1
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Guérin TM, Barrington C, Pobegalov G, Molodtsov MI, Uhlmann F. An extrinsic motor directs chromatin loop formation by cohesin. EMBO J 2024:10.1038/s44318-024-00202-5. [PMID: 39160275 DOI: 10.1038/s44318-024-00202-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/21/2024] Open
Abstract
The ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve this by actively extruding DNA loops without topologically entrapping DNA. The 'loop extrusion' hypothesis finds motivation from in vitro observations-whether this process underlies in vivo chromatin loop formation remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, and acts as an extrinsic motor that expands these loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion hypothesis. We propose that cohesin, akin to sister chromatid cohesion establishment at replication forks, forms chromatin loops by DNA-DNA capture at places of transcription, thus unifying cohesin's two roles in chromosome segregation and interphase genome organisation.
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Affiliation(s)
- Thomas M Guérin
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Université Paris Cité and Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Christopher Barrington
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Maxim I Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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2
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Hervoso JL, Amoah K, Dodson J, Choudhury M, Bhattacharya A, Quinones-Valdez G, Pasaniuc B, Xiao X. Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia. Am J Hum Genet 2024; 111:1573-1587. [PMID: 38925119 PMCID: PMC11339621 DOI: 10.1016/j.ajhg.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.
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Affiliation(s)
- Jonatan L Hervoso
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jack Dodson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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3
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Chib S, Griffin WC, Gao J, Proffitt DR, Byrd AK, Raney KD. Pif1 Helicase Mediates Remodeling of Protein-Nucleic Acid Complexes by Promoting Dissociation of Sub1 from G-Quadruplex DNA and Cdc13 from G-Rich Single-Stranded DNA. Biochemistry 2023; 62:3360-3372. [PMID: 37948114 PMCID: PMC10841737 DOI: 10.1021/acs.biochem.3c00441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Pif1 is a molecular motor enzyme that is conserved from yeast to mammals. It translocates on ssDNA with a directional bias (5' → 3') and unwinds duplexes using the energy obtained from ATP hydrolysis. Pif1 is involved in dsDNA break repair, resolution of G-quadruplex (G4) structures, negative regulation of telomeres, and Okazaki fragment maturation. An important property of this helicase is to exert force and disrupt protein-DNA complexes, which may otherwise serve as barriers to various cellular pathways. Previously, Pif1 was reported to displace streptavidin from biotinylated DNA, Rap1 from telomeric DNA, and telomerase from DNA ends. Here, we have investigated the ability of S. cerevisiae Pif1 helicase to disrupt protein barriers from G4 and telomeric sites. Yeast chromatin-associated transcription coactivator Sub1 was characterized as a G4 binding protein. We found evidence for a physical interaction between Pif1 helicase and Sub1 protein. Here, we demonstrate that Pif1 is capable of catalyzing the disruption of Sub1-bound G4 structures in an ATP-dependent manner. We also investigated Pif1-mediated removal of yeast telomere-capping protein Cdc13 from DNA ends. Cdc13 exhibits a high-affinity interaction with an 11-mer derived from the yeast telomere sequence. Our results show that Pif1 uses its translocase activity to enhance the dissociation of this telomere-specific protein from its binding site. The rate of dissociation increased with an increase in the helicase loading site length. Additionally, we examined the biochemical mechanism for Pif1-catalyzed protein displacement by mutating the sequence of the telomeric 11-mer on the 5'-end and the 3'-end. The results support a model whereby Pif1 disrupts Cdc13 from the ssDNA in steps.
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Affiliation(s)
- Shubeena Chib
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Wezley C. Griffin
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - David R. Proffitt
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Kevin D. Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
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4
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Collin A, González-Jiménez A, González-Jiménez MDC, Alfonso MJ, Calvo O. The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain. Cells 2022; 11:cells11203320. [PMID: 36291192 PMCID: PMC9600219 DOI: 10.3390/cells11203320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region.
