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Maalouf CA, Alberti A, Soutourina J. Mediator complex in transcription regulation and DNA repair: Relevance for human diseases. DNA Repair (Amst) 2024; 141:103714. [PMID: 38943827 DOI: 10.1016/j.dnarep.2024.103714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/01/2024]
Abstract
The Mediator complex is an essential coregulator of RNA polymerase II transcription. More recent developments suggest Mediator functions as a link between transcription regulation, genome organisation and DNA repair mechanisms including nucleotide excision repair, base excision repair, and homologous recombination. Dysfunctions of these processes are frequently associated with human pathologies, and growing evidence shows Mediator involvement in cancers, neurological, metabolic and infectious diseases. The detailed deciphering of molecular mechanisms of Mediator functions, using interdisciplinary approaches in different biological models and considering all functions of this complex, will contribute to our understanding of relevant human diseases.
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Affiliation(s)
- Christelle A Maalouf
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France.
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2
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Liang L, Wang D, Xu D, Xiao J, Tang W, Song X, Yu G, Liang Z, Xie M, Xu Z, Sun B, Tang Y, Huang Z, Lai Y, Li H. Comparative phylogenetic analysis of the mediator complex subunit in asparagus bean (Vigna unguiculata ssp. sesquipedialis) and its expression profile under cold stress. BMC Genomics 2024; 25:149. [PMID: 38321384 PMCID: PMC10848533 DOI: 10.1186/s12864-024-10060-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND The mediator complex subunits (MED) constitutes a multiprotein complex, with each subunit intricately involved in crucial aspects of plant growth, development, and responses to stress. Nevertheless, scant reports pertain to the VunMED gene within the context of asparagus bean (Vigna unguiculata ssp. sesquipedialis). Establishing the identification and exploring the responsiveness of VunMED to cold stress forms a robust foundation for the cultivation of cold-tolerant asparagus bean cultivars. RESULTS Within this study, a comprehensive genome-wide identification of VunMED genes was executed in the asparagus bean cultivar 'Ningjiang3', resulting in the discovery of 36 distinct VunMED genes. A phylogenetic analysis encompassing 232 MED genes from diverse species, including Arabidopsis, tomatoes, soybeans, mung beans, cowpeas, and asparagus beans, underscored the highly conserved nature of MED gene sequences. Throughout evolutionary processes, each VunMED gene underwent purification and neutral selection, with the exception of VunMED19a. Notably, VunMED9/10b/12/13/17/23 exhibited structural variations discernible across four cowpea species. Divergent patterns of temporal and spatial expression were evident among VunMED genes, with a prominent role attributed to most genes during early fruit development. Additionally, an analysis of promoter cis-acting elements was performed, followed by qRT-PCR assessments on roots, stems, and leaves to gauge relative expression after exposure to cold stress and subsequent recovery. Both treatments induced transcriptional alterations in VunMED genes, with particularly pronounced effects observed in root-based genes following cold stress. Elucidating the interrelationships between subunits involved a preliminary understanding facilitated by correlation and principal component analyses. CONCLUSIONS This study elucidates the pivotal contribution of VunMED genes to the growth, development, and response to cold stress in asparagus beans. Furthermore, it offers a valuable point of reference regarding the individual roles of MED subunits.
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Affiliation(s)
- Le Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dongmei Xu
- Mianyang Academy of Agricultural Sciences, Mianyang, 621000, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wen Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xueping Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guofeng Yu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zongxu Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minghui Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zeping Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunsong Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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3
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André KM, Giordanengo Aiach N, Martinez-Fernandez V, Zeitler L, Alberti A, Goldar A, Werner M, Denby Wilkes C, Soutourina J. Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters. Cell Rep 2023; 42:112465. [PMID: 37133993 DOI: 10.1016/j.celrep.2023.112465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/04/2023] Open
Abstract
Chromatin organization is crucial for transcriptional regulation in eukaryotes. Mediator is an essential and conserved co-activator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determine the role of Mediator-RSC interaction in their chromatin binding, nucleosome occupancy, and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.
