1
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Li T, Chao TC, Tsai KL. Structures and compositional dynamics of Mediator in transcription regulation. Curr Opin Struct Biol 2024; 88:102892. [PMID: 39067114 DOI: 10.1016/j.sbi.2024.102892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), functions as a critical coregulator during RNA polymerase II (RNAPII) transcription. cMED recruits RNAPII and facilitates the assembly of the pre-initiation complex (PIC) at promoters. In contrast, CKM prevents RNAPII binding to cMED while simultaneously exerting positive or negative influence on gene transcription through its kinase function. Recent structural studies on cMED and CKM have revealed their intricate architectures and subunit interactions. Here, we explore these structures, providing a comprehensive insight into Mediator (cMED-CKM) architecture and its potential mechanism in regulating RNAPII transcription. Additionally, we discuss the remaining puzzles that require further investigation to fully understand how cMED coordinates with CKM to regulate transcription in various events.
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Affiliation(s)
- Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX, USA
| | - Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX, USA
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX, USA.
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2
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Freytes SN, Gobbini ML, Cerdán PD. The Plant Mediator Complex in the Initiation of Transcription by RNA Polymerase II. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:211-237. [PMID: 38277699 DOI: 10.1146/annurev-arplant-070623-114005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Thirty years have passed since the discovery of the Mediator complex in yeast. We are witnessing breakthroughs and advances that have led to high-resolution structural models of yeast and mammalian Mediators in the preinitiation complex, showing how it is assembled and how it positions the RNA polymerase II and its C-terminal domain (CTD) to facilitate the CTD phosphorylation that initiates transcription. This information may be also used to guide future plant research on the mechanisms of Mediator transcriptional control. Here, we review what we know about the subunit composition and structure of plant Mediators, the roles of the individual subunits and the genetic analyses that pioneered Mediator research, and how transcription factors recruit Mediators to regulatory regions adjoining promoters. What emerges from the research is a Mediator that regulates transcription activity and recruits hormonal signaling modules and histone-modifying activities to set up an off or on transcriptional state that recruits general transcription factors for preinitiation complex assembly.
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Affiliation(s)
| | | | - Pablo D Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina; , ,
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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3
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Malik S, Roeder RG. Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genet 2023; 24:767-782. [PMID: 37532915 PMCID: PMC11088444 DOI: 10.1038/s41576-023-00630-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA
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4
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Ruoff R, Weber H, Wang Y, Huang H, Shapiro E, Fenyö D, Garabedian MJ. MED19 encodes two unique protein isoforms that confer prostate cancer growth under low androgen through distinct gene expression programs. Sci Rep 2023; 13:18227. [PMID: 37880276 PMCID: PMC10600210 DOI: 10.1038/s41598-023-45199-9] [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: 09/27/2022] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
MED19, a component of the mediator complex and a co-regulator of the androgen receptor (AR), is pivotal in prostate cancer cell proliferation. MED19 has two isoforms: a full-length "canonical" and a shorter "alternative" variant. Specific antibodies were developed to investigate these isoforms. Both exhibit similar expression in normal prostate development and adult prostate tissue, but the canonical isoform is elevated in prostate adenocarcinomas. Overexpression of canonical MED19 in LNCaP cells promotes growth under conditions of androgen deprivation in vitro and in vivo, mirroring earlier findings with alternative MED19-overexpressing LNCaP cells. Interestingly, alternative MED19 cells displayed strong colony formation in clonogenic assays under conditions of androgen deprivation, while canonical MED19 cells did not, suggesting distinct functional roles. These isoforms also modulated gene expression differently. Canonical MED19 triggered genes related to extracellular matrix remodeling while suppressing those involved in androgen-inactivating glucuronidation. In contrast, alternative MED19 elevated genes tied to cell movement and reduced those associated with cell adhesion and differentiation. The ratio of MED19 isoform expression in prostate cancers shifts with the disease stage. Early-stage cancers exhibit higher canonical MED19 expression than alternative MED19, consistent with canonical MED19's ability to promote cell proliferation under androgen deprivation. Conversely, alternative MED19 levels were higher in later-stage metastatic prostate cancer than in canonical MED19, reflecting alternative MED19's capability to enhance cell migration and autonomous cell growth. Our findings suggest that MED19 isoforms play unique roles in prostate cancer progression and highlights MED19 as a potential therapeutic target for both early and late-stage prostate cancer.