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Affiliation(s)
- Alejandro Collin
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas-INICSA, CONICET-Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, 2º piso. Ciudad Universitaria, Cordoba CP5000, Argentina
| | - Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | | | - Manuel J. Alfonso
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González, nº2, 37007 Salamanca, Spain
- Correspondence:
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5
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Rojas DA, Urbina F, Solari A, Maldonado E. The Catalytic Subunit of Schizosaccharomyces pombe CK2 (Cka1) Negatively Regulates RNA Polymerase II Transcription through Phosphorylation of Positive Cofactor 4 (PC4). Int J Mol Sci 2022; 23:ijms23169499. [PMID: 36012759 PMCID: PMC9409219 DOI: 10.3390/ijms23169499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 01/04/2023] Open
Abstract
Positive cofactor 4 (PC4) is a transcriptional coactivator that plays important roles in transcription and DNA replication. In mammals, PC4 is phosphorylated by CK2, and this event downregulates its RNA polymerase II (RNAPII) coactivator function. This work describes the effect of fission yeast PC4 phosphorylation on RNAPII transcription in a cell extract, which closely resembles the cellular context. We found that fission yeast PC4 is strongly phosphorylated by the catalytic subunit of CK2 (Cka1), while the regulatory subunit (Ckb1) downregulates the PC4 phosphorylation. The addition of Cka1 to an in vitro transcription assay can diminish the basal transcription from the Ad-MLP promoter; however, the addition of recombinant fission yeast PC4 or Ckb1 can stimulate the basal transcription in a cell extract. Fission yeast PC4 is phosphorylated in a domain which has consensus phosphorylation sites for CK2, and two serine residues were identified as critical for CK2 phosphorylation. Mutation of one of the serine residues in PC4 does not completely abolish the phosphorylation; however, when the two serine residues are mutated, CK2 is no longer able to phosphorylate PC4. The mutant which is not phosphorylated is able to stimulate transcription even though it is previously phosphorylated by Cka1, while the wild type and the point mutant are inactivated by Cka1 phosphorylation, and they cannot stimulate transcription by RNAPII in cell extracts. Those results demonstrate that CK2 can regulate the coactivator function of fission yeast PC4 and suggests that this event could be important in vivo as well.
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Affiliation(s)
- Diego A. Rojas
- Instituto de Ciencias Biomédicas (ICB), Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile
- Correspondence: (D.A.R.); (E.M.)
| | - Fabiola Urbina
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Aldo Solari
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
- Correspondence: (D.A.R.); (E.M.)
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6
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Estelle Nicolas
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Didier Trouche
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
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7
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González-Jiménez A, Campos A, Navarro F, Clemente-Blanco A, Calvo O. Regulation of Eukaryotic RNAPs Activities by Phosphorylation. Front Mol Biosci 2021; 8:681865. [PMID: 34250017 PMCID: PMC8268151 DOI: 10.3389/fmolb.2021.681865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 01/11/2023] Open
Abstract
Evolutionarily conserved kinases and phosphatases regulate RNA polymerase II (RNAPII) transcript synthesis by modifying the phosphorylation status of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII. Proper levels of Rpb1-CTD phosphorylation are required for RNA co-transcriptional processing and to coordinate transcription with other nuclear processes, such as chromatin remodeling and histone modification. Whether other RNAPII subunits are phosphorylated and influences their role in gene expression is still an unanswered question. Much less is known about RNAPI and RNAPIII phosphorylation, whose subunits do not contain functional CTDs. However, diverse studies have reported that several RNAPI and RNAPIII subunits are susceptible to phosphorylation. Some of these phosphorylation sites are distributed within subunits common to all three RNAPs whereas others are only shared between RNAPI and RNAPIII. This suggests that the activities of all RNAPs might be finely modulated by phosphorylation events and raises the idea of a tight coordination between the three RNAPs. Supporting this view, the transcription by all RNAPs is regulated by signaling pathways that sense different environmental cues to adapt a global RNA transcriptional response. This review focuses on how the phosphorylation of RNAPs might regulate their function and we comment on the regulation by phosphorylation of some key transcription factors in the case of RNAPI and RNAPIII. Finally, we discuss the existence of possible common mechanisms that could coordinate their activities.