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Affiliation(s)
- Kévin M André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Veronica Martinez-Fernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Michel Werner
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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4
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Gopaul D, Denby Wilkes C, Goldar A, Giordanengo Aiach N, Barrault MB, Novikova E, Soutourina J. Genomic analysis of Rad26 and Rad1-Rad10 reveals differences in their dependence on Mediator and RNA polymerase II. Genome Res 2022; 32:gr.276371.121. [PMID: 35738899 PMCID: PMC9435749 DOI: 10.1101/gr.276371.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/16/2022] [Indexed: 02/03/2023]
Abstract
Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/ERCC6(CSB) and Rad1-Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae Our genomic analyses reveal that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1-Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1-Rad10, Rad26, Mediator, and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1-Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, which are relevant for human diseases including cancer and XP/CS syndromes.
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Affiliation(s)
- Diyavarshini Gopaul
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elizaveta Novikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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5
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Morse RH. Function and dynamics of the Mediator complex: novel insights and new frontiers. Transcription 2022; 13:39-52. [PMID: 35708525 PMCID: PMC9467533 DOI: 10.1080/21541264.2022.2085502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The Mediator complex was discovered in the early 1990s as a biochemically fractionated factor from yeast extracts that was necessary for activator-stimulated transcriptional activation to be observed in in vitro transcription assays. The structure of this large, multi-protein complex is now understood in great detail, and novel genetic approaches have provided rich insights into its dynamics during transcriptional activation and the mechanism by which it facilitates activated transcription. Here I review recent findings and unanswered questions regarding Mediator dynamics, the roles of individual subunits, and differences between its function in yeast and metazoan cells.
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Affiliation(s)
- Randall H Morse
- Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, United States
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6
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Giustozzi M, Freytes SN, Jaskolowski A, Lichy M, Mateos J, Falcone Ferreyra ML, Rosano GL, Cerdán P, Casati P. Arabidopsis mediator subunit 17 connects transcription with DNA repair after UV-B exposure. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1047-1067. [PMID: 35220621 DOI: 10.1111/tpj.15722] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the nucleotide excision DNA repair system, but this function in plants has not been investigated. We studied the role of MED17 in Arabidopsis plants exposed to UV-B radiation. Our results demonstrate that med17 and OE MED17 plants have altered responses to UV-B, and that MED17 participates in various aspects of the DNA damage response (DDR). Comparison of the med17 transcriptome with that of wild-type (WT) plants showed that almost one-third of transcripts with altered expression in med17 plants were also changed by UV-B exposure in WT plants. Increased sensitivity to DNA damage after UV-B in med17 plants could result from the altered regulation of UV-B responsive transcripts but MED17 also physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we show that MED17 is necessary to regulate the DDR activated by ataxia telangiectasia and Rad3 related (ATR), and that programmed cell death 5 (PDCD5) overexpression reverts the deficiencies in DDR shown in med17 mutants. Our data demonstrate that MED17 is an important regulator of DDR after UV-B irradiation in Arabidopsis.
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Affiliation(s)
- Marisol Giustozzi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | | | - Aime Jaskolowski
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Micaela Lichy
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Julieta Mateos
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - María Lorena Falcone Ferreyra
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Germán L Rosano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biologia Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Pablo Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Casati
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
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7
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Abstract
The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
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8
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Mediator dynamics during heat shock in budding yeast. Genome Res 2021; 32:111-123. [PMID: 34785526 PMCID: PMC8744673 DOI: 10.1101/gr.275750.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/13/2021] [Indexed: 11/25/2022]
Abstract
The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy shows similar dependence on Mediator under normal and heat shock conditions. However, although Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Unexpectedly, Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1Δ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.
