Cited by 506Genomics and Chromatin DynamicsRNA Research and SplicingNuclear Structure and Function

The DOI matches its Crossref record; 159 of the 159 references it cites were found in a registry or an index.

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

Harlen, Kevin M., Churchman, L. Stirling·2017·Nature Reviews Molecular Cell Biology

DOI 10.1038/nrm.2017.10

Open this paper in CoChat — free account

Abstract

The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II (Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the transcription process, the CTD is dynamically modified by post-translational modifications, many of which facilitate or hinder the recruitment of key regulatory factors of Pol II that collectively constitute the 'CTD code'. Recent studies have revealed how the physicochemical properties of the CTD promote phase separation in the presence of other low-complexity domains. Here, we discuss the intricacies of the CTD code and how the newly characterized physicochemical properties of the CTD expand the function of the CTD beyond the code.

Integrity signals

Registry

Crossref · 10.1038/nrm.2017.10

Cites

159 of 159 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Liquid-Liquid Phase Separation in Biology
Hyman, A. A., Weber, C. A., & Jülicher, F. (2014) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100913-013325 · Cited by 3,155
A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation
Patel, A., Lee, H. O., Jawerth, L. M., Maharana, S., Jahnel, M., Hein, M. Y., Stoynov, S., Mahamid, J., Saha, S., Franzmann, T. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.047 · Cited by 2,927
Widespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
The economics of ribosome biosynthesis in yeast
Warner, J. R. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(99)01460-7 · Cited by 1,933
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
Adelman, K., & Lis, J. T. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3293 · Cited by 1,221
Controlling the elongation phase of transcription with P-TEFb
Peterlin, B. M., & Price, D. H. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.06.014 · Cited by 1,144
Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity
Ng, H., Robert, F., Young, R. A., & Struhl, K. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00092-3 · Cited by 1,131
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
Histone exchange, chromatin structure and the regulation of transcription
Venkatesh, S., & Workman, J. L. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3941 · Cited by 997
Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II
Burke, K. A., Janke, A. M., Rhine, C. L., & Fawzi, N. L. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.006 · Cited by 932