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Affiliation(s)
- Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Adrián Campos
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Andrés Clemente-Blanco
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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8
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Liang L, Liu R, Freed EF, Eckert CA, Gill RT. Transcriptional Regulatory Networks Involved in C3-C4 Alcohol Stress Response and Tolerance in Yeast. ACS Synth Biol 2021; 10:19-28. [PMID: 33356165 DOI: 10.1021/acssynbio.0c00253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alcohol toxicity significantly impacts the titer and productivity of industrially produced biofuels. To overcome this limitation, we must find and use strategies to improve stress tolerance in production strains. Previously, we developed a multiplex navigation of a global regulatory network (MINR) library that targeted 25 regulatory genes that are predicted to modify global regulation in yeast under different stress conditions. In this study, we expanded this concept to target the active sites of 47 transcriptional regulators using a saturation mutagenesis library. The 47 targeted regulators interact with more than half of all yeast genes. We then screened and selected for C3-C4 alcohol tolerance. We identified specific mutants that have resistance to isopropanol and isobutanol. Notably, the WAR1_K110N variant improved tolerance to both isopropanol and isobutanol. In addition, we investigated the mechanisms for improvement of isopropanol and isobutanol stress tolerance and found that genes related to glycolysis play a role in tolerance to isobutanol, while changes in ATP synthesis and mitochondrial respiration play a role in tolerance to both isobutanol and isopropanol. Overall, this work sheds light on basic mechanisms for isopropanol and isobutanol toxicity and demonstrates a promising strategy to improve tolerance to C3-C4 alcohols by perturbing the transcriptional regulatory network.
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Affiliation(s)
- Liya Liang
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder 80303, Colorado United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder 80303, Colorado United States
| | - Emily F Freed
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder 80303, Colorado United States
| | - Carrie A Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder 80303, Colorado United States
- National Renewable Energy Laboratory (NREL), Golden 80401, Colorado United States
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder 80303, Colorado United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby DK-2800, Denmark
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9
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Calvo O, Grandin N, Jordán-Pla A, Miñambres E, González-Polo N, Pérez-Ortín JE, Charbonneau M. The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription. Nucleic Acids Res 2019; 47:6250-6268. [PMID: 31006804 PMCID: PMC6614848 DOI: 10.1093/nar/gkz279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/18/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022] Open
Abstract
Specialized telomeric proteins have an essential role in maintaining genome stability through chromosome end protection and telomere length regulation. In the yeast Saccharomyces cerevisiae, the evolutionary conserved CST complex, composed of the Cdc13, Stn1 and Ten1 proteins, largely contributes to these functions. Here, we report genetic interactions between TEN1 and several genes coding for transcription regulators. Molecular assays confirmed this novel function of Ten1 and further established that it regulates the occupancies of RNA polymerase II and the Spt5 elongation factor within transcribed genes. Since Ten1, but also Cdc13 and Stn1, were found to physically associate with Spt5, we propose that Spt5 represents the target of CST in transcription regulation. Moreover, CST physically associates with Hmo1, previously shown to mediate the architecture of S-phase transcribed genes. The fact that, genome-wide, the promoters of genes down-regulated in the ten1-31 mutant are prefentially bound by Hmo1, leads us to propose a potential role for CST in synchronizing transcription with replication fork progression following head-on collisions.
