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

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Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity

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Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II

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The HIV-1 Transcriptional Program: From Initiation to Elongation Control

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Genetic screen for suppression of transcriptional interference identifies a gain-of-function mutation in Pol2 termination factor Seb1

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Mechanisms of eukaryotic transcription termination at a glance

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Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination

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The reversible inhibitor SR-4835 binds Cdk12/cyclin K in a noncanonical G-loop conformation

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Transcription and splicing dynamics during early Drosophila development

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Activation of TC10-Like Transcription by Lysine Demethylase KDM4B in Colorectal Cancer Cells

Chen, B., Zhu, Y., Chen, J., Feng, Y., & Xu, Y. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.617549 · Cited by 17

A novel, rapid and sensitive flow cytometry method reveals degradation of promoter proximal paused RNAPII in the presence and absence of UV

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Deregulations of RNA Pol II Subunits in Cancer

Sadurnì, M. M., & Saponaro, M. (2023) · Applied Biosciences · doi:10.3390/applbiosci2030029 · Cited by 17

The suppressive efficacy of THZ1 depends on KRAS mutation subtype and is associated with super‐enhancer activity and the PI3K/AKT/mTOR signalling in pancreatic ductal adenocarcinoma: A hypothesis‐generating study

Huang, L., Yang, H., Chen, K., Yuan, J., Li, J., Dai, G., Gu, M., & Shi, Y. X. (2023) · Clinical and Translational Medicine · doi:10.1002/ctm2.1500 · Cited by 17

The gammaherpesviral TATA-box-binding protein directly interacts with the CTD of host RNA Pol II to direct late gene transcription

Castañeda, A. F., Didychuk, A. L., Louder, R. K., McCollum, C. O., Davis, Z. H., Nogales, E., & Glaunsinger, B. A. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008843 · Cited by 17

Elongin A regulates transcription in vivo through enhanced RNA polymerase processivity

Wang, Y., Hou, L., Ardehali, M. B., Kingston, R. E., & Dynlacht, B. D. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.015876 · Cited by 17

Nuclear ANLN regulates transcription initiation related Pol II clustering and target gene expression

Cao, Y., Wang, H., Sun, Y., Tong, B.-B., Shi, W.-Q., Liu, P., Zhang, Y., Wu, Y.-Q., Fu, T., Zou, H.-Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56645-9 · Cited by 19

Direct targeting and regulation of RNA polymerase II by cell signaling kinases

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Nucleotide Excision Repair: Insights into Canonical and Emerging Functions of the Transcription/DNA Repair Factor TFIIH

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Longer DNA exhibits greater potential for cell-free gene expression

Nishio, T., Yoshikawa, Y., Yoshikawa, K., & Sato, S. (2021) · Scientific Reports · doi:10.1038/s41598-021-91243-x · Cited by 16

Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate C-terminal domain (CTD) phosphatase during eukaryotic transcription

Irani, S., Sipe, S. N., Yang, W., Burkholder, N. T., Lin, B., Sim, K., Matthews, W. L., Brodbelt, J. S., & Zhang, Y. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.007697 · Cited by 16

A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy

Townley, B. A., Buerer, L., Tsao, N., Bacolla, A., Mansoori, F., Rusanov, T., Clark, N. E., Goodarzi, N., Schmidt, N., Srivatsan, S. N., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.011 · Cited by 15

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

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Known types of membrane-less organelles and biomolecular condensates

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Transcription-associated cyclin-dependent kinase 12 (CDK12) as a potential target for cancer therapy

Wu, W., Yu, S., & Yu, X. (2022) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2022.188842 · Cited by 16

Distinctive interactomes of RNA polymerase II phosphorylation during different stages of transcription

Moreno, R. Y., Juetten, K. J., Panina, S., Butalewicz, J. P., Floyd, B. M., Ramani, M. K. V., Marcotte, E. M., Brodbelt, J. S., & Zhang, Y. (2023) · iScience · doi:10.1016/j.isci.2023.107581 · Cited by 15

RBM22 regulates RNA polymerase II 5′ pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5

