Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II

Dutta, Arnob; Babbarwal, Vinod; Fu, Jianhua; Brunke-Reese, Deborah; Libert, Diane M.; Willis, Jonathan; Reese, Joseph C.

doi:10.1128/mcb.00044-15

Cited by 61Genomics and Chromatin DynamicsRNA Research and SplicingNuclear Structure and Function

Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II

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Dutta, Arnob, Babbarwal, Vinod, Fu, Jianhua, Brunke-Reese, Deborah, Libert, Diane M., Willis, Jonathan, Reese, Joseph C.·2015·Molecular and Cellular Biology

DOI 10.1128/mcb.00044-15PMC PMC4420917

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Abstract

Expression of the genome requires RNA polymerase II (RNAPII) to transcribe across many natural and unnatural barriers, and this transcription across barriers is facilitated by protein complexes called elongation factors (EFs). Genetic studies in Saccharomyces cerevisiae yeast suggest that multiple EFs collaborate to assist RNAPII in completing the transcription of genes, but the molecular mechanisms of how they cooperate to promote elongation are not well understood. The Ccr4-Not complex participates in multiple steps of mRNA metabolism and has recently been shown to be an EF. Here we describe how Ccr4-Not and TFIIS cooperate to stimulate elongation. We find that Ccr4-Not and TFIIS mutations show synthetically enhanced phenotypes, and biochemical analyses indicate that Ccr4-Not and TFIIS work synergistically to reactivate arrested RNAPII. Ccr4-Not increases the recruitment of TFIIS into elongation complexes and enhances the cleavage of the displaced transcript in backtracked RNAPII. This is mediated by an interaction between Ccr4-Not and the N terminus of TFIIS. In addition to revealing insights into how these two elongation factors cooperate to promote RNAPII elongation, our study extends the growing body of evidence suggesting that the N terminus of TFIIS acts as a docking/interacting site that allows it to synergize with other EFs to promote RNAPII transcription.

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Ccr4-Not can rescue backtracked RNA Pol II in the absence of TFIIS.
“While Ccr4‐Not can rescue backtracked RNA Pol II in the absence of TFIIS, further in vitro characterization showed that Ccr4‐Not also interacts with TFIIS and recruits it to the arrested elongation complex resulting in enhanced transcript cleavage (Dutta et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Dutta et al, 2015
Ccr4-Not interacts with TFIIS and recruits it to the arrested elongation complex, resulting in enhanced transcript cleavage.
“While Ccr4‐Not can rescue backtracked RNA Pol II in the absence of TFIIS, further in vitro characterization showed that Ccr4‐Not also interacts with TFIIS and recruits it to the arrested elongation complex resulting in enhanced transcript cleavage (Dutta et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Dutta et al, 2015