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Transcriptional Stress Induces Chromatin Relocation of the Nucleotide Excision Repair Factor XPG. Int J Mol Sci 2021; 22:ijms22126589. [PMID: 34205418 PMCID: PMC8235791 DOI: 10.3390/ijms22126589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
Endonuclease XPG participates in nucleotide excision repair (NER), in basal transcription, and in the processing of RNA/DNA hybrids (R-loops): the malfunction of these processes may cause genome instability. Here, we investigate the chromatin association of XPG during basal transcription and after transcriptional stress. The inhibition of RNA polymerase II with 5,6-dichloro-l-β-D-ribofuranosyl benzimidazole (DRB), or actinomycin D (AD), and of topoisomerase I with camptothecin (CPT) resulted in an increase in chromatin-bound XPG, with concomitant relocation by forming nuclear clusters. The cotranscriptional activators p300 and CREB-binding protein (CREBBP), endowed with lysine acetyl transferase (KAT) activity, interact with and acetylate XPG. Depletion of both KATs by RNA interference, or chemical inhibition with C646, significantly reduced XPG acetylation. However, the loss of KAT activity also resulted in increased chromatin association and the relocation of XPG, indicating that these processes were induced by transcriptional stress and not by reduced acetylation. Transcription inhibitors, including C646, triggered the R-loop formation and phosphorylation of histone H2AX (γ-H2AX). Proximity ligation assay (PLA) showed that XPG colocalized with R-loops, indicating the recruitment of the protein to these structures. These results suggest that transcriptional stress-induced XPG relocation may represent recruitment to sites of R-loop processing.
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Fattal-Valevski A, Ben Sira L, Lerman-Sagie T, Strausberg R, Bloch-Mimouni A, Edvardson S, Kaufman R, Chernuha V, Schneebaum Sender N, Heimer G, Ben Zeev B. Delineation of the phenotype of MED17-related disease in Caucasus-Jewish families. Eur J Paediatr Neurol 2021; 32:40-45. [PMID: 33756211 DOI: 10.1016/j.ejpn.2020.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND and Purpose: Postnatal progressive microcephaly, with seizures and brain atrophy (OMIM # 613668) is a rare disorder caused by a homozygous founder missense mutation c.1112T>C (p.L371P) in the MED17 gene on chromosome 11 that was identified in 2010 in Caucasus Jewish families. The present study aimed to delineate the phenotype and developmental outcomes in patients diagnosed with this mutation to date. METHODS We conducted a medical charts review to collect the clinical, laboratory and neuroimaging findings in patients from several unrelated families of Caucasus-Jewish origin, who were diagnosed with the same homozygous c.1112T>C MED17 mutation. RESULTS The study cohort, including the previously reported patients, comprised 10 males and 5 females from 11 families. All subjects had at birth a normal head circumference, which steeply declined to -6SD within a few months. None of the patients achieved developmental milestones. All patients had progressive spasticity and were wheelchair bound due to spastic quadriplegia. All of them eventually developed profound intellectual disability. Epilepsy of varied severity was present in all patients. Most patients required enteral feeding due to aspirations. Eight patients died before puberty (age range 2-13 years). Brain MRI showed marked cerebral atrophy and early prominent cerebellar atrophy (vermian > hemispheres) accompanied by pontine ventral flattening. CONCLUSIONS The founder c.1112T>C mutation in MED17 gene is expressed by a unique and homogeneous clinical phenotype with distinctive MRI findings. This mutation should be considered in patients of Caucasus-Jewish ancestry presenting with clinical features and a MRI pattern of progressive cerebral and cerebellar atrophy.
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Affiliation(s)
- Aviva Fattal-Valevski
- Pediatric Neurology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel.
| | - Liat Ben Sira
- Department of Radiology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Tally Lerman-Sagie
- Pediatric Neurology, Fetal Neurology Clinic, Obstetrics-Gynecology Ultrasound Unit, Department of Obstetrics and Gynecology, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Strausberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Neurology, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Aviva Bloch-Mimouni
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Neurology and Developmental Unit, Loewenstein Rehabilitation Hospital, Raanana, Israel
| | - Simon Edvardson
- Pediatric Neurology, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel; Monique and Jacques Roboh Department of Genetic Research, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rami Kaufman
- Monique and Jacques Roboh Department of Genetic Research, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Veronika Chernuha
- Pediatric Neurology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Nira Schneebaum Sender
- Pediatric Neurology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Gali Heimer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Bruria Ben Zeev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
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11
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Yang L, Chen R, Goodison S, Sun Y. An efficient and effective method to identify significantly perturbed subnetworks in cancer. NATURE COMPUTATIONAL SCIENCE 2021; 1:79-88. [PMID: 37346964 PMCID: PMC10284573 DOI: 10.1038/s43588-020-00009-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/02/2020] [Indexed: 06/23/2023]
Abstract
The identification of key functional biological networks from high-dimensional genomics data is pivotal for cancer research. Here, we introduce FDRnet, a method for the detection of molecular subnetworks in cancer, which addresses several challenges in pathway analysis. FDRnet detects key subnetworks by solving a mixed-integer linear programming problem, using a given upper bound of false discovery rate (FDR) as a budget constraint, and minimizing a conductance score to find dense subgraphs around seed genes. A large-scale benchmark study was performed on both simulation and cancer genomics data. FDRnet outperformed other methods in the ability to detect functionally homogeneous subnetworks in a scale-free biological network, to control FDRs of the genes in detected subnetworks, to improve computational efficiency and to integrate multi-omics data. By overcoming the limitations of existing approaches, FDRnet can facilitate the detection of key functional pathways in cancer and other genetic diseases.