Flagged first, then by citations

Show all 159 references

Sorted by citations

Items 301–400 of 506

Cell-type specific concentration regulation of the basal transcription factor TFIIH in XPBy/y mice model
Donnio, L., Miquel, C., Vermeulen, W., Giglia‐Mari, G., & Mari, P. (2019) · Cancer Cell International · doi:10.1186/s12935-019-0945-4 · Cited by 7
Physiochemical Mechanisms of Biomolecular Liquid-Liquid Phase Separation
Zhang, C., & Lai, L. (2020) · Acta Physico-Chimica Sinica · doi:10.3866/pku.whxb201907053 · Cited by 7
Liquid-liquid phase separation as triggering factor of fibril formation
Khorsand, F. R., & Uversky, V. N. (2024) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2024.03.006 · Cited by 6
RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cells
Hisler, V., Bardot, P., Detilleux, D., Bernardini, A., Stierlé, M., Sánchez, E. G., Richard, C., Arab, L. H., Ehrhard, C., Morlet, B., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114791 · Cited by 6
Unique features of transcription termination and initiation at closely spaced tandem human genes
Nissani, N., & Ulitsky, I. (2022) · Molecular Systems Biology · doi:10.15252/msb.202110682 · Cited by 5
Dual function of SF3B2 on chromatin and RNA to regulate transcription in head and neck squamous cell carcinoma
Kitamura, K., Suzuki, H., Abe, R., Inohara, H., Kaneda, Y., Takahashi, H., & Nimura, K. (2022) · Cell & Bioscience · doi:10.1186/s13578-022-00812-8 · Cited by 6
Systematic mutagenesis of TFIIH subunit p52/Tfb2 identifies residues required for XPB/Ssl2 subunit function and genetic interactions with TFB6
Bassett, J., Rimel, J. K., Basu, S., Basnet, P., Luo, J., Engel, K. L., Nagel, M., Woyciehowsky, A., Ebmeier, C. C., Kaplan, C. D., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102433 · Cited by 7
Elongation rate of RNA polymerase II affects pausing patterns across 3′ UTRs
Khitun, A., Brion, C., Moqtaderi, Z., Geisberg, J. V., Churchman, L. S., & Struhl, K. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105289 · Cited by 7
Self-citation
Spt5 C-terminal repeat domain phosphorylation and length negatively regulate heterochromatin through distinct mechanisms
MacKinnon, S., Pagé, V., Chen, J. J., SHARIAT, A., Martin, R., Hébert, T. E., & Tanny, J. C. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010492 · Cited by 6
Protein phosphatase PP1 regulation of RNA polymerase II transcription termination and allelic exclusion of VSG genes in trypanosomes
Kieft, R., Zhang, Y., Yan, H., Schmitz, R. J., & Sabatini, R. S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae392 · Cited by 6
Macromolecular and cytological changes in fission yeast G0 nuclei
Tan, Z. Y., Cai, S., Paithankar, S. A., Liu, T., Nie, X., Shi, J. R., & Gan, L. (2025) · Journal of Cell Science · doi:10.1242/jcs.263654 · Cited by 6
A novel RNA pol II CTD interaction site on the mRNA capping enzyme is essential for its allosteric activation
Bage, M., Almohammed, R., Cowling, V. H., & Pisliakov, A. V. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab130 · Cited by 6
Methods for the analysis of transcriptome dynamics
Rodrigues, D. F., Costa, V. M., Silvestre, R., Bastos, M. D. L., & Carvalho, F. D. (2019) · Toxicology Research · doi:10.1039/c9tx00088g · Cited by 6
Dynamics of transcription-dependent H3K36me3 marking by the SETD2:IWS1:SPT6 ternary complexPreprint
Čermáková, K., Smith, E. A., Veverka, V., & Hodges, H. C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/636084 · Cited by 8
Tracking chromatin state changes using μ Map photo-proximity labelingPreprint
Seath, C. P., Burton, A. J., MacMillan, D. W. C., & Muir, T. W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.28.462236 · Cited by 6
Targeting processive transcription for Myc-driven circuitry in medulloblastoma
Sobral, L. M., Walker, F. M., Madhavan, K. P. C., Janko, E., Donthula, S., Danis, E. P., Bompada, P., Balakrishnan, I., Wang, D., Pierce, A. M., et al. (2025) · Neuro-Oncology · doi:10.1093/neuonc/noaf121 · Cited by 5
Bromodomain-containing proteins interact with a non-canonical RNA polymerase II kinase to maintain gene expression upon heat stress
Zheng, X., Zuo, Z., Peng, Y., Li, X., Zhang, Q., & Chen, X. (2025) · Nature Plants · doi:10.1038/s41477-025-02044-3 · Cited by 5
A regulatory role for the unstructured C-terminal domain of the CtBP transcriptional corepressor
Raicu, A., Suresh, M., & Arnosti, D. N. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105490 · Cited by 5
The deubiquitylase Ubp15 couples transcription to mRNA export
Eyboulet, F., Jerónimo, C., Côté, J., & Robert, F. (2020) · eLife · doi:10.7554/elife.61264 · Cited by 5
Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation
Ford, K. M., Munson, B. P., Fong, S. H., Panwala, R., Chu, W. K., Rainaldi, J., Plongthongkum, N., Vinayagam, A., Kostrowicki, J., Meluzzi, D., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-33329-2 · Cited by 5