Designer deletion strains derived fromSaccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications
Brachmann, C. B., Davies, A., Cost, G. J., Caputo, E. M., Li, J., Hieter, P., & Boeke, J. D. (1998) · Yeast · doi:10.1002/(sici)1097-0061(19980130)14:2 · Cited by 3,411 · see citing works
Elongation by RNA polymerase II: the short and long of itPreprint
Sims, R. J., Belotserkovskaya, R., & Reinberg, D. (2004) · Genes & Development · doi:10.1101/gad.1235904 · Cited by 709 · see citing works
Uniform transitions of the general RNA polymerase II transcription complex
Mayer, A., Lidschreiber, M., Siebert, M., Leike, K., Söding, J., & Cramer, P. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1903 · Cited by 446 · see citing works
Structural basis of RNA polymerase II backtracking, arrest and reactivation
Cheung, A. C. M., & Cramer, P. (2011) · Nature · doi:10.1038/nature09785 · Cited by 373 · see citing works
Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo
Mason, P. B., & Struhl, K. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.017 · Cited by 359 · see citing works
Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage
Kettenberger, H., Armache, K., & Cramer, P. (2003) · Cell · doi:10.1016/s0092-8674(03)00598-1 · Cited by 355 · see citing works
Structure of Eukaryotic RNA Polymerases
Cramer, P., Armache, K., Baumli, S., Benkert, S., Brueckner, F., Buchen, C., Damsma, G. E., Dengl, S., Geiger, S. R., Jasiak, A. J., et al. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.130008 · Cited by 305 · see citing works
The Ccr4–Not complex
Collart, M. A., & Panasenko, O. O. (2011) · Gene · doi:10.1016/j.gene.2011.09.033 · Cited by 295 · see citing works
A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces
Venters, B. J., Wachi, S., Mavrich, T. N., Andersen, B. E., Jena, P., Sinnamon, A. J., Jain, P., Rolleri, N. S., Jiang, C., Hemeryck, C. S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.01.015 · Cited by 294 · see citing works
The Human PAF1 Complex Acts in Chromatin Transcription Elongation Both Independently and Cooperatively with SII/TFIIS
Kim, J., Guermah, M., & Roeder, R. G. (2010) · Cell · doi:10.1016/j.cell.2009.12.050 · Cited by 273 · see citing works
Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution
Wang, D., Bushnell, D. A., Huang, X., Westover, K. D., Levitt, M., & Kornberg, R. D. (2009) · Science · doi:10.1126/science.1168729 · Cited by 241 · see citing works
Gcn5 Promotes Acetylation, Eviction, and Methylation of Nucleosomes in Transcribed Coding Regions
Govind, C. K., Zhang, F., Qiu, H., Hofmeyer, K., & Hinnebusch, A. G. (2007) · Molecular Cell · doi:10.1016/j.molcel.2006.11.020 · Cited by 238 · see citing works
Promoting elongation with transcript cleavage stimulatory factors
Fish, R. N., & Kane, C. M. (2002) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(02)00459-1 · Cited by 236 · see citing works
Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates.
Izban, M. G., & Luse, D. S. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)42262-4 · Cited by 233 · see citing works
Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II.
Reines, D. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)50596-8 · Cited by 198 · see citing works
The multifunctional Ccr4–Not complex directly promotes transcription elongation
Kruk, J. A., Dutta, A., Fu, J., Gilmour, D. S., & Reese, J. C. (2011) · Genes & Development · doi:10.1101/gad.2020911 · Cited by 177 · see citing works
Self-citation
Ccr4-Not complex: the control freak of eukaryotic cells
Miller, J. E., & Reese, J. C. (2012) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2012.667214 · Cited by 176 · see citing works
Self-citation
RNA Polymerase Active Center: The Molecular Engine of Transcription
Nudler, E. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.76.052705.164655 · Cited by 168 · see citing works
Properties of RNA Polymerase II Elongation Complexes Before and After the P-TEFb-mediated Transition into Productive Elongation
Cheng, B. W., & Price, D. H. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702936200 · Cited by 165 · see citing works
To be or not to be active: the stochastic nature of enhancer action
Fiering, S., Whitelaw, E., & Martin, D. I. K. (2000) · BioEssays · doi:10.1002/(sici)1521-1878(200004)22:4 · Cited by 159 · see citing works
Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex