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Affiliation(s)
- Le Yang
- Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Steve Goodison
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Yijun Sun
- Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
- Department of Microbiology and Immunology, The State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, The State University of New York at Buffalo, Buffalo, NY, USA
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12
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Forey R, Barthe A, Tittel-Elmer M, Wery M, Barrault MB, Ducrot C, Seeber A, Krietenstein N, Szachnowski U, Skrzypczak M, Ginalski K, Rowicka M, Cobb JA, Rando OJ, Soutourina J, Werner M, Dubrana K, Gasser SM, Morillon A, Pasero P, Lengronne A, Poli J. A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization. Mol Cell 2020; 81:183-197.e6. [PMID: 33278361 DOI: 10.1016/j.molcel.2020.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023]
Abstract
Mre11-Rad50-Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. MRX restricts transcription of coding and noncoding DNA by a mechanism that does not require the nuclease activity of Mre11. MRX is required to tether transcriptionally active loci to the nuclear pore complex (NPC), and it also promotes large-scale gene-NPC interactions. Moreover, MRX-mediated chromatin anchoring to the NPC contributes to chromosome folding and helps to control gene expression. Together, these findings indicate that MRX has a role in transcription and chromosome organization that is distinct from its known function in DNA repair.
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Affiliation(s)
- Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Mireille Tittel-Elmer
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Maxime Wery
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cécile Ducrot
- Institute of Molecular and Cellular Radiobiology, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF), 92260 Fontenay-aux-Roses Cedex, France
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ugo Szachnowski
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Jennifer A Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Michel Werner
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Karine Dubrana
- Institute of Molecular and Cellular Radiobiology, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF), 92260 Fontenay-aux-Roses Cedex, France
| | - Susan M Gasser
- University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Antonin Morillon
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France.
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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13
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Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome? Int J Mol Sci 2020; 21:ijms21218360. [PMID: 33171795 PMCID: PMC7664663 DOI: 10.3390/ijms21218360] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
The most frequent DNA lesion resulting from an oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoG). 8-oxoG is a premutagenic base modification due to its capacity to pair with adenine. Thus, the repair of 8-oxoG is critical for the preservation of the genetic information. Nowadays, 8-oxoG is also considered as an oxidative stress-sensor with a putative role in transcription regulation. In mammalian cells, the modified base is excised by the 8-oxoguanine DNA glycosylase (OGG1), initiating the base excision repair (BER) pathway. OGG1 confronts the massive challenge that is finding rare occurrences of 8-oxoG among a million-fold excess of normal guanines. Here, we review the current knowledge on the search and discrimination mechanisms employed by OGG1 to find its substrate in the genome. While there is considerable data from in vitro experiments, much less is known on how OGG1 is recruited to chromatin and scans the genome within the cellular nucleus. Based on what is known of the strategies used by proteins searching for rare genomic targets, we discuss the possible scenarios allowing the efficient detection of 8-oxoG by OGG1.
