., Xu, W. M., Li, K., Wang, Z., & Sun, Q. (2019) · The Plant Journal · doi:10.1111/tpj.14584 · Cited by 13

Elongation factor-specific capture of RNA polymerase II complexes

Gregersen, L. H., Mitter, R., & Svejstrup, J. Q. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2022.100368 · Cited by 13

Bioinformatics and HIV Latency

Ciuffi, A., Mohammadi, P., Golumbeanu, M., di Iulio, J., & Telenti, A. (2015) · Current HIV/AIDS Reports · doi:10.1007/s11904-014-0240-x · Cited by 13

Genetic and structural analysis of the essential fission yeast RNA polymerase II CTD phosphatase Fcp1

Schwer, B., Ghosh, A., Sánchez, A. M., Lima, C. D., & Shuman, S. (2015) · RNA · doi:10.1261/rna.050286.115 · Cited by 13

Structural studies of the endogenous spliceosome – The supraspliceosome

Sperling, J. M., & Sperling, R. (2017) · Methods · doi:10.1016/j.ymeth.2017.04.005 · Cited by 13

RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression

Calvo, O. (2020) · Current Genetics · doi:10.1007/s00294-020-01084-w · Cited by 13

Cdk7 mediates RPB1-driven mRNA synthesis in Toxoplasma gondii

Deshmukh, A. S., Mitra, P., & Maruthi, M. (2016) · Scientific Reports · doi:10.1038/srep35288 · Cited by 13

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language ModelsPreprint

Wang, C., Karimzadeh, M., Ravindra, N. G., Bounds, L. R., Alerasool, N., Huang, A., Ma, S., Gulbranson, D. R., Cui, H., Lee, Y., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.18.712807 · Cited by 18

Expanding roles of circRNAs in cardiovascular diseases

Liu, X., Yao, X., & Chen, L. (2024) · Non-coding RNA Research · doi:10.1016/j.ncrna.2024.02.001 · Cited by 12

Assembling the RNA therapeutics toolbox

Teng, M., Xia, Z. J., Lo, N., Daud, K., & He, H. H. (2024) · Medical Review · doi:10.1515/mr-2023-0062 · Cited by 12

Lin28a forms an RNA ‐binding complex with Igf2bp3 to regulate m6A ‐modified stress response genes in stress granules of muscle stem cells

Song, D., Chen, Y., Wang, P., Cheng, Y., & Shyh‐Chang, N. (2024) · Cell Proliferation · doi:10.1111/cpr.13707 · Cited by 12

OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs

Sheinboim, D., Maza, I., Dror, I., Parikh, S., Krupalnik, V., Bell, R. E., Zviran, A., Suita, Y., Hakim, O., Mandel‐Gutfreund, Y., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01122-1 · Cited by 11

Blocking late stages of splicing quickly limits pre-spliceosome assembly in vivo

Mendoza‐Ochoa, G. I., Barrass, J. D., Maudlin, I. E., & Beggs, J. D. (2019) · RNA Biology · doi:10.1080/15476286.2019.1657788 · Cited by 12

Quantitative proteomics and phosphoproteomics of Trypanosoma cruzi epimastigote cell cycle

Júnior, A. D. C. M. D. S., Melo, R. M., Ferreira, B. V. G., Pontes, A. H., de Lima, C. M. R., Fontes, W., de Sousa, M. V., de Lima, B. D., & Ricart, C. A. O. (2021) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2021.140619 · Cited by 12

Evolution of the Early Spliceosomal Complex—From Constitutive to Regulated Splicing

Borao, S., Ayté, J., & Hümmer, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222212444 · Cited by 15

SR Splicing Factors Promote Cancer via Multiple Regulatory Mechanisms

Wan, L., Deng, M., & Zhang, H. (2022) · Genes · doi:10.3390/genes13091659 · Cited by 12

SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data

Yague‐Sanz, C., & Hermand, D. (2018) · GigaScience · doi:10.1093/gigascience/giy084 · Cited by 12

Mapping transcriptome‐wide protein‐RNA interactions to elucidate RNA regulatory programs

Hannigan, M. M., Zagore, L. L., & Licatalosi, D. D. (2018) · Quantitative Biology · doi:10.1007/s40484-018-0145-6 · Cited by 13

Multi-omics approach reveals posttranscriptionally regulated genes are essential for human pluripotent stem cells

Iwasaki, M., Kawahara, Y., Okubo, C., Yamakawa, T., Nakamura, M., Tabata, T., Nishi, Y., Narita, M., Ohta, A., Saito, H., et al. (2022) · iScience · doi:10.1016/j.isci.2022.104289 · Cited by 11

Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase

Figueiredo, A. S., Loureiro, J. R., Macedo‐Ribeiro, S., & Silveira, I. (2023) · Cells · doi:10.3390/cells12060826 · Cited by 14

A WYL domain transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP

Guo, Q., Wang, G., Zheng, L., Xue, H. F., Wang, R., Fang, Y., & Zhang, J. (2025) · Nature Communications · doi:10.1038/s41467-025-57581-4 · Cited by 11