Phase separation of RNA-binding protein promotes polymerase engagement and transcriptionPreprint
Shao, W., Bi, X., Gao, B., Wu, J. F., Pan, Y., Yin, Y., Liu, Z., Zhang, W., Jiang, X., Ren, W., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.26.436939 · Cited by 5
Transcription machinery clustering by Integrator synchronizes histone gene expressionPreprint
Lu, F., Park, B. J., Fujiwara, R., Wilusz, J. E., Gilmour, D. S., Lehmann, R., & Lionnet, T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.07.561364 · Cited by 6
Monitoring transcription by nascent RNA sequencing in crop plants
Zhu, M., Liu, M., & Dong, Z. (2024) · New Crops · doi:10.1016/j.ncrops.2024.100031 · Cited by 4
Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation
Tei, S., Bando, M., Sakata, T., Yoshimura, A., Natsume, T., Kanemaki, M. T., Sutani, T., & Shirahige, K. (2026) · Nature Communications · doi:10.1038/s41467-026-76738-3 · Cited by 4
FeaSion decodes the regulatory landscape and functional diversity of RNA polymerase II CTD phosphorylation
Zhu, J., Bao, L., Xu, S., & Ji, X. (2025) · Science Advances · doi:10.1126/sciadv.adz2345 · Cited by 5
The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate
Hyder, U., & Bentley, D. L. (2026) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051424-053703 · Cited by 5
Phase separation in synthetic biology
Shuyu, S., Si, W., Xiaoyi, O., & Ping, W. (2021) · Quantitative Biology · doi:10.15302/j-qb-021-0262 · Cited by 4
Transcriptional pausing induced by ionizing radiation enables the acquisition of radioresistance in nasopharyngeal carcinoma
Liu, H., Fu, H., Yu, C., Zhang, N., Huang, C., Lv, L., Hu, C., Chen, F., Xiao, Z., Zhang, Z., et al. (2023) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjad044 · Cited by 7
Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription
Bhandare, P., Narain, A., Hofstetter, J., Rummel, T., Wenzel, J., Schülein‐Völk, C., Lamer, S., Eilers, U., Schlösser, A., Eilers, M., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1219 · Cited by 4
Cyclin-dependent kinases as mediators of aberrant transcription in prostate cancer
Rahman, R., & Selth, L. A. (2025) · Translational Oncology · doi:10.1016/j.tranon.2025.102378 · Cited by 5
Phosphorylation modulates secondary structure of intrinsically disorder regions in RNA polymerase II
Chen, W., Laremore, T. N., Yennawar, N. H., & Showalter, S. A. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108533 · Cited by 4
N-terminal intrinsic disorder is an ancestral feature of Gγ subunits that influences the balance between different Gβγ signaling axes in yeast
Su, X., Pang, Y. T., Li, W., Gumbart, J. C., Kelley, J. B., & Torres, M. P. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104947 · Cited by 4
The Long and the Short of the RNA Polymerase C-Terminal Domain and Phase Separation
Isaac, R. S., & Churchman, L. S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.004 · Cited by 4
Self-citation
Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in ArabidopsisPreprint
Mori, S., Oya, S., Takahashi, M. M., Takashima, K., Inagaki, S., & Kakutani, T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.17.528985 · Cited by 4
Mixed Messages: Dynamic and Compositional Heterogeneity of Nuclear Messenger Ribonucleoprotein ( mRNP ) Complexes
Wechsler, T., Asada, R., & Montpetit, B. (2025) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.70032 · Cited by 3
CDK9 is a dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas
Wang, C., Abdelrahman, S., Geng, X., Burgess, A., Hu, Y., Rauf, M. A., Kady, N., Fu, Y., Reilly, T. A., Maine, I. P., et al. (2025) · Blood Cancer Journal · doi:10.1038/s41408-025-01427-1 · Cited by 3
DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID
Subramani, P. G., Seija, N., Ridani, J., Boulais, J., Donnelly, P. A., Provencher, M., Bagci, H., Poitras, C., Côté, J., Robert, F., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68332-4 · Cited by 3
Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation
McGeoch, A. J. S., Cushing, V. I., Roumeliotis, T. I., Cronin, N., Hearnshaw, S. J., Choudhary, J. S., Alfieri, C., & Greber, B. J. (2026) · Nature Communications · doi:10.1038/s41467-026-72329-4 · Cited by 3
DNA-binding, multivalent interactions and phase separation in transcriptional activation
Smith, N. C., & Matthews, J. M. (2023) · Australian Journal of Chemistry · doi:10.1071/ch22269 · Cited by 3
NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit
Kang, Z., Xu, C., Lü, S., Gong, J., Yan, R., Luo, G., Wang, Y., He, Q., Wu, Y., Yan, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-55579-y · Cited by 3
FUBP3 enhances HIV-1 transcriptional activity and regulates immune response pathways in T cells
Gibaut, Q. M. R., Li, C., Cheng, A., Moranguinho, I., Mori, L., & Valente, S. T. (2025) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2025.102525 · Cited by 3