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14
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Lebraud E, Pinna G, Siberchicot C, Depagne J, Busso D, Fantini D, Irbah L, Robeska E, Kratassiouk G, Ravanat JL, Epe B, Radicella JP, Campalans A. Chromatin recruitment of OGG1 requires cohesin and mediator and is essential for efficient 8-oxoG removal. Nucleic Acids Res 2020; 48:9082-9097. [PMID: 32710616 PMCID: PMC7498353 DOI: 10.1093/nar/gkaa611] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 12/29/2022] Open
Abstract
One of the most abundant DNA lesions induced by oxidative stress is the highly mutagenic 8-oxoguanine (8-oxoG), which is specifically recognized by 8-oxoguanine DNA glycosylase 1 (OGG1) to initiate its repair. How DNA glycosylases find small non-helix-distorting DNA lesions amongst millions of bases packaged in the chromatin-based architecture of the genome remains an open question. Here, we used a high-throughput siRNA screening to identify factors involved in the recognition of 8-oxoG by OGG1. We show that cohesin and mediator subunits are required for re-localization of OGG1 and other base excision repair factors to chromatin upon oxidative stress. The association of OGG1 with euchromatin is necessary for the removal of 8-oxoG. Mediator subunits CDK8 and MED12 bind to chromatin and interact with OGG1 in response to oxidative stress, suggesting they participate in the recruitment of the DNA glycosylase. The oxidative stress-induced association between the cohesin and mediator complexes and OGG1 reveals an unsuspected function of those complexes in the maintenance of genomic stability.
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Affiliation(s)
- Emilie Lebraud
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Guillaume Pinna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Capucine Siberchicot
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Jordane Depagne
- Institute of Cellular and Molecular Radiobiology, U1274 INSERM, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Didier Busso
- Institute of Cellular and Molecular Radiobiology, U1274 INSERM, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Damiano Fantini
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Lamya Irbah
- Institute of Cellular and Molecular Radiobiology, U1274 INSERM, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Elena Robeska
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Gueorgui Kratassiouk
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS IRIG/SyMMES, F-38054 Grenoble, France
| | - Bernd Epe
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Germany
| | - J Pablo Radicella
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
| | - Anna Campalans
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 18 route du Panorama, F-92265 Fontenay-aux-Roses, France
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15
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André KM, Sipos EH, Soutourina J. Mediator Roles Going Beyond Transcription. Trends Genet 2020; 37:224-234. [PMID: 32921511 DOI: 10.1016/j.tig.2020.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022]
Abstract
Dysfunctions of nuclear processes including transcription and DNA repair lead to severe human diseases. Gaining an understanding of how these processes operate in the crowded context of chromatin can be particularly challenging. Mediator is a large multiprotein complex conserved in eukaryotes with a key coactivator role in the regulation of RNA polymerase (Pol) II transcription. Despite intensive studies, the molecular mechanisms underlying Mediator function remain to be fully understood. Novel findings have provided insights into the relationship between Mediator and chromatin architecture, revealed its role in connecting transcription with DNA repair and proposed an emerging mechanism of phase separation involving Mediator condensates. Recent developments in the field suggest multiple functions of Mediator going beyond transcriptional processes per se that would explain its involvement in various human pathologies.
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Affiliation(s)
- Kévin M André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Eliet H Sipos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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16
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Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin. Proc Natl Acad Sci U S A 2020; 117:18608-18616. [PMID: 32690696 DOI: 10.1073/pnas.2003868117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that removes RNA polymerase (RNAP)-stalling DNA damage from the transcribed strand (TS) of active genes. TC-NER deficiency in humans is associated with the severe neurological disorder Cockayne syndrome. Initiation of TC-NER is mediated by specific factors such as the human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in the context of the chromatin organization, is unclear. Here, we used single-nucleotide resolution UV damage mapping data to show that Rad26 and its ATPase activity is critical for TC-NER downstream of the first (+1) nucleosome in gene coding regions. However, TC-NER on the transcription start site (TSS)-proximal half of the +1 nucleosome is largely independent of Rad26, likely due to high occupancy of the transcription initiation/repair factor TFIIH in this nucleosome. Downstream of the +1 nucleosome, the combination of low TFIIH occupancy and high occupancy of the transcription elongation factor Spt4/Spt5 suppresses TC-NER in Rad26-deficient cells. We show that deletion of SPT4 significantly restores TC-NER across the genome in a rad26∆ mutant, particularly in the downstream nucleosomes. These data demonstrate that the requirement for Rad26 in TC-NER is modulated by the distribution of TFIIH and Spt4/Spt5 in transcribed chromatin and Rad26 mainly functions downstream of the +1 nucleosome to remove TC-NER suppression by Spt4/Spt5.