Du, X., Qin, W., Yang, C., Dai, L., San, M., Xia, Y., Zhou, S., Wang, M., Wu, S., Zhang, S., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03242-6 · Cited by 17

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

First Come, First Served: Sui Generis Features of the First Intron

Zalabák, D., & Ikeda, Y. (2020) · Plants · doi:10.3390/plants9070911 · Cited by 17

The CTD Is Not Essential for the Post-Initiation Control of RNA Polymerase II Activity

Gerber, A., & Roeder, R. G. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.07.010 · Cited by 15

TOX4 Promotes Promoter Proximal Pause of RNA Polymerase Ii by Facilitating the Recruitment of DSIF and NELF

Liu, Z., Wu, A., Wu, Z., Wang, T., Pan, Y., Li, B., Zhang, X., & Yu, M. (2021) · Communications Biology · doi:10.1038/s42003-022-03214-1 · Cited by 15

Targeting the C-Terminal Domain Small Phosphatase 1

Rallabandi, H. R., Ganesan, P., & Kim, Y. J. (2020) · Life · doi:10.3390/life10050057 · Cited by 15

Control of non-productive RNA polymerase II transcription via its early termination in metazoans

Rouvière, J. O., Lykke‐Andersen, S., & Jensen, T. H. (2022) · Biochemical Society Transactions · doi:10.1042/bst20201140 · Cited by 14

Surface condensation of a pioneer transcription factor on DNAPreprint

Morín, J. A., Wittmann, S., Choubey, S., Kłosin, A., Golfier, S., Hyman, A. A., Jülicher, F., & Grill, S. W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.24.311712 · 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

Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae

Singh, P., Chaudhuri, A., Banerjea, M., Marathe, N., & Das, B. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab930 · Cited by 14

Phase separation drives tumor pathogenesis and evolution: all roads lead to Rome

Gu, X., Zhuang, A., Yu, J., Chai, P., Jia, R., & Ruan, J. (2022) · Oncogene · doi:10.1038/s41388-022-02195-z · Cited by 15

Genome-wide mapping of protein–DNA damage interaction by PADD-seq

Zhu, Y., Tan, Y., Li, L., Xiang, Y., Huang, Y., Zhang, X., Yin, J., Li, J., Lan, F., Qian, M., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad008 · Cited by 15

Regulation of HSF1 transcriptional complexes under proteotoxic stress

Fujimoto, M., Takii, R., & Nakai, A. (2023) · BioEssays · doi:10.1002/bies.202300036 · Cited by 14

RNA polymerase II promotes the organization of chromatin following DNA replication

Bandau, S., Álvarez, V., Jiang, H., Graff, S., Sundaramoorthy, R., Gierliński, M., Toman, M., Owen‐Hughes, T., Sidoli, S., Lamond, A. I., et al. (2024) · EMBO Reports · doi:10.1038/s44319-024-00085-x · Cited by 12

Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation

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Intact Arabidopsis RPB 1 functions in stem cell niches maintenance and cell cycling control

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Design, synthesis and anticancer evaluation of selective 2,4-disubstituted pyrimidine CDK9 inhibitors

Xu, Z., Zhang, B., Liu, Z., & Gou, S. (2022) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2022.114875 · Cited by 14

Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management

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Cytoplasmic Mislocalization of RNA Polymerase II Subunit RPB1 in Alzheimer Disease Is Linked to Pathologic Tau

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Never a dull enzyme, RNA polymerase II

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Biomolecular condensates in kidney physiology and disease

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Super-enhancers: drivers of cells’ identities and cells’ debacles

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CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing

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Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis

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A live imaging system to analyze spatiotemporal dynamics of RNA polymerase II modification in Arabidopsis thaliana

Shibuta, M. K., Sakamoto, T., Yamaoka, T., Yoshikawa, M., Kasamatsu, S., Yagi, N., Fujimoto, S., Suzuki, T., Uchino, S., Sato, Y., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02106-0 · Cited by 16

Emerging roles of protein phosphorylation in regulation of stomatal development

Liang, C. (2022) · Journal of Plant Physiology · doi:10.1016/j.jplph.2022.153882 · Cited by 13