Murakami, K., Elmlund, H., Kalisman, N., Bushnell, D. A., Adams, C. M., Azubel, M., Elmlund, D., Levi‐Kalisman, Y., Liu, X., Gibbons, B. J., et al. (2013) · Science · doi:10.1126/science.1238724 · Cited by 155 · see citing works
The CCR4–NOT Complex Plays Diverse Roles in mRNA Metabolism
Denis, C. L., & Chen, J. (2003) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(03)01007-9 · Cited by 149 · see citing works
Evidence that Transcript Cleavage Is Essential for RNA Polymerase II Transcription and Cell Viability
Sigurðsson, S., Dirac-Svejstrup, A. B., & Svejstrup, J. Q. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.02.026 · Cited by 141 · see citing works
NuA4 Lysine Acetyltransferase Esa1 Is Targeted to Coding Regions and Stimulates Transcription Elongation with Gcn5
Ginsburg, D. S., Govind, C. K., & Hinnebusch, A. G. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01033-09 · Cited by 113 · see citing works
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes
Kim, B., Nesvizhskii, A. I., Rani, P. G., Hahn, S., Aebersold, R. H., & Ranish, J. A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704573104 · Cited by 108 · see citing works
Contending with transcriptional arrest during RNAPII transcript elongation
Svejstrup, J. Q. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.02.005 · Cited by 107 · see citing works
Structural basis of transcription elongation
Martínez-Rucobo, F. W., & Cramer, P. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.09.002 · Cited by 96 · see citing works
Genome-Wide Analysis of Factors Affecting Transcription Elongation and DNA Repair: A New Role for PAF and Ccr4-Not in Transcription-Coupled Repair
Gaillard, H., Tous, C., Botet, J., González‐Aguilera, C., Quintero, M., Viladevall, L., García-Rubio, M. L., Rodríguez‐Gil, A., Marín, A., Ariño, J., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000364 · Cited by 93 · see citing works
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
Schweikhard, V., Meng, C., Murakami, K., Kaplan, C. D., Kornberg, R. D., & Block, S. M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405181111 · Cited by 92 · see citing works
SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments
Izban, M. G., & Luse, D. S. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)31467-4 · Cited by 88 · see citing works
Genetic Evidence Supports a Role for the Yeast CCR4-NOT Complex in Transcriptional Elongation
Denis, C. L., Chiang, Y. C., Cui, Y., & Chen, J. (2001) · Genetics · doi:10.1093/genetics/158.2.627 · Cited by 85 · see citing works
Dual Roles for Transcription Factor IIF in Promoter Escape by RNA Polymerase II
Yan, Q., Moreland, R. J., Conaway, J. W., & Conaway, R. C. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.50.35668 · Cited by 84 · see citing works
Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA.
Gu, W., Powell, W. H., Mote, J., & Reines, D. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)74433-0 · Cited by 81 · see citing works
Large‐scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6‐azauracil
Riles, L., Shaw, R. J., Johnston, M., & Reines, D. (2004) · Yeast · doi:10.1002/yea.1068 · Cited by 77 · see citing works
The transcription factor TFIIS zinc ribbon dipeptide Asp-Glu is critical for stimulation of elongation and RNA cleavage by RNA polymerase II.
Jeon, C., Yoon, H. S., & Agarwal, K. L. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.19.9106 · Cited by 77 · see citing works
Yeast Transcript Elongation Factor (TFIIS), Structure and Function
Awrey, D. E., Shimasaki, N., Koth, C. M., Weilbaecher, R., Olmsted, V. K., Kazanis, S., Shan, X., Arellano, J., Arrowsmith, C. H., Kane, C. M., et al. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.35.22595 · Cited by 73 · see citing works
A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS
Palangat, M., Renner, D. B., Price, D. H., & Landick, R. C. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409405102 · Cited by 70 · see citing works
Studies on transcription of 3'-extended templates by mammalian RNA polymerase II. Parameters that affect the initiation and elongation reactions
Dedrick, R. L., & Chamberlin, M. J. (1985) · Biochemistry · doi:10.1021/bi00330a019 · Cited by 68 · see citing works
The structure of an Iws1/Spt6 complex reveals an interaction domain conserved in TFIIS, Elongin A and Med26
Diebold, M.-L., Koch, M., Loeliger, E., Cura, V., Winston, F., Cavarelli, J., & Romier, C. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.272 · Cited by 67 · see citing works
Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcriptionPreprint