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17
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Georges A, Gopaul D, Denby Wilkes C, Giordanengo Aiach N, Novikova E, Barrault MB, Alibert O, Soutourina J. Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin. Nucleic Acids Res 2019; 47:8988-9004. [PMID: 31299084 PMCID: PMC6753472 DOI: 10.1093/nar/gkz598] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.
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Affiliation(s)
- Adrien Georges
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Diyavarshini Gopaul
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Giordanengo Aiach
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Elizaveta Novikova
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Bénédicte Barrault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | | | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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18
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Abstract
Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.
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Affiliation(s)
- Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, Commissariat à l'énergie Atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), University Paris Sud, University Paris Saclay, F-91198 Gif-sur-Yvette, France
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19
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Jeronimo C, Robert F. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol 2017; 27:765-783. [DOI: 10.1016/j.tcb.2017.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/15/2022]
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20
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Med15B Regulates Acid Stress Response and Tolerance in Candida glabrata by Altering Membrane Lipid Composition. Appl Environ Microbiol 2017; 83:AEM.01128-17. [PMID: 28710262 DOI: 10.1128/aem.01128-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/04/2017] [Indexed: 12/16/2022] Open
Abstract
Candida glabrata is a promising producer of organic acids. To elucidate the physiological function of the Mediator tail subunit Med15B in the response to low-pH stress, we constructed a deletion strain, C. glabratamed15BΔ, and an overexpression strain, C. glabrata HTUΔ/CgMED15B Deletion of MED15B caused biomass production, glucose consumption rate, and cell viability to decrease by 28.3%, 31.7%, and 26.5%, respectively, compared with those of the parent (HTUΔ) strain at pH 2.0. Expression of lipid metabolism-related genes was significantly downregulated in the med15BΔ strain, whereas key genes of ergosterol biosynthesis showed abnormal upregulation. This caused the proportion of C18:1 fatty acids, the ratio of unsaturated to saturated fatty acids (UFA/SFA), and the total phospholipid content to decrease by 11.6%, 27.4%, and 37.6%, respectively. Cells failed to synthesize fecosterol and ergosterol, leading to the accumulation and a 60.3-fold increase in the concentration of zymosterol. Additionally, cells showed reductions of 69.2%, 11.6%, and 21.8% in membrane integrity, fluidity, and H+-ATPase activity, respectively. In contrast, overexpression of Med15B increased the C18:1 levels, total phospholipids, ergosterol content, and UFA/SFA by 18.6%, 143.5%, 94.5%, and 18.7%, respectively. Membrane integrity, fluidity, and H+-ATPase activity also increased by 30.2%, 6.9%, and 51.8%, respectively. Furthermore, in the absence of pH buffering, dry weight of cells and pyruvate concentrations were 29.3% and 61.2% higher, respectively, than those of the parent strain. These results indicated that in C. glabrata, Med15B regulates tolerance toward low pH via transcriptional regulation of acid stress response genes and alteration in lipid composition.IMPORTANCE This study explored the role of the Mediator tail subunit Med15B in the metabolism of Candida glabrata under acidic conditions. Overexpression of MED15B enhanced yeast tolerance to low pH and improved biomass production, cell viability, and pyruvate yield. Membrane lipid composition data indicated that Med15B might play a critical role in membrane integrity, fluidity, and H+-ATPase activity homeostasis at low pH. Thus, controlling membrane composition may serve to increase C. glabrata productivity at low pH.
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21
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Eychenne T, Werner M, Soutourina J. Toward understanding of the mechanisms of Mediator function in vivo: Focus on the preinitiation complex assembly. Transcription 2017; 8:328-342. [PMID: 28841352 DOI: 10.1080/21541264.2017.1329000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation.
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Affiliation(s)
- Thomas Eychenne
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France.,b Institut Pasteur, (Epi)genomics of Animal Development Unit , Development and Stem Cell Biology Department, CNRS UMR3778 , Paris , France
| | - Michel Werner
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
| | - Julie Soutourina
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
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22
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Abstract
Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical complex and raised new questions about its role in the regulation of gene expression.
