1
|
Rengachari S, Schilbach S, Cramer P. Mediator structure and function in transcription initiation. Biol Chem 2023; 404:829-837. [PMID: 37078249 DOI: 10.1515/hsz-2023-0158] [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: 03/10/2023] [Accepted: 04/06/2023] [Indexed: 04/21/2023]
Abstract
Recent advances in cryo-electron microscopy have led to multiple structures of Mediator in complex with the RNA polymerase II (Pol II) transcription initiation machinery. As a result we now hold in hands near-complete structures of both yeast and human Mediator complexes and have a better understanding of their interactions with the Pol II pre-initiation complex (PIC). Herein, we provide a summary of recent achievements and discuss their implications for future studies of Mediator and its role in gene regulation.
Collapse
Affiliation(s)
- Srinivasan Rengachari
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Sandra Schilbach
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| |
Collapse
|
2
|
Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023; 290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
Abstract
Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.
Collapse
Affiliation(s)
- Élie Lambert
- Institut de recherches cliniques de Montréal, Canada
| | | | - Yi Fei Tao
- Institut de recherches cliniques de Montréal, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Canada
| |
Collapse
|
3
|
Tanemoto F, Nangaku M, Mimura I. Epigenetic memory contributing to the pathogenesis of AKI-to-CKD transition. Front Mol Biosci 2022; 9:1003227. [PMID: 36213117 PMCID: PMC9532834 DOI: 10.3389/fmolb.2022.1003227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Epigenetic memory, which refers to the ability of cells to retain and transmit epigenetic marks to their daughter cells, maintains unique gene expression patterns. Establishing programmed epigenetic memory at each stage of development is required for cell differentiation. Moreover, accumulating evidence shows that epigenetic memory acquired in response to environmental stimuli may be associated with diverse diseases. In the field of kidney diseases, the “memory” of acute kidney injury (AKI) leads to progression to chronic kidney disease (CKD); epidemiological studies show that patients who recover from AKI are at high risk of developing CKD. The underlying pathological processes include nephron loss, maladaptive epithelial repair, inflammation, and endothelial injury with vascular rarefaction. Further, epigenetic alterations may contribute as well to the pathophysiology of this AKI-to-CKD transition. Epigenetic changes induced by AKI, which can be recorded in cells, exert long-term effects as epigenetic memory. Considering the latest findings on the molecular basis of epigenetic memory and the pathophysiology of AKI-to-CKD transition, we propose here that epigenetic memory contributing to AKI-to-CKD transition can be classified according to the presence or absence of persistent changes in the associated regulation of gene expression, which we designate “driving” memory and “priming” memory, respectively. “Driving” memory, which persistently alters the regulation of gene expression, may contribute to disease progression by activating fibrogenic genes or inhibiting renoprotective genes. This process may be involved in generating the proinflammatory and profibrotic phenotypes of maladaptively repaired tubular cells after kidney injury. “Priming” memory is stored in seemingly successfully repaired tubular cells in the absence of detectable persistent phenotypic changes, which may enhance a subsequent transcriptional response to the second stimulus. This type of memory may contribute to AKI-to-CKD transition through the cumulative effects of enhanced expression of profibrotic genes required for wound repair after recurrent AKI. Further understanding of epigenetic memory will identify therapeutic targets of future epigenetic intervention to prevent AKI-to-CKD transition.
Collapse
|
4
|
Cevher MA. Reconstitution of Pol II (G) responsive form of the human Mediator complex. Turk J Biol 2021; 45:253-261. [PMID: 34377050 PMCID: PMC8313941 DOI: 10.3906/biy-2009-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/16/2021] [Indexed: 01/15/2023] Open
Abstract
RNA polymerase II (Pol II) is a 12 subunit protein complex from yeast to human that is required for gene expression. Gdown1 containing Pol II [Pol II (G)] is a special form of Pol II that is catalytically inactive and heavily depends on the 30-subunit Mediator complex for its activator and basal dependent function in vitro. Here we report for the first time, the identification and the generation of a 15-subunit human Mediator complex via the novel multibac baculovirus expression system that is fully responsive to Pol II (G). Our results show complete recovery of Pol II (G) dependent transcription both with full 30-subunit Mediator and also with 15-subunit recombinant Mediator that we synthesized. Moreover, we also show that the recombinant Mediator interacts with Pol II (G) as well. These results enlighten us towards understanding how a certain population of Pol II that is involved in selected gene regulation is activated by Mediator complex.