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Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-USAL, Salamanca, Spain
| | - Nathalie Grandin
- GReD laboratory, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
| | - Antonio Jordán-Pla
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | | | | | - José E Pérez-Ortín
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Michel Charbonneau
- GReD laboratory, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
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10
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Martínez-Fernández V, Garrido-Godino AI, Mirón-García MC, Begley V, Fernández-Pévida A, de la Cruz J, Chávez S, Navarro F. Rpb5 modulates the RNA polymerase II transition from initiation to elongation by influencing Spt5 association and backtracking. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:1-13. [DOI: 10.1016/j.bbagrm.2017.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 12/13/2022]
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11
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Neves LT, Douglass S, Spreafico R, Venkataramanan S, Kress TL, Johnson TL. The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae. Genes Dev 2017; 31:702-717. [PMID: 28446598 PMCID: PMC5411710 DOI: 10.1101/gad.295188.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/27/2017] [Indexed: 01/01/2023]
Abstract
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation. Here we show that splicing of intron-containing genes in cells lacking H2A.Z is impaired, particularly under suboptimal splicing conditions. Cells lacking H2A.Z are especially dependent on a functional U2 snRNP (small nuclear RNA [snRNA] plus associated proteins), as H2A.Z shows extensive genetic interactions with U2 snRNP-associated proteins, and RNA sequencing (RNA-seq) reveals that introns with nonconsensus branch points are particularly sensitive to H2A.Z loss. Consistently, H2A.Z promotes efficient spliceosomal rearrangements involving the U2 snRNP, as H2A.Z loss results in persistent U2 snRNP association and decreased recruitment of downstream snRNPs to nascent RNA. H2A.Z impairs transcription elongation, suggesting that spliceosome rearrangements are tied to H2A.Z's role in elongation. Depletion of disassembly factor Prp43 suppresses H2A.Z-mediated splice defects, indicating that, in the absence of H2A.Z, stalled spliceosomes are disassembled, and unspliced RNAs are released. Together, these data demonstrate that H2A.Z is required for efficient pre-mRNA splicing and indicate a role for H2A.Z in coordinating the kinetics of transcription elongation and splicing.
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Affiliation(s)
- Lauren T Neves
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA.,Graduate Program in Molecular Biology Interdepartmental Program, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Stephen Douglass
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Srivats Venkataramanan
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA
| | - Tracy L Kress
- Department of Biology, The College of New Jersey, Ewing, New Jersey 08628, USA
| | - Tracy L Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA.,Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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12
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Abstract
Sub1 was initially identified as a coactivator factor with a role during transcription initiation. However, over the last years, many evidences showed that it influences processes downstream during mRNA biogenesis, such as elongation, termination, and RNAPII phosphorylation. The recent discover that Sub1 directly interacts with the RNAPII stalk adds new insights into how it achieves all these tasks.
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Affiliation(s)
- Olga Calvo
- a Instituto de Biología Funcional y Genómica (CSIC) , Salamanca , Spain
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13
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Garavís M, González-Polo N, Allepuz-Fuster P, Louro JA, Fernández-Tornero C, Calvo O. Sub1 contacts the RNA polymerase II stalk to modulate mRNA synthesis. Nucleic Acids Res 2017; 45:2458-2471. [PMID: 27924005 PMCID: PMC5389574 DOI: 10.1093/nar/gkw1206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
Biogenesis of messenger RNA is critically influenced by the phosphorylation state of the carboxy-terminal domain (CTD) in the largest RNA polymerase II (RNAPII) subunit. Several kinases and phosphatases are required to maintain proper CTD phosphorylation levels and, additionally, several other proteins modulate them, including Rpb4/7 and Sub1. The Rpb4/7 heterodimer, constituting the RNAPII stalk, promote phosphatase functions and Sub1 globally influences CTD phosphorylation, though its mechanism remains mostly unknown. Here, we show that Sub1 physically interacts with the RNAPII stalk domain, Rpb4/7, likely through its C-terminal region, and associates with Fcp1. While Rpb4 is not required for Sub1 interaction with RNAPII complex, a fully functional heterodimer is required for Sub1 association to promoters. We also demonstrate that a complete CTD is necessary for proper association of Sub1 to chromatin and to the RNAPII. Finally, genetic data show a functional relationship between Sub1 and the RNAPII clamp domain. Altogether, our results indicate that Sub1, Rpb4/7 and Fcp1 interaction modulates CTD phosphorylation. In addition, Sub1 interaction with Rpb4/7 can also modulate transcription start site selection and transcription elongation rate likely by influencing the clamp function.