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Affiliation(s)
- Sebastian Grünberg
- a Basic Sciences Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
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23
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Grünberg S, Henikoff S, Hahn S, Zentner GE. Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters. EMBO J 2016; 35:2435-2446. [PMID: 27797823 DOI: 10.15252/embj.201695020] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 11/09/2022] Open
Abstract
Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes. Using the same approach to map TFIID, we find that TFIID is associated with both TFIID- and SAGA-dependent genes and that TFIID and Mediator occupancy is cooperative. Our results clarify Mediator recruitment and binding to the genome, showing that Mediator binding to UASs is widespread, partially uncoupled from transcription, and mediated in part by TFIID.
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Affiliation(s)
- Sebastian Grünberg
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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24
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Eychenne T, Novikova E, Barrault MB, Alibert O, Boschiero C, Peixeiro N, Cornu D, Redeker V, Kuras L, Nicolas P, Werner M, Soutourina J. Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture. Genes Dev 2016; 30:2119-2132. [PMID: 27688401 PMCID: PMC5066617 DOI: 10.1101/gad.285775.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022]
Abstract
Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator-TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts.
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Affiliation(s)
- Thomas Eychenne
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
| | - Elizaveta Novikova
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
| | - Marie-Bénédicte Barrault
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
| | - Olivier Alibert
- Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Institut de Radiobiologie Cellulaire et Moléculaire (IRCM), CEA, Genopole G2, F-91057 Evry Cedex, France
| | - Claire Boschiero
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
| | - Nuno Peixeiro
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
| | - David Cornu
- Service d'Identification et de Caractérisation des Protéines par Spectrométrie de Masse (SICaPS), CNRS, F-91198 Gif-sur-Yvette Cedex, France
| | - Virginie Redeker
- Service d'Identification et de Caractérisation des Protéines par Spectrométrie de Masse (SICaPS), CNRS, F-91198 Gif-sur-Yvette Cedex, France.,Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS, F-91198 Gif-sur-Yvette Cedex, France
| | - Laurent Kuras
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France
| | - Pierre Nicolas
- Mathematiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Michel Werner
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
| | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Université Paris Saclay, F-91198 Gif-sur-Yvette Cedex, France.,Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191 Gif-sur-Yvette Cedex, France
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25
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Avila AI, Illing A, Becker F, Maerz LD, Morita Y, Philipp M, Burkhalter MD. Xpg limits the expansion of haematopoietic stem and progenitor cells after ionising radiation. Nucleic Acids Res 2016; 44:6252-61. [PMID: 27137888 PMCID: PMC5291257 DOI: 10.1093/nar/gkw376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/25/2016] [Indexed: 12/17/2022] Open
Abstract
Reduced capacity of genome maintenance represents a problem for any organism, potentially causing premature death, carcinogenesis, or accelerated ageing. Strikingly though, loss of certain genome stability factors can be beneficial, especially for the maintenance of tissue stem cells of the intestine and the haematopoietic system. We therefore screened for genome stability factors negatively impacting maintenance of haematopoietic stem cells (HSC) in the context of ionising radiation (IR). We found that in vivo knock down of Xeroderma pigmentosum, complementation group G (Xpg) causes elevation of HSC numbers after IR treatment, while numbers of haematopoietic progenitors are elevated to a lesser extent. IR rapidly induces Xpg both on mRNA and on protein level. Prevention of this induction does not influence activation of the checkpoint cascade, yet attenuates late checkpoint steps such as induction of p21 and Noxa. This causes a leaky cell cycle arrest and lower levels of apoptosis, both contributing to increased colony formation and transformation rates. Xpg thus helps to adequately induce DNA damage responses after IR, thereby keeping the expansion of damaged cells under control. This represents a new function of Xpg in the response to IR, in addition to its well-characterized role in nucleotide excision repair.