Elongation factor-specific capture of RNA polymerase II complexes

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Biomolecule-Based Coacervates with Modulated Physiological Functions

Huang, Y., & Huang, X. C. (2023) · Langmuir · doi:10.1021/acs.langmuir.3c00628 · Cited by 12

Balanced between order and disorder: a new phase in transcription elongation control and beyond

Lu, H., Liu, R., & Zhou, Q. (2019) · Transcription · doi:10.1080/21541264.2019.1570812 · Cited by 12

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

Single-cell nascent transcription reveals sparse genome usage and plasticity

Ma, S., Hong, Y., Chen, J., Xu, J., & Shen, X. (2025) · Cell · doi:10.1016/j.cell.2025.09.003 · Cited by 12

Ssu72 Dual-Specific Protein Phosphatase: From Gene to Diseases

Hwang, S., Kim, M., & Lee, C. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073791 · Cited by 11

Oxidative stress induces Ser 2 dephosphorylation of the RNA polymerase II CTD and premature transcription termination

Yamazaki, T., Liu, L., & Manley, J. L. (2021) · Transcription · doi:10.1080/21541264.2021.2009421 · Cited by 12

Lighting up Nobel Prize-winning studies with protein intrinsic disorder

Piersimoni, L., el Malek, M. A., Bhatia, T., Bender, J., Brankatschk, C., Sánchez, J. C., Dayhoff, G. W., Ianni, A. D., Parra, J. O. F., Martínez, D. G., et al. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04468-y · Cited by 11

Phosphorylation and specific DNA improved the incorporation ability of p53 into functional condensates

Chen, Q., Wu, Y., Dai, Z., Zhang, Z., & Yang, X. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.123221 · Cited by 12

Removing quote marks from the RNA polymerase II CTD ‘code’

Dieci, G. (2021) · Biosystems · doi:10.1016/j.biosystems.2021.104468 · Cited by 12

A CDK11-dependent RNA polymerase II pause-checkpoint precedes CDK9-mediated transition to transcriptional elongation

Devlin, J. R., Martin, B. P., Bartoniček, N., Ting, K., Fan, Z., Todorovski, I., Bjelosevic, F., Verschoor, S., Ciccone, A., Trapani, J. A., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.08.001 · Cited by 12

De Novo Polycomb Recruitment and Repressive Domain Formation

Hernández-Romero, I. A., & Valdés, V. J. (2022) · Epigenomes · doi:10.3390/epigenomes6030025 · Cited by 11

Tox4 regulates transcriptional elongation and reinitiation during murine T cell development

Wang, T., Zhao, R., Zhi, J., Liu, Z., Wu, A., Yang, Z., Wang, W., Ni, T., Jing, L., & Yu, M. (2023) · Communications Biology · doi:10.1038/s42003-023-04992-y · Cited by 10

Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics

Yang, Y.-L., Duan, Z., Liu, X., Li, Z., Shen, Z., Gong, S., Hu, Y., Hu, Y., Song, L., Wang, Z., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf162 · Cited by 12

Multifaceted Roles of ICP22/ORF63 Proteins in the Life Cycle of Human Herpesviruses

Wu, Y., Yang, Q., Wang, M., Chen, S., Jia, R., Yang, Q., Zhu, D., Liu, M., Zhao, X., Zhang, S., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.668461 · Cited by 11

Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains

Gibbons, M. D., Fang, Y., Spicola, A. P., Linzer, N., Jones, S. M., Johnson, B. R., Li, L., Xie, M., & Bungert, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23169290 · Cited by 12

MDC1 maintains active elongation complexes of RNA polymerase II

Pappas, G. D., Munk, S. H. N., Watanabe, K., Thomas, Q. A., Gál, Z., Gram, H. H., Lee, M., Gómez-Cabello, D., Kanellis, D. C., Olivares‐Chauvet, P., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2022.111979 · Cited by 12

The role of O-GlcNAcylation in RNA polymerase II transcription

Lewis, B. A. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.105705 · Cited by 11