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Affiliation(s)
- Miguel Garavís
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Noelia González-Polo
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Paula Allepuz-Fuster
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Jaime Alegrio Louro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Olga Calvo
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
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14
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Sub1/PC4, a multifaceted factor: from transcription to genome stability. Curr Genet 2017; 63:1023-1035. [DOI: 10.1007/s00294-017-0715-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 10/19/2022]
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15
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Hot1 factor recruits co-activator Sub1 and elongation complex Spt4/5 to osmostress genes. Biochem J 2016; 473:3065-79. [DOI: 10.1042/bcj20160463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Hyperosmotic stress response involves the adaptative mechanisms needed for cell survival. Under high osmolarity conditions, many stress response genes are activated by several unrelated transcription factors that are controlled by the Hog1 kinase. Osmostress transcription factor Hot1 regulates the expression of several genes involved in glycerol biosynthesis, and the presence of this transcription factor in their promoters is essential for RNApol II recruitment. The physical association between Hog1 and Hot1 activates this transcription factor and directs the RNA polymerase II localization at these promoters. We, herein, demonstrate that physical and genetic interactions exist between Hot1 and several proteins involved in transcriptional and posttranscriptional processes: for example, transcription co-activator Sub1 and elongation complex Spt4/5. The results presented in this work demonstrate that Hot1 enrichment is not detected through the coding regions of its target genes and rule out a direct role in transcription elongation. Instead, other data presented herein indicate a key function of the Hot1 transcription factor in the recruitment of these proteins to the promoter or the 5′-coding region of the genes under its control.
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16
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Sliva A, Kuang Z, Meluh PB, Boeke JD. Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes. G3 (BETHESDA, MD.) 2016; 6:881-92. [PMID: 26837954 PMCID: PMC4825658 DOI: 10.1534/g3.115.026757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 01/27/2016] [Indexed: 11/18/2022]
Abstract
The yeast pheromone response pathway serves as a valuable model of eukaryotic mitogen-activated protein kinase (MAPK) pathways, and transcription of their downstream targets. Here, we describe application of a screening method combining two technologies: fluorescence-activated cell sorting (FACS), and barcode analysis by sequencing (Bar-Seq). Using this screening method, and pFUS1-GFP as a reporter for MAPK pathway activation, we readily identified mutants in known mating pathway components. In this study, we also include a comprehensive analysis of the FUS1 induction properties of known mating pathway mutants by flow cytometry, featuring single cell analysis of each mutant population. We also characterized a new source of false positives resulting from the design of this screen. Additionally, we identified a deletion mutant, sub1Δ, with increased basal expression of pFUS1-GFP. Here, in the first ChIP-Seq of Sub1, our data shows that Sub1 binds to the promoters of about half the genes in the genome (tripling the 991 loci previously reported), including the promoters of several pheromone-inducible genes, some of which show an increase upon pheromone induction. Here, we also present the first RNA-Seq of a sub1Δ mutant; the majority of genes have no change in RNA, but, of the small subset that do, most show decreased expression, consistent with biochemical studies implicating Sub1 as a positive transcriptional regulator. The RNA-Seq data also show that certain pheromone-inducible genes are induced less in the sub1Δ mutant relative to the wild type, supporting a role for Sub1 in regulation of mating pathway genes. The sub1Δ mutant has increased basal levels of a small subset of other genes besides FUS1, including IMD2 and FIG1, a gene encoding an integral membrane protein necessary for efficient mating.