Coupling between nucleotide excision repair and gene expression
Botto, A. E. C., Muñoz, J. C., & Muñoz, M. J. (2018) · RNA Biology · doi:10.1080/15476286.2018.1464354 · Cited by 3
Transcriptionally active regions are highly limited in the nucleus of the plant sperm cell
Shibuta, M. K., & Matsunaga, S. (2023) · CYTOLOGIA · doi:10.1508/cytologia.88.273 · Cited by 3
Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription
Rajan, S. S., Ebegboni, V. J., Pichling, P., Ludwig, K. R., Jones, T. L., Chari, R., Tran, A. D., Kruhlak, M. J., Lončarek, J., & Caplen, N. J. (2024) · Molecular and Cellular Biology · doi:10.1080/10985549.2024.2315425 · Cited by 4
ZmSSRP1 facilitates the progression of RNA polymerase II and is essential for kernel development in maize
Wang, J., Wang, Q., Peng, Y.-X., Jiang, L., Lu, Z., Zheng, L.-M., Li, X., Liu, J., Long, J., Liu, J., et al. (2025) · The Plant Cell · doi:10.1093/plcell/koaf071 · Cited by 3
The Elongation Regulators and Architectural Proteins as New Participants of Eukaryotic Gene Transcription
Vorobyeva, N. E., & Mazina, M. Y. (2021) · Russian Journal of Genetics · doi:10.1134/s1022795421060144 · Cited by 3
Ras and Rho GTPase regulation of Pol II transcription: A shortcut model revisited
Zheng, Z. (2017) · Transcription · doi:10.1080/21541264.2017.1321612 · Cited by 3
The gammaherpesviral TATA-box-binding protein directly interacts with the CTD of host RNA Pol II to direct late gene transcriptionPreprint
Castañeda, A. F., Didychuk, A. L., Louder, R. K., McCollum, C. O., Davis, Z. H., Nogales, E., & Glaunsinger, B. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.28.922526 · Cited by 3
Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiaePreprint
Singh, P., Chaudhuri, A., Banerjea, M., Marathe, N., & Das, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.02.129106 · Cited by 3
Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in TrypanosomesPreprint
Kieft, R., Zhang, Y., Yan, H., Schmitz, R. J., & Sabatini, R. S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.21.563358 · Cited by 3
CDK8 fine-tunes IL-6 transcriptional activities by limiting STAT3 resident time at the gene loci
Martinez-Fabregas, J., Wang, L., Pohler, E., Cozzani, A., Kazemian, M., Mitra, S., & Moraga, I. (2020) · doi:10.1101/2020.03.19.998351 · Cited by 2
Phosphorylation Dynamics and Kinase Interaction in mRNA Transcription-Associated Kinases: Autophosphorylation of CDK12 and its Modulation by CDK7 and CDK9
Yamakawa, H., Ebara, S., Yoshida, M., Yamamoto, K., Hayashi, K., Shimokawa, K., Araki, S., Tauchi, H., & Morishita, D. (2024) · BPB Reports · doi:10.1248/bpbreports.7.5_170 · Cited by 2
PNUTS:PP1 recruitment to Tox4 regulates chromosomal dispersal in Drosophila germline development
Duncalf, L., Wang, X., Aljabri, A. A., Campbell, A. E., Alharbi, R. Q., Donaldson, I. J., Hayes, A., Peti, W., Page, R., & Bennett, D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115693 · Cited by 2
Chromatin Regulatory Targets for Anticancer Therapeutics
Barta, P. A., Carter, T. R., & Erb, M. A. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.5c00231 · Cited by 2
CPSF73 activation and 3′ RNA polymerase II pausing are lost during readthrough transcription after heat shock
Walsh, K. E., Goodrich, J. A., & Kugel, J. F. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117039 · Cited by 2
BRD4: From molecular understanding to therapeutics development
Wu, S.-Y., & Chiang, C. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.07.004 · Cited by 2
Association of peptidyl prolyl cis/trans isomerase Rrd1 with C terminal domain of RNA polymerase II
Kashif, M., Kumar, B., Bharati, A. P., Altayeb, H. N., Asalam, M., Akhtar, M. S., Khan, M. I., Ahmad, A., Chaudhary, H., Hosawi, S. B. I., et al. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.124653 · Cited by 2
Ceg1 depletion reveals mechanisms governing degradation of non-capped RNAs in Saccharomyces cerevisiae
Zanin, O., Eastham, M., Winczura, K., Ashe, M., Martínez-Nuñez, R. T., Hebenstreit, D., & Grzechnik, P. (2023) · Communications Biology · doi:10.1038/s42003-023-05495-6 · Cited by 2
An alpha-herpesvirus employs host HEXIM1 to promote viral transcription
Wu, Y., Sun, A., Yang, Q., Wang, M., Tian, B., Yang, Q., Jia, R., Chen, S., Ou, X., Huang, J., et al. (2024) · Journal of Virology · doi:10.1128/jvi.01392-23 · Cited by 2
PRC2 primes bivalent genes for transcription induction independent of histone methyltransferase activity
Gong, M., Yuan, Y., Dai, Z., Lv, X., Su, J., Huo, D., Niu, L., Chen, X., & Wu, X. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2573-2 · Cited by 2
Exploring the Role of Unconventional Post-Translational Modifications in Cancer Diagnostics and Therapy
Sharma, S., Sarkar, O., & Ghosh, R. (2024) · Current Protein and Peptide Science · doi:10.2174/0113892037274615240528113148 · Cited by 3