Post‐Transcriptional Regulation of Gene Expression and the Intricate Life of Eukaryotic mRNAs

Lancaster, C. L., Moberg, K. H., & Corbett, A. H. (2025) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.70007 · Cited by 14

U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation

Kim, G., Carroll, C. L., Wakefield, Z. P., Tuncay, M., & Fiszbein, A. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.04.021 · Cited by 13

Race with virus evolution: The development and application of mRNA vaccines against SARS-CoV-2

Lee, K.-M., Lin, S., Wu, C.-J., & Kuo, R. (2023) · Biomedical Journal · doi:10.1016/j.bj.2023.01.002 · Cited by 14

TRAP150 activates splicing in composite terminal exons

Lee, K.-M., & Tarn, W. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku963 · Cited by 11

Trinucleotide-repeat expanded and normal DMPK transcripts contain unusually long poly(A) tails despite differential nuclear residence

Gudde, A. E. E. G., van Kessel, I. D. G., André, L. M., Wieringa, B., & Wansink, D. G. (2017) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2017.04.002 · Cited by 12

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome

Moreau, K., Dantec, A. L., Mosrin-Huaman, C., Bigot, Y., Piégu, B., & Rahmouni, A. R. (2019) · RNA Biology · doi:10.1080/15476286.2019.1593745 · Cited by 12

Cell-free transcription in Xenopus egg extract

Barrows, J. K., & Long, D. T. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.011350 · Cited by 12

Multiplex PCR and NGS-based identification of mRNA splicing variants: Analysis of BRCA1 splicing pattern as a model

Hojny, J., Zemánková, P., Lhota, F., Sevcik, J., Stránecký, V., Hartmannová, H., Hodaňová, K., Měšťák, O., Pavlista, D., Janatová, M., et al. (2017) · Gene · doi:10.1016/j.gene.2017.09.025 · Cited by 11

RNAi-Based Identification of Gene-Specific Nuclear Cofactor Networks Regulating Interleukin-1 Target Genes

Meier‐Soelch, J., Jurida, L., Weber, A., Newel, D., Kim, J., Braun, T. W., Schmitz, M. L., & Kracht, M. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00775 · Cited by 11

SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

Ungerleider, N., & Flemington, E. K. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2865-7 · Cited by 11

Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release

Wang, Z., Himanen, S. V., Haikala, H. M., Friedel, C. C., Vihervaara, A., & Barborič, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad792 · Cited by 14

WRN modulates translation by influencing nuclear mRNA export in HeLa cancer cells

Iglesias‐Pedraz, J. M., Fossatti-Jara, D. M., Valle-Riestra-Felice, V., Cruz-Visalaya, S. R., Felix, J. A. A., & Comai, L. (2020) · BMC Molecular and Cell Biology · doi:10.1186/s12860-020-00315-9 · Cited by 10

Modeling by disruption and a selected-for partner for the nude locus

Li, J., Lee, Y., Fu, W.-Y., Whalen, A. M., Estable, M. C., Raftery, L. A., White, K., Weiner, L., & Brissette, J. L. (2020) · EMBO Reports · doi:10.15252/embr.201949804 · Cited by 10

Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution

Kolev, S. K., Petkov, P. S., Milenov, T. I., & Vayssilov, G. N. (2022) · ACS Omega · doi:10.1021/acsomega.2c01327 · Cited by 10

The Phantom Mark: Enigmatic roles of phospho‐Threonine 4 modification of the C‐terminal domain of RNA polymerase II

Kempen, R. P., Dabas, P., & Ansari, A. Z. (2023) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1771 · Cited by 10

Roles of alternative splicing in infectious diseases: from hosts, pathogens to their interactions

Lyu, M., Lai, H., Wang, Y., Zhou, Y., Chen, Y., Wu, D., Chen, J., & Ying, B. (2023) · Chinese Medical Journal · doi:10.1097/cm9.0000000000002621 · Cited by 12

The conserved RNA-binding protein Seb1 promotes cotranscriptional ribosomal RNA processing by controlling RNA polymerase I progression

Duval, M., Yague‐Sanz, C., Turowski, T. W., Petfalski, E., Tollervey, D. W., & Bachand, F. (2023) · Nature Communications · doi:10.1038/s41467-023-38826-6 · Cited by 10

FUS reads histone H3K36me3 to regulate alternative polyadenylation

Jia, J., Fan, H., Wan, X., Fang, Y., Li, Z., Tang, Y., Zhang, Y., Huang, J., & Dong, F. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae184 · Cited by 10

Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast

Inada, M., Nichols, R. J., Parsa, J., Homer, C. M., Benn, R. A., Hoxie, R. S., Madhani, H. D., Shuman, S., Schwer, B., & Pleiss, J. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw603 · Cited by 10