Collapse
Affiliation(s)
- Murat Alper Cevher
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara Turkey.,Visiting Assistant Professor, Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Tourigny JP, Schumacher K, Saleh MM, Devys D, Zentner GE. Architectural Mediator subunits are differentially essential for global transcription in Saccharomyces cerevisiae. Genetics 2021; 217:iyaa042. [PMID: 33789343 PMCID: PMC8045717 DOI: 10.1093/genetics/iyaa042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator is a modular coactivator complex involved in the transcription of the majority of RNA polymerase II-regulated genes. However, the degrees to which individual core subunits of Mediator contribute to its activity have been unclear. Here, we investigate the contribution of two essential architectural subunits of Mediator to transcription in Saccharomyces cerevisiae. We show that acute depletion of the main complex scaffold Med14 or the head module nucleator Med17 is lethal and results in global transcriptional downregulation, though Med17 removal has a markedly greater negative effect. Consistent with this, Med17 depletion impairs preinitiation complex (PIC) assembly to a greater extent than Med14 removal. Co-depletion of Med14 and Med17 reduced transcription and TFIIB promoter occupancy similarly to Med17 ablation alone, indicating that the contributions of Med14 and Med17 to Mediator function are not additive. We propose that, while the structural integrity of complete Mediator and the head module are both important for PIC assembly and transcription, the head module plays a greater role in this process and is thus the key functional module of Mediator in this regard.
Collapse
Affiliation(s)
- Jason P Tourigny
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kenny Schumacher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Moustafa M Saleh
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| |
Collapse
|
7
|
Al-Husini N, Medler S, Ansari A. Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194657. [PMID: 33246184 DOI: 10.1016/j.bbagrm.2020.194657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
The transcription cycle of RNAPII is comprised of three consecutive steps; initiation, elongation and termination. It has been assumed that the initiation and termination steps occur in spatial isolation, essentially as independent events. A growing body of evidence, however, has challenged this dogma. First, factors involved in initiation and termination exhibit both a genetic and a physical interaction during transcription. Second, the initiation and termination factors have been found to occupy both ends of a transcribing gene. Third, physical interaction of initiation and termination factors occupying distal ends of a gene sometime results in the entire terminator region of a genes looping back and contact its cognate promoter, thereby forming a looped gene architecture during transcription. A logical interpretation of these findings is that the initiation and termination steps of transcription do not occur in isolation. There is extensive communication of factors occupying promoter and terminator ends of a gene during transcription cycle. This review entails a discussion of the promoter-terminator crosstalk and its implication in the context of transcription.
Collapse
Affiliation(s)
- Nadra Al-Husini
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Scott Medler
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America.
| |
Collapse
|
8
|
Legrand N, Bretscher CL, Zielke S, Wilke B, Daude M, Fritz B, Diederich WE, Adhikary T. PPARβ/δ recruits NCOR and regulates transcription reinitiation of ANGPTL4. Nucleic Acids Res 2019; 47:9573-9591. [PMID: 31428774 PMCID: PMC6765110 DOI: 10.1093/nar/gkz685] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/20/2019] [Accepted: 07/28/2019] [Indexed: 12/24/2022] Open
Abstract
In the absence of ligands, the nuclear receptor PPARβ/δ recruits the NCOR and SMRT corepressors, which form complexes with HDAC3, to canonical target genes. Agonistic ligands cause dissociation of corepressors and enable enhanced transcription. Vice versa, synthetic inverse agonists augment corepressor recruitment and repression. Both basal repression of the target gene ANGPTL4 and reinforced repression elicited by inverse agonists are partially insensitive to HDAC inhibition. This raises the question how PPARβ/δ represses transcription mechanistically. We show that the PPARβ/δ inverse agonist PT-S264 impairs transcription initiation by decreasing recruitment of activating Mediator subunits, RNA polymerase II, and TFIIB, but not of TFIIA, to the ANGPTL4 promoter. Mass spectrometry identifies NCOR as the main PT-S264-dependent interactor of PPARβ/δ. Reconstitution of knockout cells with PPARβ/δ mutants deficient in basal repression results in diminished recruitment of NCOR, SMRT, and HDAC3 to PPAR target genes, while occupancy by RNA polymerase II is increased. PT-S264 restores binding of NCOR, SMRT, and HDAC3 to the mutants, resulting in reduced polymerase II occupancy. Our findings corroborate deacetylase-dependent and -independent repressive functions of HDAC3-containing complexes, which act in parallel to downregulate transcription.