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Affiliation(s)
- Anna Sliva
- Institute for Systems Genetics, New York University Langone School of Medicine, New York 10016 Human Genetics Program, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Zheng Kuang
- Institute for Systems Genetics, New York University Langone School of Medicine, New York 10016
| | - Pamela B Meluh
- Calico Life Sciences, Google Inc., San Francisco, California 94080
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Langone School of Medicine, New York 10016
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17
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Cruz OHDL, Marchat LA, Guillén N, Weber C, Rosas IL, Díaz-Chávez J, Herrera L, Rojo-Domínguez A, Orozco E, López-Camarillo C. Multinucleation and Polykaryon Formation is Promoted by the EhPC4 Transcription Factor in Entamoeba histolytica. Sci Rep 2016; 6:19611. [PMID: 26792358 PMCID: PMC4726151 DOI: 10.1038/srep19611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/14/2015] [Indexed: 02/01/2023] Open
Abstract
Entamoeba histolytica is the intestinal parasite responsible for human amoebiasis that is a leading cause of death in developing countries. In this protozoan, heterogeneity in DNA content, polyploidy and genome plasticity have been associated to alterations in mechanisms controlling DNA replication and cell division. Studying the function of the transcription factor EhPC4, we unexpectedly found that it is functionally related to DNA replication, and multinucleation. Site-directed mutagenesis on the FRFPKG motif revealed that the K127 residue is required for efficient EhPC4 DNA-binding activity. Remarkably, overexpression of EhPC4 significantly increased cell proliferation, DNA replication and DNA content of trophozoites. A dramatically increase in cell size resulting in the formation of giant multinucleated trophozoites (polykaryon) was also found. Multinucleation event was associated to cytokinesis failure leading to abortion of ongoing cell division. Consistently, genome-wide profiling of EhPC4 overexpressing trophozoites revealed the up-regulation of genes involved in carbohydrates and nucleic acids metabolism, chromosome segregation and cytokinesis. Forced overexpression of one of these genes, EhNUDC (nuclear movement protein), led to alterations in cytokinesis and partially recapitulated the multinucleation phenotype. These data indicate for the first time that EhPC4 is associated with events related to polyploidy and genome stability in E. histolytica.
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Affiliation(s)
| | - Laurence A. Marchat
- National Polytechnic Institute, National School of Medicine and Homeopathy, Institutional Program of Molecular Biomedicine, Biotechnology Program, Mexico City, Mexico
| | - Nancy Guillén
- Institut Pasteur, Cellular Biology of Parasitism Unit, Paris, France
- INSERM U786, Paris, France
| | - Christian Weber
- Institut Pasteur, Cellular Biology of Parasitism Unit, Paris, France
- INSERM U786, Paris, France
| | - Itzel López Rosas
- Universidad Autonoma de la Ciudad de Mexico, Genomics Sciences Program, Mexico City, Mexico
| | - José Díaz-Chávez
- National Institute of Cancerology, Carcinogenesis Laboratory, Mexico City, Mexico
| | - Luis Herrera
- National Institute of Cancerology, Carcinogenesis Laboratory, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Metropolitan Autonomous University, Natural Sciences Department, Mexico City, Mexico
| | - Esther Orozco
- Center for Research and Advanced Studies of the National Polytechnic Institute, Department of Infectomics and Molecular Pathogenesis, Mexico City, Mexico
| | - César López-Camarillo
- Universidad Autonoma de la Ciudad de Mexico, Genomics Sciences Program, Mexico City, Mexico
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18
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Gao J, Zybailov BL, Byrd AK, Griffin WC, Chib S, Mackintosh SG, Tackett AJ, Raney KD. Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb) 2015; 51:7242-4. [PMID: 25813861 DOI: 10.1039/c5cc00742a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using a G-quadruplex bait, we identified the transcription co-activator Sub1 as a G-quadruplex binding protein by quantitative LC-MS/MS and demonstrated in vivo G-quadruplex binding by ChIP. In vitro, Sub1, and its human homolog PC4, bind preferentially to G-quadruplexes. This provides a possible mechanism by which G-quadruplexes can influence gene transcription.