Ghavi-Helm, Y., Michaut, M., Acker, J., Aude, J.-C., Thuriaux, P., Werner, M., & Soutourina, J. (2008) · Genes & Development · doi:10.1101/gad.471908 · Cited by 67 · see citing works
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics
Ishibashi, T., Dangkulwanich, M., Coello, Y., Lionberger, T. A., Lubkowska, L., Ponticelli, A. S., Kashlev, M., & Bustamante, C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401611111 · Cited by 55 · see citing works
Running with RNA polymerase: eukaryotic transcript elongation
Arndt, K. M., & Kane, C. M. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.08.008 · Cited by 54 · see citing works
The control of elongation by the yeast Ccr4–Not complex
Reese, J. C. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.09.001 · Cited by 54 · see citing works
Self-citation
Elongation by Drosophila RNA polymerase II. Transcription of 3′-extended DNA templates.
Sluder, A. E., Price, D. H., & Greenleaf, A. L. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)81605-8 · Cited by 53 · see citing works
Basic Mechanisms of RNA Polymerase II Activity and Alteration of Gene Expression in Saccharomyces cerevisiae
Kaplan, C. (2012) · Biochimica et Biophysica Acta · doi:10.1016/j.bbagrm.2012.09.007 · Cited by 53 · see citing works
A simple in vivo assay for measuring the efficiency of gene length‐dependent processes in yeast mRNA biogenesis
Morillo‐Huesca, M., Vanti, M., & Chávez, S. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2005.05108.x · Cited by 51 · see citing works
The Rpb4/7 Module of RNA Polymerase II Is Required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) Complex to Promote Elongation
BABBARWAL, V. K., Fu, J., & Reese, J. C. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.c114.601088 · Cited by 51 · see citing works
Self-citation
Combinatorial Control of Human RNA Polymerase II (RNAP II) Pausing and Transcript Cleavage by Transcription Factor IIF, Hepatitis δ Antigen, and Stimulatory Factor II
Zhang, C., Honggao Yan, A., & Burton, Z. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m307590200 · Cited by 43 · see citing works
Variation in the Size of Nascent RNA Cleavage Products as a Function of Transcript Length and Elongation Competence
Gu, W., & Reines, D. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.51.30441 · Cited by 42 · see citing works
Cleavage of the nascent transcript induced by TFIIS is insufficient to promote read-through of intrinsic blocks to elongation by RNA polymerase II.
Cipres-Palacin, G., & Kane, C. M. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.17.8087 · Cited by 42 · see citing works
Transcription Factors TFIIF, ELL, and Elongin Negatively Regulate SII-induced Nascent Transcript Cleavage by Non-arrested RNA Polymerase II Elongation Intermediates
Elmendorf, B. J., Shilatifard, A., Yan, Q., Conaway, J. W., & Conaway, R. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101445200 · Cited by 39 · see citing works
One step back before moving forward: Regulation of transcription elongation by arrest and backtracking
Gómez-Herreros, F., de Miguel-Jiménez, L., Millán-Zambrano, G., Peñate, X., Delgado-Ramos, L., Muñoz-Centeno, M. C., & Chávez, S. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.07.030 · Cited by 37 · see citing works
Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD
Suh, M.-H., Ye, P., Zhang, M., Hausmann, S., Shuman, S., Gnatt, A. L., & Fu, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507987102 · Cited by 28 · see citing works
Self-citation
Analysis of Polymerase II Elongation Complexes by Native Gel Electrophoresis
Zhang, Z., Wu, C.-H., & Gilmour, D. S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m402956200 · Cited by 23 · see citing works
The Functions of TFIIF during Initiation and Transcript Elongation Are Differentially Affected by Phosphorylation by Casein Kinase 2
Újvári, A., Pal, M., & Luse, D. S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.205658 · Cited by 22 · see citing works
Functional Analysis of TFIID Components Using Conditional Mutants
Reese, J. C., & Green, M. R. (2003) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(03)70036-6 · Cited by 12 · see citing works
Self-citation
Genetic Interactions Between TFIIF and TFIIS
Fish, R. N., Ammerman, M. L., Davie, J. K., Lu, B., Pham, C. C., Howe, L. J., Ponticelli, A. S., & Kane, C. M. (2006) · Genetics · doi:10.1534/genetics.106.058834 · Cited by 11 · see citing works