Collapse
Affiliation(s)
- Nathalie Legrand
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Clemens L Bretscher
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Svenja Zielke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Bernhard Wilke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Michael Daude
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Barbara Fritz
- Centre for Human Genetics, Universitätsklinikum Giessen und Marburg GmbH, Baldingerstrasse, 35043 Marburg, Germany
| | - Wibke E Diederich
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Pharmacy, Institute for Pharmaceutical Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Till Adhikary
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| |
Collapse
|
9
|
Knoll ER, Zhu ZI, Sarkar D, Landsman D, Morse RH. Role of the pre-initiation complex in Mediator recruitment and dynamics. eLife 2018; 7:39633. [PMID: 30540252 PMCID: PMC6322861 DOI: 10.7554/elife.39633] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022] Open
Abstract
The Mediator complex stimulates the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that yeast lacking Med2-Med3-Med15 are viable and that Mediator and PolII are recruited to promoters genome-wide in these cells, albeit at reduced levels. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.
Collapse
Affiliation(s)
- Elisabeth R Knoll
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Z Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, United States
| | - Debasish Sarkar
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, United States
| | - Randall H Morse
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States.,Wadsworth Center, New York State Department of Health, Albany, United States
| |
Collapse
|
10
|
Mediator, known as a coactivator, can act in transcription initiation in an activator-independent manner in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:687-696. [DOI: 10.1016/j.bbagrm.2018.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 01/20/2023]
|
11
|
Putlyaev EV, Ibragimov AN, Lebedeva LA, Georgiev PG, Shidlovskii YV. Structure and Functions of the Mediator Complex. BIOCHEMISTRY (MOSCOW) 2018; 83:423-436. [PMID: 29626929 DOI: 10.1134/s0006297918040132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
Collapse
Affiliation(s)
- E V Putlyaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | | | | | | | | |
Collapse
|
12
|
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]
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Petrenko N, Jin Y, Wong KH, Struhl K. Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo. eLife 2017; 6. [PMID: 28699889 PMCID: PMC5529107 DOI: 10.7554/elife.28447] [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: 12/24/2016] [Accepted: 07/09/2017] [Indexed: 12/27/2022] Open
Abstract
The Mediator complex has been described as a general transcription factor, but it is unclear if it is essential for Pol II transcription and/or is a required component of the preinitiation complex (PIC) in vivo. Here, we show that depletion of individual subunits, even those essential for cell growth, causes a general but only modest decrease in transcription. In contrast, simultaneous depletion of all Mediator modules causes a drastic decrease in transcription. Depletion of head or middle subunits, but not tail subunits, causes a downstream shift in the Pol II occupancy profile, suggesting that Mediator at the core promoter inhibits promoter escape. Interestingly, a functional PIC and Pol II transcription can occur when Mediator is not detected at core promoters. These results provide strong evidence that Mediator is essential for Pol II transcription and stimulates PIC formation, but it is not a required component of the PIC in vivo. DOI:http://dx.doi.org/10.7554/eLife.28447.001
Collapse
Affiliation(s)
- Natalia Petrenko
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Boston, United States
| | - Yi Jin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Boston, United States
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Boston, United States
| |
Collapse
|
15
|
Amorim AF, Pinto D, Kuras L, Fernandes L. Absence of Gim proteins, but not GimC complex, alters stress-induced transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:773-781. [PMID: 28457997 DOI: 10.1016/j.bbagrm.2017.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 02/08/2023]
Abstract
Saccharomyces cerevisiae GimC (mammalian Prefoldin) is a hexameric (Gim1-6) cytoplasmic complex involved in the folding pathway of actin/tubulin. In contrast to a shared role in GimC complex, we show that absence of individual Gim proteins results in distinct stress responses. No concomitant alteration in F-actin integrity was observed. Transcription of stress responsive genes is altered in gim2Δ, gim3Δ and gim6Δ mutants: TRX2 gene is induced in these mutants but with a profile diverging from type cells, whereas CTT1 and HSP26 fail to be induced. Remaining gimΔ mutants display stress transcript abundance comparable to wild type cells. No alteration in the nuclear localization of the transcriptional activators for TRX2 (Yap1) and CTT1/HSP26 (Msn2) was observed in gim2Δ. In accordance with TRX2 induction, RNA polymerase II occupancy at TRX2 discriminates the wild type from gim2Δ and gim6Δ. In contrast, RNA polymerase II occupancy at CTT1 is similar in wild type and gim2Δ, but higher in gim6Δ. The absence of active RNA polymerase II at CTT1 in gim2Δ, but not in wild type and gim1Δ, explains the respective CTT1 transcript outputs. Altogether our results put forward the need of Gim2, Gim3 and Gim6 in oxidative and osmotic stress activated transcription; others Gim proteins are dispensable. Consequently, the participation of Gim proteins in activated-transcription is independent from the GimC complex.