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Affiliation(s)
- Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Slot 516, Little Rock, AR 72205, USA.
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19
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Gupta R, Sadhale PP, Vijayraghavan U. SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae. PLoS One 2015; 10:e0132350. [PMID: 26147804 PMCID: PMC4492983 DOI: 10.1371/journal.pone.0132350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/14/2015] [Indexed: 01/29/2023] Open
Abstract
Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1Δ cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1Δ sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation.
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Affiliation(s)
- Ritu Gupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Parag P. Sadhale
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
- * E-mail:
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20
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NandyMazumdar M, Artsimovitch I. Ubiquitous transcription factors display structural plasticity and diverse functions: NusG proteins - Shifting shapes and paradigms. Bioessays 2015; 37:324-34. [PMID: 25640595 DOI: 10.1002/bies.201400177] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Numerous accessory factors modulate RNA polymerase response to regulatory signals and cellular cues and establish communications with co-transcriptional RNA processing. Transcription regulators are astonishingly diverse, with similar mechanisms arising via convergent evolution. NusG/Spt5 elongation factors comprise the only universally conserved and ancient family of regulators. They bind to the conserved clamp helices domain of RNA polymerase, which also interacts with non-homologous initiation factors in all domains of life, and reach across the DNA channel to form processivity clamps that enable uninterrupted RNA chain synthesis. In addition to this ubiquitous function, NusG homologs exert diverse, and sometimes opposite, effects on gene expression by competing with each other and other regulators for binding to the clamp helices and by recruiting auxiliary factors that facilitate termination, antitermination, splicing, translation, etc. This surprisingly diverse range of activities and the underlying unprecedented structural changes make studies of these "transformer" proteins both challenging and rewarding.
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Affiliation(s)
- Monali NandyMazumdar
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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21
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Acker J, Nguyen NTT, Vandamme M, Tavenet A, Briand-Suleau A, Conesa C. Sub1 and Maf1, two effectors of RNA polymerase III, are involved in the yeast quiescence cycle. PLoS One 2014; 9:e114587. [PMID: 25531541 PMCID: PMC4273968 DOI: 10.1371/journal.pone.0114587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/11/2014] [Indexed: 12/30/2022] Open
Abstract
Sub1 and Maf1 exert an opposite effect on RNA polymerase III transcription interfering with different steps of the transcription cycle. In this study, we present evidence that Sub1 and Maf1 also exhibit an opposite role on yeast chronological life span. First, cells lacking Sub1 need more time than wild type to exit from resting and this lag in re-proliferation is correlated with a delay in transcriptional reactivation. Second, our data show that the capacity of the cells to properly establish a quiescent state is impaired in the absence of Sub1 resulting in a premature death that is dependent on the Ras/PKA and Tor1/Sch9 signalling pathways. On the other hand, we show that maf1Δ cells are long-lived mutant suggesting a connection between Pol III transcription and yeast longevity.