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Multisubunit DNA-Dependent RNA Polymerases from Vaccinia Virus and Other Nucleocytoplasmic Large-DNA Viruses: Impressions from the Age of Structure
Mirzakhanyan, Y., & Gershon, P. D. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00010-17 · Cited by 26 · see citing works
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Rodríguez‐Gil, A., Ritter, O., Hornung, J., Stekman, H., Krüger, M., Braun, T. W., Kremmer, E., Kracht, M., & Schmitz, M. L. (2016) · Molecular Biology of the Cell · doi:10.1091/mbc.e15-09-0629 · Cited by 19 · see citing works
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Allen, G., Weiss, B., Panasenko, O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P. M., Liao, S. E., et al. (2022) · bioRxiv · doi:10.1186/s13059-023-02871-7 · Cited by 16 · see citing works
Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance
Shimo, H. M., Terassi, C., Silva, C. C. D. L., Zanella, J. D. L., Mercaldi, G. F., Rocco, S. A., & Benedetti, C. E. (2019) · Molecular Plant Pathology · doi:10.1111/mpp.12815 · Cited by 15 · see citing works
Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved?
Zhang, Y., Najmi, S. M., & Schneider, D. A. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.10.010 · Cited by 14 · see citing works
Transcription Blockage Leads to New Beginnings
de Andrade-Lima, L. C., Veloso, A., & Ljungman, M. E. (2015) · Biomolecules · doi:10.3390/biom5031600 · Cited by 14 · see citing works
Disruption of the Mammalian Ccr4–Not Complex Contributes to Transcription-Mediated Genome Instability
Hagkarim, N. C., Hajkarim, M. C., Suzuki, T., Fujiwara, T., Winkler, G. S., Stewart, G. S., & Grand, R. J. A. (2023) · Cells · doi:10.3390/cells12141868 · Cited by 12 · see citing works
SILAC-based quantitative mass spectrometry-based proteomics quantifies endoplasmic reticulum stress in whole HeLa cells
Itzhak, D. N., Sacco, F., Nagaraj, N., Tyanova, S., Mann, M., & Murgia, M. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.040741 · Cited by 12 · see citing works
New roles for elongation factors in RNA polymerase II ubiquitylation and degradation
Reese, J. C. (2023) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2023.194956 · Cited by 10 · see citing works
Self-citation
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Akinniyi, O. T., & Reese, J. C. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103202 · Cited by 9 · see citing works
Self-citation
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Laribee, R. N. (2021) · Current Genetics · doi:10.1007/s00294-021-01180-5 · Cited by 8 · see citing works
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Self-citation
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Barman, P., Ferdoush, J., Kaja, A., Chakraborty, P., Uprety, B., Bhaumik, R., Bhaumik, R., & Bhaumik, S. R. (2023) · Gene · doi:10.1016/j.gene.2023.148004 · Cited by 7 · see citing works
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational eventsPreprint
Allen, G. E., Weiss, B., Panasenko, O. O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.14.484207 · Cited by 6 · see citing works
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Pulido, V., Rodríguez-Peña, J. M., Alonso, G., Sanz, A. B., Arroyo, J., & García, R. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168570 · Cited by 5 · see citing works
Diverse functions of deadenylases in DNA damage response and genomic integrity
Yan, Y. (2020) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1621 · Cited by 5 · see citing works
A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading
Challal, D., Menant, A., Goksal, C., Leroy, E., Al‐Sady, B., & Rougemaille, M. (2023) · Genetics · doi:10.1093/genetics/iyad108 · Cited by 4 · see citing works
The Legionella pneumophila effector PieF modulates mRNA stability through association with eukaryotic CCR4−NOT
Mount, H. O., Urbanus, M. L., Zangari, F., Gingras, A., & Ensminger, A. W. (2024) · mSphere · doi:10.1128/msphere.00891-24 · Cited by 4 · see citing works
FAIR approaches applied to unraveling Plant-Pathogen Interactions Data and RNA Processing Evolution
Iglesias, A. R. (2016) · doi:10.20868/upm.thesis.44220 · Cited by 1 · see citing works
Investigation of NOT1 proteins in regulating gene expression in plasmodium falciparum
Liu, Y. (2019) · doi:10.32657/10220/49669 · Cited by 1 · see citing works
The L. pneumophila effector PieF modulates mRNA stability through association with eukaryotic CCR4-NOTPreprint
Mount, H. O., Zangari, F., Gingras, A., & Ensminger, A. W. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.06.494580 · Cited by 1 · see citing works
The influence of chromatin in DNA-RNA hybrid metabolism
Martínez, C., & Carlos, J. (2020) · Deposito de Investigacion Universidad de Sevilla (University of Seville)
Ccr4-Not complex reduces transcription efficiency in heterochromatinPreprint
Monteagudo-Mesas, P., Brönner, C., Kohvaei, P., Amedi, H., Canzar, S., & Halić, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.08.455218
Novel insights into RNA polymerase II transcription regulation: transcription factors, phase separation, and their roles in cardiovascular diseases
Liu, M., Li, Y., Yuan, X. H., Rong, S., & Du, J. (2024) · Biochemistry and Cell Biology · doi:10.1139/bcb-2024-0094
Growth rate regulates RNA polymerase II transcription elongation in Saccharomyces cerevisiaePreprint
Garrido-Godino, A. I., González, R., Martín-Expósito, M., Chávez, S., Pérez-Ortín, J. E., & Navarro, F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.26.625403
Growth rate is related to elongation of RNA polymerase II transcription in Saccharomyces cerevisiae
Garrido-Godino, A. I., González, R., Martín‐Expósito, M., Chávez, S., Pérez-Ortín, J. E., & Navarro, F. (2025) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2025.195100
Additional file 6 of Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Allen, G. E., Weiss, B., Panasenko, O. O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. E., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22614337
Additional file 1 of Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Allen, G. E., Weiss, B., Panasenko, O. O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. E., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22614322
Additional file 7 of Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Allen, G. E., Weiss, B., Panasenko, O. O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. E., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22614340
Study of the mechanisms of sexual differentiation in the fission yeast S. pombe
Simonetti, F. (2017) · doi:10.70675/53c7a46ezf12fz42dfza4d0z1ba256e14ca2
La réparation par excision de nucléotides à la croisée des chemins avec la transcription
Cerutti, E. (2019) · doi:10.70675/7981b4d3zd54bz440azb76azb293aa83e753
Contrôle de l'expression génique par la RNP 7SK
Studniarek, C. (2019) · theses.fr (ABES) · doi:10.70675/4bab1779z812bz45d6zbcd4z9eea765b52e7
Study of the mechanisms of sexual differentiation in the fission yeast Schizosaccharomyces pombe
Andrić, V. (2020) · doi:10.70675/b0f4a1b2z13caz4b6dz918ez814c52ed380e
CCR4-NOT is required for suppressing pervasive transcription and retrotransposable elements
Kulkarni, S. D., Morrissey, A., Sebastian, A., Akinniyi, O. T., Keller, C. A., Albert, I. U., Mahony, S., & Reese, J. C. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.113289
Self-citation