Collapse
Affiliation(s)
- Ana Fátima Amorim
- Instituto Gulbenkian de Ciência, Oeiras, Portugal; Universidade de Lisboa, Faculdade de Ciências, Biosystems & Integrative Sciences Institute (BioISI), Lisboa, Portugal
| | - Dora Pinto
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Laurent Kuras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Lisete Fernandes
- Instituto Gulbenkian de Ciência, Oeiras, Portugal; Universidade de Lisboa, Faculdade de Ciências, Biosystems & Integrative Sciences Institute (BioISI), Lisboa, Portugal; Instituto Politécnico de Lisboa, ESTeSL-Escola Superior de Tecnologia da Saúde de Lisboa, Lisboa, Portugal.
| |
Collapse
|
16
|
Viscarra JA, Wang Y, Hong IH, Sul HS. Transcriptional activation of lipogenesis by insulin requires phosphorylation of MED17 by CK2. Sci Signal 2017; 10:eaai8596. [PMID: 28223413 PMCID: PMC5376069 DOI: 10.1126/scisignal.aai8596] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
De novo lipogenesis is precisely regulated by nutritional and hormonal conditions. The genes encoding various enzymes involved in this process, such as fatty acid synthase (FASN), are transcriptionally activated in response to insulin. We showed that USF1, a key transcription factor for FASN activation, directly interacted with the Mediator subunit MED17 at the FASN promoter. This interaction recruited Mediator, which can bring POL II and other general transcription machinery to the complex. Moreover, we showed that MED17 was phosphorylated at Ser53 by casein kinase 2 (CK2) in the livers of fed mice or insulin-stimulated hepatocytes, but not in the livers of fasted mice or untreated hepatocytes. Furthermore, activation of the FASN promoter in response to insulin required this CK2-mediated phosphorylation event, which occurred only in the absence of p38 MAPK-mediated phosphorylation at Thr570 Overexpression of a nonphosphorylatable S53A MED17 mutant or knockdown of MED17, as well as CK2 knockdown or inhibition, impaired hepatic de novo fatty acid synthesis and decreased triglyceride content in mice. These results demonstrate that CK2-mediated phosphorylation of Ser53 in MED17 is required for the transcriptional activation of lipogenic genes in response to insulin.
Collapse
Affiliation(s)
- Jose A Viscarra
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yuhui Wang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Il-Hwa Hong
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hei Sook Sul
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
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.
Collapse
|
21
|
Ansari SA, Paul E, Sommer S, Lieleg C, He Q, Daly AZ, Rode KA, Barber WT, Ellis LC, LaPorta E, Orzechowski AM, Taylor E, Reeb T, Wong J, Korber P, Morse RH. Mediator, TATA-binding protein, and RNA polymerase II contribute to low histone occupancy at active gene promoters in yeast. J Biol Chem 2014; 289:14981-95. [PMID: 24727477 DOI: 10.1074/jbc.m113.529354] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transcription by RNA polymerase II (Pol II) in eukaryotes requires the Mediator complex, and often involves chromatin remodeling and histone eviction at active promoters. Here we address the role of Mediator in recruitment of the Swi/Snf chromatin remodeling complex and its role, along with components of the preinitiation complex (PIC), in histone eviction at inducible and constitutively active promoters in the budding yeast Saccharomyces cerevisiae. We show that recruitment of the Swi/Snf chromatin remodeling complex to the induced CHA1 promoter, as well as its association with several constitutively active promoters, depends on the Mediator complex but is independent of Mediator at the induced MET2 and MET6 genes. Although transcriptional activation and histone eviction at CHA1 depends on Swi/Snf, Swi/Snf recruitment is not sufficient for histone eviction at the induced CHA1 promoter. Loss of Swi/Snf activity does not affect histone occupancy of several constitutively active promoters; in contrast, higher histone occupancy is seen at these promoters in Mediator and PIC component mutants. We propose that an initial activator-dependent, nucleosome remodeling step allows PIC components to outcompete histones for occupancy of promoter sequences. We also observe reduced promoter association of Mediator and TATA-binding protein in a Pol II (rpb1-1) mutant, indicating mutually cooperative binding of these components of the transcription machinery and indicating that it is the PIC as a whole whose binding results in stable histone eviction.
Collapse
Affiliation(s)
- Suraiya A Ansari
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Emily Paul
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Sebastian Sommer
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Corinna Lieleg
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Qiye He
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| | - Alexandre Z Daly
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Kara A Rode
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Wesley T Barber
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Laura C Ellis
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Erika LaPorta
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| | - Amanda M Orzechowski
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Emily Taylor
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Tanner Reeb
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Jason Wong
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Philipp Korber
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Randall H Morse
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| |
Collapse
|