Development of CDK12 as a Cancer Therapeutic Target and Related Inhibitors
Chen, B., & Liu, J. (2024) · Current Cancer Drug Targets · doi:10.2174/0115680096307629240611104728 · Cited by 2
An oncoprotein CREPT functions as a co-factor in MYC-driven transformation and tumor growth
Li, M., Li, J., He, C., Jiang, G., Ma, D., Guan, H., Lin, Y.-T., Li, M., Jia, J., Duan, X., et al. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.108030 · Cited by 2
The role of RNA polymerase II transcript elongation factors in plant stress responses
Grasser, K. D. (2024) · Journal of Experimental Botany · doi:10.1093/jxb/erae472 · Cited by 3
Chemical Tools for Studying the Impact of cis/trans Prolyl Isomerization on Signaling: A Case Study on RNA Polymerase II Phosphatase Activity and Specificity
Burkholder, N. T., Medellin, B. P., Irani, S., Matthews, W. L., Showalter, S. A., & Zhang, Y. (2018) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2018.04.020 · Cited by 2
Methods for Identification of Substrates/Inhibitors of FCP/SCP Type Protein Ser/Thr Phosphatases
Mizunuma, M., Kaneko, A., Imai, S., Furukawa, K., & Chuman, Y. (2020) · Processes · doi:10.3390/pr8121598 · Cited by 2
Dynamic regulation of promoter-proximal RNA polymerase II pausing
Guo, C., Luo, Z., & Lin, C. (2020) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/tb-2020-0581 · Cited by 2
NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolutionPreprint
Mylonas, C., & Tessarz, P. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/246827 · Cited by 2
RNA polymerase II transcription with partially assembled TFIID complexesPreprint
Hisler, V., Bardot, P., Detilleux, D., Stierlé, M., Sánchez, E. G., Richard, C., Arab, L. H., Ehrhard, C., Morlet, B., Hadzhiev, Y., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.27.567046 · Cited by 2
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5Preprint
Šebesta, M., Skubnik, K., Morton, W., Kravec, M., Linhartova, K., Klapstova, V., Nováček, J., Kubíček, K., Bryja, V., Vácha, R., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.05.636647 · Cited by 2
Stalling of elongating Pol II triggers Ser7 phosphorylation in trans to drive transcription recoveryPreprint
Shlamovitz, I., Bao, Y., Toteva, T., Crisp, A., Ye, S., Wingett, S., Cacioppo, R., Edmondson, A., Castiblanco, D., Boemo, M. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.04.692291 · Cited by 2
CDK12/13 inhibitor, CTX-439, suppresses tumor growth and potentiates BCL-2 family blockadePreprint
Yamakawa, H., Khatab, R., Mizutani, A., Ebara, S., Hirayama, T., Tanaka, S., Tarumoto, Y., Sugiyama, M., Sugino, S., Takano, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.20.706902 · Cited by 3
Glc7/PP1 triggers Paf1 complex dissociation from RNA polymerase II to enable transcription terminationPreprint
Namjilsuren, S., & Arndt, K. M. (2026) · Genes & Development · doi:10.1101/gad.353379.125 · Cited by 2
Regulation of gene expression in mammals
Goswami, S. K. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91305-8.00019-3 · Cited by 1
N-terminal tagging of RNA Polymerase II shapes transcriptomes more than C-terminal alterations
Callan-Sidat, A., Zewdu, E., Cavallaro, M., Liu, J., & Hebenstreit, D. (2024) · iScience · doi:10.1016/j.isci.2024.109914 · Cited by 1
Interaction of CDK12 with NXF1 is a new node for the linking mechanism between transcription and transportation of mRNA
Ebara, S., Yoshida, M., Yamakawa, H., Shimokawa, K., Inoue, Y., Tauchi, H., & Morishita, D. (2024) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2024.150608 · Cited by 1
Dynamic changes in chromatin structure and transcriptional activity in the generative cells of Lilium longiflorum
Shibuta, M. K., Aso, T., & Okawa, Y. (2025) · Journal of Plant Research · doi:10.1007/s10265-025-01637-5 · Cited by 1
Targeting CDK7/12/13 functional synergism reverses myofibroblast activation and ameliorates lung fibrosis
Ma, H., Huang, Z., Jeet, S., Emerson, C., Bender, H. S., Ren, Q., & Ding, N. (2025) · iScience · doi:10.1016/j.isci.2025.112778 · Cited by 1
Unraveling gene expression: a beginner’s guide from chromatin modifications to mRNA export in Saccharomyces cerevisiae
Serrano‐Quílez, J., & Rodríguez‐Navarro, S. (2025) · Nucleus · doi:10.1080/19491034.2025.2516909 · Cited by 1
Transcriptional Condensates: Epigenetic Reprogramming and Therapeutic Targets in Hematologic Malignancies
Qiu, K., Yin, Q., Zang, C., & Tao, J. (2025) · Cancers · doi:10.3390/cancers17193148 · Cited by 1
The Loss-and-Gain Strategy for Functional Specialization of Plant-Specific RNA Polymerases
Wu, X., Huang, K., Zhang, H., Sun, S., Zz, G., Sun, H., Zhang, Y., Liu, X., Mu, W., Xu, W., et al. (2026) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-063025-102003 · Cited by 1
Targeting super-enhancer-driven SKIL transcription by CDK7 inhibitor THZ1 to suppress gastric cancer progression