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Affiliation(s)
- Joël Acker
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- * E-mail: (CC); (JA)
| | - Ngoc-Thuy-Trinh Nguyen
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Marie Vandamme
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Arounie Tavenet
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Audrey Briand-Suleau
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Christine Conesa
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- * E-mail: (CC); (JA)
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22
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Akimoto Y, Yamamoto S, Iida S, Hirose Y, Tanaka A, Hanaoka F, Ohkuma Y. Transcription cofactor PC4 plays essential roles in collaboration with the small subunit of general transcription factor TFIIE. Genes Cells 2014; 19:879-90. [PMID: 25308091 DOI: 10.1111/gtc.12187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/01/2014] [Indexed: 11/27/2022]
Abstract
In eukaryotes, positive cofactor 4 (PC4) stimulates activator-dependent transcription by facilitating transcription initiation and the transition from initiation to elongation. It also forms homodimers and binds to single-stranded DNA and various transcriptional activators, including the general transcription factor TFIIH. In this study, we further investigated PC4 from Homo sapiens and the nematode Caenorhabditis elegans (hPC4 and cePC4, respectively). hPC4 strongly stimulated transcription on a linearized template, whereas it alleviated transcription on a supercoiled template. Transcriptional stimulation by PC4 was also alleviated by increasing the amount of TFIID. GST pull-down studies with general transcription factors indicated that both hPC4 and cePC4 bind strongly to TFIIB, TFIIEβ, TFIIFα, TFIIFβ and TFIIH XPB subunits and weakly to TBP and TFIIH p62. However, only hPC4 bound to CDK7. The effect of each PC4 on transcription was studied in combination with TFIIEβ. hPC4 stimulated both basal and activated transcription, whereas cePC4 primarily stimulated activated transcription, especially in the presence of TFIIEβ from C. elegans. Finally, hPC4 bound to the C-terminal region of hTFIIEβ adjacent to the basic region. These results indicate that PC4 plays essential roles in the transition step from transcription initiation to elongation by binding to melted DNA in collaboration with TFIIEβ.
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Affiliation(s)
- Yusuke Akimoto
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
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23
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Moehle EA, Braberg H, Krogan NJ, Guthrie C. Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. RNA Biol 2014; 11:313-9. [PMID: 24717535 PMCID: PMC4075515 DOI: 10.4161/rna.28646] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Control of pre-mRNA splicing is a critical part of the eukaryotic gene expression process. Extensive evidence indicates that transcription and splicing are spatiotemporally coordinated and that most splicing events occur co-transcriptionally. A kinetic coupling model has been proposed in metazoans to describe how changing RNA Polymerase II (RNAPII) elongation rate can impact which alternative splice sites are used. In Saccharomyces cerevisiae, in which most spliced genes have only a single intron and splice sites adhere to a strong consensus sequence, we recently observed that splicing efficiency was sensitive to mutations in RNAPII that increase or decrease its elongation rate. Our data revealed that RNAPII speed and splicing efficiency are generally anti-correlated: at many genes, increased elongation rate caused decreased splicing efficiency, while decreased elongation rate increased splicing efficiency. An improved splicing phenotype was also observed upon deletion of SUB1, a condition in which elongation rate is slowed. We discuss these data in the context of a growing field and expand the kinetic coupling model to apply to both alternative splicing and splicing efficiency.
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Affiliation(s)
- Erica A Moehle
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA; California Institute for Quantitative Biosciences; QB3; San Francisco, CA USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA; California Institute for Quantitative Biosciences; QB3; San Francisco, CA USA; J. David Gladstone Institutes; San Francisco, CA USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
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24
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From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell 2013; 154:775-88. [PMID: 23932120 DOI: 10.1016/j.cell.2013.07.033] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 05/16/2013] [Accepted: 07/22/2013] [Indexed: 01/22/2023]
Abstract
RNA polymerase II (RNAPII) lies at the core of dynamic control of gene expression. Using 53 RNAPII point mutants, we generated a point mutant epistatic miniarray profile (pE-MAP) comprising ∼60,000 quantitative genetic interactions in Saccharomyces cerevisiae. This analysis enabled functional assignment of RNAPII subdomains and uncovered connections between individual regions and other protein complexes. Using splicing microarrays and mutants that alter elongation rates in vitro, we found an inverse relationship between RNAPII speed and in vivo splicing efficiency. Furthermore, the pE-MAP classified fast and slow mutants that favor upstream and downstream start site selection, respectively. The striking coordination of polymerization rate with transcription initiation and splicing suggests that transcription rate is tuned to regulate multiple gene expression steps. The pE-MAP approach provides a powerful strategy to understand other multifunctional machines at amino acid resolution.
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