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Affiliation(s)
- Rachel Ruoff
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Hannah Weber
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ying Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Hongying Huang
- Department of Urology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ellen Shapiro
- Department of Urology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Michael J Garabedian
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Urology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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5
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Yang DL, Huang K, Deng D, Zeng Y, Wang Z, Zhang Y. DNA-dependent RNA polymerases in plants. THE PLANT CELL 2023; 35:3641-3661. [PMID: 37453082 PMCID: PMC10533338 DOI: 10.1093/plcell/koad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/09/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
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Affiliation(s)
- Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenxing Wang
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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6
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Jeon J, Friedman LJ, Seo HD, Adeleke A, Graham B, Patteson E, Gelles J, Buratowski S. Single-molecule analysis of transcription activation: dynamics of SAGA co-activator recruitment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552353. [PMID: 37609355 PMCID: PMC10441308 DOI: 10.1101/2023.08.07.552353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Transcription activators are said to stimulate gene expression by "recruiting" coactivators to promoters, yet this term fits several different kinetic models. To directly analyze dynamics of activator-coactivator interactions, single-molecule microscopy was used to image promoter DNA, a transcription activator, and the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex within nuclear extract. SAGA readily, but transiently, binds nucleosome-free DNA without activator, while chromatin template association occurs nearly exclusively when activator is present. On both templates, activator increases SAGA association rates by up to an order of magnitude, and dramatically extends its dwell times. These effects reflect direct interactions with the transactivation domain, as VP16 or Rap1 activation domains produce different SAGA dynamics. Despite multiple bromodomains, acetyl-CoA or histone H3/H4 tail acetylation only modestly improves SAGA binding. Unexpectedly, histone acetylation more strongly affects activator residence. Our studies thus reveal two modes of SAGA interaction with the genome: a short-lived activator-independent interaction with nucleosome-free DNA, and a state tethered to promoter-bound transcription activators that can last up to several minutes.
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7
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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.
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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
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8
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Gorbea Colón JJ, Palao L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K. Structural basis of a transcription pre-initiation complex on a divergent promoter. Mol Cell 2023; 83:574-588.e11. [PMID: 36731470 PMCID: PMC10162435 DOI: 10.1016/j.molcel.2023.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
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Affiliation(s)
- Jose J Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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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.
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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
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10
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Yang D, Alphey MS, MacNeill SA. Non-canonical binding of the Chaetomium thermophilum PolD4 N-terminal PIP motif to PCNA involves Q-pocket and compact 2-fork plug interactions but no 3 10 helix. FEBS J 2023; 290:162-175. [PMID: 35942639 PMCID: PMC10087552 DOI: 10.1111/febs.16590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 01/14/2023]
Abstract
DNA polymerase δ (Pol δ) is a key enzyme for the maintenance of genome integrity in eukaryotic cells, acting in concert with the sliding clamp processivity factor PCNA (proliferating cell nuclear antigen). Three of the four subunits of human Pol δ interact directly with the PCNA homotrimer via a short, conserved protein sequence known as a PCNA interacting protein (PIP) motif. Here, we describe the identification of a PIP motif located towards the N terminus of the PolD4 subunit of Pol δ (equivalent to human p12) from the thermophilic filamentous fungus Chaetomium thermophilum and present the X-ray crystal structure of the corresponding peptide bound to PCNA at 2.45 Å. Like human p12, the fungal PolD4 PIP motif displays non-canonical binding to PCNA. However, the structures of the human p12 and fungal PolD4 PIP motif peptides are quite distinct, with the fungal PolD4 PIP motif lacking the 310 helical segment that characterises most previously identified PIP motifs. Instead, the fungal PolD4 PIP motif binds PCNA via conserved glutamine that inserts into the Q-pocket on the surface of PCNA and with conserved leucine and phenylalanine sidechains forming a compact 2-fork plug that inserts into the hydrophobic pocket on PCNA. Despite the unusual binding mode of the fungal PolD4, isothermal calorimetry (ITC) measurements show that its affinity for PCNA is similar to that of its human orthologue. These observations add to a growing body of information on how diverse proteins interact with PCNA and highlight how binding modes can vary significantly between orthologous PCNA partner proteins.