Targeting General Transcriptional Machinery as a Therapeutic Strategy for Adult T-Cell Leukemia

Wong, R. W. J., Ishida, T., & Sanda, T. (2018) · Molecules · doi:10.3390/molecules23051057 · Cited by 11

Nanoscale analysis of human G1 and metaphase chromatin in situPreprint

Chen, J. K., Liu, T., Cai, S., Ruan, W., Ng, C. T., Shi, J. R., Surana, U., & Gan, L. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.31.551204 · Cited by 11

Nuclear patterns of phosphatidylinositol 4,5‐ and 3,4‐bisphosphate revealed by super‐resolution microscopy differ between the consecutive stages of RNA polymerase II transcription

Hoboth, P., Sztacho, M., & Hozák, P. (2024) · FEBS Journal · doi:10.1111/febs.17136 · Cited by 9

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

HIV-1 transcriptional modulation: novel host factors and prospective therapeutic strategies

Gibaut, Q. M. R., Mori, L., & Valente, S. T. (2023) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000808 · Cited by 11

Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation

Amith, W. D., & Dutagaci, B. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c02655 · Cited by 8

Structure and Functions of the Mediator Complex

Putlyaev, E. V., Ibragimov, A. N., Lebedeva, L. A., Georgiev, P. G., & Shidlovskii, Y. V. (2018) · Biochemistry (Moscow) · doi:10.1134/s0006297918040132 · Cited by 12

Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast

Aristizabal, M. J., Dever, K., Negri, G. L., Shen, M., Hawe, N., Benschop, J. J., Holstege, F. C. P., Krogan, N. J., Sadowski, I., & Kobor, M. S. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.008515 · Cited by 10

Low complexity domains, condensates, and stem cell pluripotency

Vodnala, M., Choi, E., & Fong, Y. W. (2021) · World Journal of Stem Cells · doi:10.4252/wjsc.v13.i5.416 · Cited by 10

Promoter and Gene-Body RNA-Polymerase II co-exist in partial demixed condensatesPreprint

Changiarath, A., Flores‐Solis, D., Michels, J. J., Herrera-Rodríguez, R., Hanson, S. M., Schmid, F., Zweckstetter, M., Padeken, J., & Stelzl, L. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.16.585180 · Cited by 13

Phase separation and transcriptional regulation in cancer development

Gu, Y., Wei, K., & Wang, J. (2024) · Journal of Biomedical Research · doi:10.7555/jbr.37.20230214 · Cited by 8

Regulation of Eukaryotic RNAPs Activities by Phosphorylation

González-Jiménez, A., Campos, A., Navarro, F., Clemente‐Blanco, A., & Calvo, O. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.681865 · Cited by 10

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

Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly

Kasiliauskaitė, A., Kubíček, K., Klumpler, T., Zanova, M., Zapletal, D., Koutná, E., Nováček, J., & Štefl, R. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac451 · Cited by 7

Cellular state landscape and herpes simplex virus type 1 infection progression are connected

Pietilä, M. K., Bachmann, J. J., Ravantti, J., Pelkmans, L., & Fraefel, C. (2023) · Nature Communications · doi:10.1038/s41467-023-40148-6 · Cited by 9

Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis

Obermeyer, S., Schrettenbrunner, L., Stöckl, R., Schwartz, U., & Grasser, K. D. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad825 · Cited by 8

EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism

Olmedo-Pelayo, J., Granado-Calle, E., Delgado‐Bellido, D., Lobo-Selma, L., Jordán-Pérez, C., Amaral, A. T., Ehlers, A. C., Ohmura, S., García-Domínguez, D. J., Mackintosh, C., et al. (2025) · Oncogene · doi:10.1038/s41388-025-03496-9 · Cited by 9

CVB3 VP1 interacts with MAT1 to inhibit cell proliferation by interfering with Cdk-activating kinase complex activity in CVB3-induced acute pancreatitis

Zhang, H., Zeng, L., Liu, Q., Jin, G., Zhang, J., Li, Z., Xu, Y., Tian, H., Deng, S., Shi, Q., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1008992 · Cited by 9

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