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Affiliation(s)
- Alush I Avila
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Anett Illing
- Department of Internal Medicine I, Ulm University, 89081 Ulm, Germany
| | - Friedrich Becker
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Lars D Maerz
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Yohei Morita
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Melanie Philipp
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Martin D Burkhalter
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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26
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Eyboulet F, Wydau-Dematteis S, Eychenne T, Alibert O, Neil H, Boschiero C, Nevers MC, Volland H, Cornu D, Redeker V, Werner M, Soutourina J. Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo. Nucleic Acids Res 2015; 43:9214-31. [PMID: 26240385 PMCID: PMC4627066 DOI: 10.1093/nar/gkv782] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/21/2015] [Indexed: 12/20/2022] Open
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes, which has a crucial coregulator function in transcription by RNA polymerase II (Pol II). However, the molecular mechanisms of its action in vivo remain to be understood. Med17 is an essential and central component of the Mediator head module. In this work, we utilised our large collection of conditional temperature-sensitive med17 mutants to investigate Mediator's role in coordinating preinitiation complex (PIC) formation in vivo at the genome level after a transfer to a non-permissive temperature for 45 minutes. The effect of a yeast mutation proposed to be equivalent to the human Med17-L371P responsible for infantile cerebral atrophy was also analyzed. The ChIP-seq results demonstrate that med17 mutations differentially affected the global presence of several PIC components including Mediator, TBP, TFIIH modules and Pol II. Our data show that Mediator stabilizes TFIIK kinase and TFIIH core modules independently, suggesting that the recruitment or the stability of TFIIH modules is regulated independently on yeast genome. We demonstrate that Mediator selectively contributes to TBP recruitment or stabilization to chromatin. This study provides an extensive genome-wide view of Mediator's role in PIC formation, suggesting that Mediator coordinates multiple steps of a PIC assembly pathway.
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Affiliation(s)
- Fanny Eyboulet
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Sandra Wydau-Dematteis
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Thomas Eychenne
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | | | - Helen Neil
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Claire Boschiero
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Marie-Claire Nevers
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, F-91191 Gif sur Yvette cedex, France
| | - Hervé Volland
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, F-91191 Gif sur Yvette cedex, France
| | - David Cornu
- CNRS, Centre de Recherche de Gif, SICaPS, F-91198 Gif-sur-Yvette cedex, France
| | - Virginie Redeker
- CNRS, Centre de Recherche de Gif, SICaPS, F-91198 Gif-sur-Yvette cedex, France
| | - Michel Werner
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
| | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, CNRS, Université Paris Sud, F-91191 Gif-sur-Yvette cedex, France
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27
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Kikuchi Y, Umemura H, Nishitani S, Iida S, Fukasawa R, Hayashi H, Hirose Y, Tanaka A, Sugasawa K, Ohkuma Y. Human mediator MED17 subunit plays essential roles in gene regulation by associating with the transcription and DNA repair machineries. Genes Cells 2014; 20:191-202. [DOI: 10.1111/gtc.12210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/02/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Yuko Kikuchi
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Hiroyasu Umemura
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Saori Nishitani
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Satoshi Iida
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Rikiya Fukasawa
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Hiroto Hayashi
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Aki Tanaka
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Kaoru Sugasawa
- Biosignal Research Center; Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
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Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol 2014; 21:1028-34. [PMID: 25383669 PMCID: PMC4259101 DOI: 10.1038/nsmb.2914] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/09/2014] [Indexed: 01/01/2023]
Abstract
The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here, we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to mass spectrometry (CX-MS). Whereas the reconstituted head and middle modules can stably associate, only with incorporation of MED14 into the bi-modular complex does it acquire basal and coactivator functions. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematically dissecting the multiple layers of functionalities associated with the Mediator complex.
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Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast. Mol Cell Biol 2014; 35:331-42. [PMID: 25368384 DOI: 10.1128/mcb.00991-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that in Saccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised in med17 temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complex in vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.
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Affiliation(s)
- Julie Soutourina
- CEA; iBiTec-S; FRE3377, Gif-sur-Yvette, France; CNRS; FRE3377; Gif-sur-Yvette, France; Univ Paris-Sud; FRE3377; Gif-sur-Yvette, France
| | - Michel Werner
- CEA; iBiTec-S; FRE3377, Gif-sur-Yvette, France; CNRS; FRE3377; Gif-sur-Yvette, France; Univ Paris-Sud; FRE3377; Gif-sur-Yvette, France
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31
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Schuldt A. A mediator for DNA repair. Nat Rev Mol Cell Biol 2013. [DOI: 10.1038/nrm3728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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