Competing RNA pairings in complex alternative splicing of a 3′ variable region

Pan, H., Shi, Y., Chen, S., Yang, Y., Yue, Y., Zhan, L., Dai, L., Dong, H., Hong, W., Shi, F., et al. (2018) · RNA · doi:10.1261/rna.066225.118 · Cited by 10

Revisiting the window of opportunity for cotranscriptional splicing in budding yeast

Aslanzadeh, V., & Beggs, J. D. (2020) · RNA · doi:10.1261/rna.075895.120 · Cited by 8

Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf

Zhu, J., Zhao, H. Q., Kong, F., Liu, B., Liu, M., & Dong, Z. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.649634 · Cited by 10

Pbp1, the yeast ortholog of human Ataxin-2, functions in the cell growth on non-fermentable carbon sources

Dang, T. T. V., Fujii, S., Valderrama, A. L., Ito, A., Matsuura, E., Nishihata, A., Irie, K., Suda, Y., Mizuno, T., & Irie, K. (2021) · PLoS ONE · doi:10.1371/journal.pone.0251456 · Cited by 8

Dissecting the Role of Circular RNAs in Sarcomas with Emphasis on Osteosarcomas

Lakiotaki, E., Kanakoglou, D. S., Pampalou, A., Karatrasoglou, E. A., Piperi, C., & Korkolopoulou, P. A. (2021) · Biomedicines · doi:10.3390/biomedicines9111642 · Cited by 10

Emerging value of the viroid model in molecular biology and beyond

Ma, J., Mudiyanselage, S. D. D., & Wang, Y. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198730 · Cited by 10

P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway

Wang, Z., Mačáková, M., Bugai, A., Kuznetsov, S. G., Hassinen, A., Lenasi, T., Potdar, S., Friedel, C. C., & Barborič, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad001 · Cited by 11

A Nuclear Zip Code in SKS1 mRNA Promotes Its Slow Export, Nuclear Retention, and Degradation by the Nuclear Exosome/DRN in Saccharomyces cerevisiae

Das, S., Biswas, S., Chaudhuri, S., Bhattacharyya, A., & Das, B. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.005 · Cited by 10

Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin LevelsPreprint

Chen, J., Lim, D., & Fu, X. (2019) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2019.84.039222 · Cited by 10

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavagePreprint

Liu, J., Hansen, D., Eck, E., Kim, Y. J., Turner, M. A., Álamos, S., & García, H. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.29.273474 · Cited by 10

DNA methylation affects pre-mRNA transcriptional initiation and processing in ArabidopsisPreprint

Li, Q., Chen, S., Leung, A. W.-S., Liu, Y., Xin, Y., Zhang, L., Lam, H., Luo, R., & Zhang, S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.29.441938 · Cited by 10

A direct interaction between CPF and Pol II links RNA 3ʹ-end processing to transcriptionPreprint

Carminati, M., Manav, M. C., Bellini, D., & Passmore, L. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.28.501803 · Cited by 10

Aerocyte specification and lung adaptation to breathing is dependent on alternative splicing changes

Fidalgo, M., Fonseca, C. G., Caldas, P., Raposo, A. A. S. F., Balboni, T., Misikova, L. H., Grosso, A. R., Vasconcelos, F. F., & Franco, C. A. (2022) · Life Science Alliance · doi:10.26508/lsa.202201554 · Cited by 11

RNF20-mediated transcriptional pausing and VEGFA splicing orchestrate vessel growth

Tetik-Elsherbiny, N., Elsherbiny, A., Setya, A., Gahn, J., Tang, Y., Gupta, P., Dou, Y., Serke, H., Wieland, T., Dubrac, A., et al. (2024) · Nature Cardiovascular Research · doi:10.1038/s44161-024-00546-5 · Cited by 11

Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription

Heo, D., Kuś, K., Grzechnik, P., Tan‐Wong, S. M., Birot, A., Kecman, T., Nielsen, S., Zenkin, N., & Vasiljeva, L. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109671 · Cited by 9

Targeting strategies for modulating pre-mRNA splicing with small molecules: Recent advances

Barraza, S. J., Bhattacharyya, A., Trotta, C. R., & Woll, M. G. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.103431 · Cited by 9

CircAMOTL1 RNA and AMOTL1 Protein: Complex Functions of AMOTL1 Gene Products

Sadlak, J., Joshi, I., Prószyński, T. J., & Kischel, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032103 · Cited by 9

The U1 antisense morpholino oligonucleotide (AMO) disrupts U1 snRNP structure to promote intronic PCPA modification of pre-mRNAs

Feng, Q., Lin, Z., Deng, Y., Ran, Y., Yu, R., Xiang, A. P., Ye, C., & Yao, C. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104854 · Cited by 9

Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo

Björk, P., Persson, J., & Wieslander, L. (2015) · The Journal of Cell Biology · doi:10.1083/jcb.201412017 · Cited by 9

Functional Interplay between PPM1G and the Transcription Elongation Machinery

Gudipaty, S. A., & D’Orso, I. (2016) · RNA & DISEASE · doi:10.14800/rd.1215 · Cited by 9

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