Lan, B., Zhou, T., Pan, L., Cui, M., Tan, Q., Pu, T., Ran, L., Wei, S., Zhu, X., & Huang, H. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-07721-1 · Cited by 1
Cytoplasmic mRNA decay by the antiviral nuclease RNase L promotes transcriptional repression
Mao, X., Tokamov, S. A., Pahmeier, F., Lari, A., Xu, J., Harris, E., & Glaunsinger, B. A. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117028 · Cited by 1
An H3K4me3 reader recruits the positive transcription elongation factor B complex to facilitate transcription elongation in Arabidopsis
Yu, X., Lu, X., Huang, C., Deng, Z., Chai, S., Du, J., Yang, Z., Zheng, X., Wang, L., & Yan, S. (2026) · Developmental Cell · doi:10.1016/j.devcel.2026.02.005 · Cited by 1
The molecular basis of transcription initiation by RNA polymerase II
Chen, X., & Xu, Y. (2026) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-026-01019-2 · Cited by 1
Visualization, Quantification, and Modeling of Endogenous RNA Polymerase II Phosphorylation at a Single-copy Gene in Living Cells
Forero-Quintero, L. S., Raymond, W., Munsky, B. E., & Stasevich, T. J. (2022) · BIO-PROTOCOL · doi:10.21769/bioprotoc.4482 · Cited by 1
Multiple Fra-1-bound enhancers showing different molecular and functional features can cooperate to repress gene transcription
Bejjani, F., Evanno, E., Mahfoud, S., Tolza, C., Zibara, K., Piechaczyk, M., & Jariel‐Encontre, I. (2023) · Cell & Bioscience · doi:10.1186/s13578-023-01077-5 · Cited by 2
Inhibitory function of CDK12i combined with WEE1i on castration-resistant prostate cancer cells in vitro and in vivo
Qin, Z., Liu, D., Zhang, Y., Chen, X., Zhu, X., Xu, S., Peng, B., Dong, S., Hou, D., Zhu, L., et al. (2023) · ONCOLOGIE · doi:10.1515/oncologie-2023-0233 · Cited by 1
A missing link in male meiotic sex chromosome inactivation: the effectors of DDR factors
Li, M., Li, H., & Liu, H. (2023) · Scientia Sinica Vitae · doi:10.1360/ssv-2023-0198 · Cited by 1
A critical role for Pol II CTD phosphorylation in heterochromatic gene activation
Kainth, A. S., Zhang, H., & Gross, D. S. (2024) · Gene · doi:10.1016/j.gene.2024.148473 · Cited by 1
Assembly of the Xrn2/Rat1–Rai1–Rtt103 termination complexes in mesophilic and thermophilic organisms
Dikunová, A., Noskova, N. V., Overbeck, J. H., Polak, M., Stelzig, D., Zapletal, D., Kubíček, K., Nováček, J., Sprangers, R., & Štefl, R. (2024) · Structure · doi:10.1016/j.str.2024.11.010 · Cited by 1
Conducting the CTD orchestra
Robles, C. M. G., & Coin, F. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0201-6 · Cited by 1
Arginine citrullination at the C-terminal domain controls RNA polymerase II transcriptionPreprint
Sharma, P., Lioutas, A., Fernandez-Fuentes, N., Quilez, J., Carbonell‐Caballero, J., Wright, R. H. G., Vona, C. D., Dily, F. L., Schüller, R., Eick, D., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/216143 · Cited by 1
Human TFIIH Kinase CDK7 Regulates Transcription-Associated Epigenetic ModificationsPreprint
Ebmeier, C. C., Erickson, B., Allen, B., Allen, M. A., Kim, H., Fong, N., Jacobsen, J. R., Liang, K., Shilatifard, A., Dowell, R. D., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3155590 · Cited by 1
New link between the RNA polymerase II-CTD and replication stress
Landsverk, H. B., Sandquist, L. E., Bay, L. T. E., & Syljuåsen, R. G. (2021) · Molecular & Cellular Oncology · doi:10.1080/23723556.2021.1910008 · Cited by 1
The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulatorsPreprint
Appel, L.-M., Grishkovskaya, I., Benedum, J., Franke, V., Polyansky, A. A., Neudolt, A., Wunder, A., Žagrović, B., Akalin, A., Djinović‐Carugo, K., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.26.482114 · Cited by 1
Spt6 directly interacts with Cdc73 and is required for Paf1C recruitment to active genesPreprint
Ellison, M. A., Blacksmith, M. S., Namjilsuren, S., Shirra, M. K., Schusteff, R. A., Kerr, E. M., Fang, F., Xiang, Y., Shi, Y., & Arndt, K. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.04.490663 · Cited by 1
A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophyPreprint
Townley, B. A., Buerer, L., Bacolla, A., Rusanov, T., Schmidt, N., Srivatsan, S. N., Clark, N. E., Mansoori, F., Sample, R. A., Brickner, J. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.03.515106 · Cited by 1
Fine tuning of Rpb4 phosphorylation modulates Rpb4/7 stoichiometry within yeast RNA polymerase II and regulates gene expressionPreprint
González-Jiménez, A., González-Jiménez, M. D. C., Jordán‐Pla, A., Medina, I., Alfonso, M. J., Richard, S., Fernández‐Tornero, C., Choder, M., & Calvo, O. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.15.571801 · Cited by 2
Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modificationsPreprint
Francette, A. M., & Arndt, K. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.25.591159 · Cited by 1