The multifunctional Ccr4–Not complex directly promotes transcription elongation
Kruk, J. A., Dutta, A., Fu, J., Gilmour, D. S., & Reese, J. C. (2011) · Genes & Development · doi:10.1101/gad.2020911 · Cited by 177 · see citing works
Self-citation
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
Schweikhard, V., Meng, C., Murakami, K., Kaplan, C. D., Kornberg, R. D., & Block, S. M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405181111 · Cited by 92 · see citing works
Ccr4‐Not complex directly regulates transcription elongation
Reese, J. C., Kruk, J. A., Dutta, A., & Gilmour, D. S. (2010) · The FASEB Journal · doi:10.1096/fasebj.24.1_supplement.186.2
Self-citation
The control of elongation by the yeast Ccr4–Not complex
Reese, J. C. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.09.001 · Cited by 54 · see citing works
Self-citation
Transcript elongation mechanisms
Svejstrup, J. Q., Aygün, O., Sigurðsson, S., & Saeki, H. (2009) · The FASEB Journal · doi:10.1096/fasebj.23.1_supplement.430.1

Authors: Dutta, A., Babbarwal, V., Fu, J., Brunke-Reese, D., Libert, D. M., Willis, J., & Reese, J. C.
Affiliations: Pennsylvania State University (US)
Medical College of Wisconsin (US)
ORCID: Dutta, Arnob
Fu, Jianhua
Brunke-Reese, Deborah
Libert, Diane M.
Reese, Joseph C.
Venue: Molecular and Cellular Biology
Publisher: Informa UK Limited
Published: 2015-06-01
Volume: 35
Issue: 11
Pages: 1915-1925
ISSN: 0270-7306 (ISSN-L)
1098-5549
DOI: 10.1128/mcb.00044-15
PMC: PMC4420917
OpenAlex: W2105576664
Cited by: 61
References: 57
Citations by year: 2026: 1 · 2025: 1 · 2024: 5 · 2023: 8 · 2022: 3 · 2021: 4 · 2020: 8 · 2019: 9 · 2018: 3 · 2017: 8 · 2016: 9 · 2015: 2
FWCI: 3.19
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Molecular and Cellular Biology (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institute of General Medical Sciences (R01GM100997, GM58672, GM100997, R01GM058672)
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: CCR4-NOT complex, TFIIS, RNA polymerase II, transcription elongation, elongation factors, transcript cleavage, elongation complex, protein-protein interaction, synthetic genetic interactions, Saccharomyces cerevisiae
MeSH terms: Peptide Elongation Factors, Ribonucleases, RNA Polymerase II, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Saccharomyces cerevisiae Proteins, Transcriptional Elongation Factors

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Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II

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