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Affiliation(s)
- Dongxiao Yang
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, UK
| | - Magnus S Alphey
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, UK
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, UK
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11
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Warfield L, Donczew R, Mahendrawada L, Hahn S. Yeast Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism. Mol Cell 2022; 82:4033-4048.e7. [PMID: 36208626 PMCID: PMC9637718 DOI: 10.1016/j.molcel.2022.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022]
Abstract
Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. In contrast, at most Tail-independent genes, we find MED primarily at promoters but not at the UASs. These results suggest that MED Tail and activator-mediated MED recruitment regulates only a small subset of genes. Furthermore, we define three classes of genes that differ in PIC assembly pathways and the requirements for MED Tail, SAGA, TFIID, and BET factors Bdf1/2. Our combined results have broad implications for the roles of MED, other coactivators, and mechanisms of transcriptional regulation at different gene classes.
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Affiliation(s)
- Linda Warfield
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA
| | - Rafal Donczew
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA
| | - Lakshmi Mahendrawada
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA
| | - Steven Hahn
- Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Mailstop A1-162, Seattle, WA 98109, USA.
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12
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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13
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Bick G, Zhang J, Lower EE, Zhang X. Transcriptional coactivator MED1 in the interface of anti-estrogen and anti-HER2 therapeutic resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:498-510. [PMID: 35800368 PMCID: PMC9255246 DOI: 10.20517/cdr.2022.33] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 11/18/2022]
Abstract
Breast cancer is one of the most common cancer and leading causes of death in women in the United States and Worldwide. About 90% of breast cancers belong to ER+ or HER2+ subtypes and are driven by key breast cancer genes Estrogen Receptor and HER2, respectively. Despite the advances in anti-estrogen (endocrine) and anti-HER2 therapies for the treatment of these breast cancer subtypes, unwanted side effects, frequent recurrence and resistance to these treatments remain major clinical challenges. Recent studies have identified ER coactivator MED1 as a key mediator of ER functions and anti-estrogen treatment resistance. Interestingly, MED1 is also coamplified with HER2 and activated by the HER2 signaling cascade, and plays critical roles in HER2-mediated tumorigenesis and response to anti-HER2 treatment as well. Thus, MED1 represents a novel crosstalk point of the HER2 and ER pathways and a highly promising new therapeutic target for ER+ and HER2+ breast cancer treatment. In this review, we will discuss the recent progress on the role of this key ER/HER2 downstream effector MED1 in breast cancer therapy resistance and our development of an innovative RNA nanotechnology-based approach to target MED1 for potential future breast cancer therapy to overcome treatment resistance.
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Affiliation(s)
- Gregory Bick
- Department of Cancer Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jasmine Zhang
- Department of Cancer Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Elyse E. Lower
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA. ,University of Cincinnati Cancer Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaoting Zhang
- Department of Cancer Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA. ,University of Cincinnati Cancer Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Correspondence to: Prof. Xiaoting Zhang, Professor and Thomas Boat Endowed Chair, Department of Cancer Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267, USA. E-mail:
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14
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Farnung L, Vos SM. Assembly of RNA polymerase II transcription initiation complexes. Curr Opin Struct Biol 2022; 73:102335. [DOI: 10.1016/j.sbi.2022.102335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 11/03/2022]
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15
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Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y. Structures of the human Mediator and Mediator-bound preinitiation complex. Science 2021; 372:science.abg0635. [DOI: 10.1126/science.abg0635] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022]
Abstract
The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)–mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)–mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module–extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yilun Qi
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, He Y. Structure of the human Mediator-bound transcription preinitiation complex. Science 2021; 372:52-56. [PMID: 33707221 PMCID: PMC8117670 DOI: 10.1126/science.abg3074] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 12/24/2022]
Abstract
Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.
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Affiliation(s)
- R Abdella
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - A Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - S Chen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - C J Inouye
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - R Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Y He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA
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