Authors: Harlen, K. M., & Churchman, L. S.
Affiliations: Harvard University (US)
Corresponding author: Churchman, L. Stirling
ORCID: Harlen, Kevin M.
Churchman, L. Stirling
Venue: Nature Reviews Molecular Cell Biology
Publisher: Springer Science and Business Media LLC
Published: 2017-03-01
Volume: 18
Issue: 4
Pages: 263-273
ISSN: 1471-0072 (ISSN-L)
1471-0080
DOI: 10.1038/nrm.2017.10
OpenAlex: W2594707272
Cited by: 499
References: 159
Citations by year: 2026: 40 · 2025: 46 · 2024: 70 · 2023: 65 · 2022: 51 · 2021: 66 · 2020: 65 · 2019: 44 · 2018: 35 · 2017: 17
FWCI: 4.15
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Reviews Molecular Cell Biology (publishedVersion)
PubMed (publishedVersion)
Funders: National Human Genome Research Institute (R01HG007173)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords: RNA polymerase II, C-terminal domain, post-translational modification, transcriptional regulation, phase separation, low-complexity domains
MeSH terms: Protein Domains, Gene Expression Regulation, Humans, Phosphorylation, Protein Processing, Post-Translational, RNA Polymerase II, Transcription, Genetic

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks