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Li YW, Tu SX, Li ZX, Ding YQ, Hu L. Manifold functions of Mediator complex in neurodevelopmental disorders. Neurobiol Dis 2025; 210:106913. [PMID: 40246246 DOI: 10.1016/j.nbd.2025.106913] [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: 04/14/2025] [Accepted: 04/14/2025] [Indexed: 04/19/2025] Open
Abstract
Neurodevelopmental disorders (NDDs) encompass a diverse range of impairments affecting brain development and functions, often presenting as deficits in motor skills, cognitive abilities, language development and neuropsychiatric health. The emergence of next-generation sequencing has unveiled numerous genetic variants linked to NDDs, implicating molecular pathways involved in essential neuronal processes such as synaptic plasticity, neuronal architecture and proteostasis. Central to these processes is the Mediator complex, a highly conserved multi-subunit assembly crucial for RNA polymerase II (Pol II)-dependent transcription. The Mediator functions as a key regulator of gene expression, playing a pivotal role in coordinating cellular processes essential for neuronal differentiation and developmental signaling cascades. Increasingly evidence has shown that its dysfunction is highly associated with the pathogenesis of NDDs. This review aims to comprehensively examine the structural and functional characteristics of individual mediator subunits. We will focus on clinical case reports and recent preclinical studies that highlight the connection between genetic abnormalities in the Mediator complex and specific neurodevelopmental phenotypes, ultimately guiding the development of enhanced diagnostic tools and therapeutic interventions. Furthermore, this review will advance our understanding of the general role transcriptional regulation plays in the etiology of NDDs.
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Affiliation(s)
- Yi-Wei Li
- Laboratory Animal Center, Fudan University, Shanghai 200032, China
| | - Si-Xin Tu
- Laboratory Animal Center, Fudan University, Shanghai 200032, China
| | - Ze-Xuan Li
- Laboratory Animal Center, Fudan University, Shanghai 200032, China
| | - Yu-Qiang Ding
- Laboratory Animal Center, Fudan University, Shanghai 200032, China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Brain Science, Fudan University, Shanghai 200032, China.
| | - Ling Hu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Laboratory Animal Center, Fudan University, Shanghai 200032, China.
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2
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Nagel M, Taatjes DJ. Regulation of RNA polymerase II transcription through re-initiation and bursting. Mol Cell 2025; 85:1907-1919. [PMID: 40378829 DOI: 10.1016/j.molcel.2025.04.011] [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: 12/20/2024] [Revised: 03/13/2025] [Accepted: 04/07/2025] [Indexed: 05/19/2025]
Abstract
The regulation of RNA polymerase II (RNAPII) activity requires orchestrated responses among genomic regulatory sequences and an expansive set of proteins and protein complexes. Despite intense study over five decades, mechanistic insights continue to emerge. Within the past 10 years, live-cell imaging and single-cell transcriptomics experiments have yielded new information about enhancer-promoter communication, transcription factor dynamics, and the kinetics of RNAPII transcription activation. These insights have established RNAPII re-initiation and bursting as a common regulatory phenomenon with widespread implications for gene regulation in health and disease. Here, we summarize regulatory strategies that help control RNAPII bursting in eukaryotic cells, which is defined as short periods of active transcription followed by longer periods of inactivity. We focus on RNAPII re-initiation (i.e., a "burst" of two or more polymerases that initiate from the same promoter), with an emphasis on molecular mechanisms, open questions, and controversies surrounding this distinct regulatory stage.
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Affiliation(s)
- Michael Nagel
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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3
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Bhuiyan T, Arecco N, Mendoza Sanchez PK, Kim J, Schwan C, Weyrauch S, Nizamuddin S, Prunotto A, Tekman M, Biniossek ML, Knapp B, Koidl S, Drepper F, Huesgen PF, Grosse R, Hugel T, Arnold SJ. TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors. Cell Rep 2025; 44:115616. [PMID: 40287942 DOI: 10.1016/j.celrep.2025.115616] [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: 02/05/2024] [Revised: 11/22/2024] [Accepted: 04/01/2025] [Indexed: 04/29/2025] Open
Abstract
TFIID is an essential basal transcription factor, crucial for RNA polymerase II (pol II) promoter recognition and transcription initiation. The TFIID complex consists of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs) that contain intrinsically disordered regions (IDRs) with currently unknown functions. Here, we show that a conserved IDR drives TAF2 to nuclear speckle condensates independently of other TFIID subunits. Quantitative mass spectrometry analyses reveal TAF2 proximity to RNA splicing factors including specific interactions of the TAF2 IDR with SRRM2 in nuclear speckles. Deleting the IDR from TAF2 does not majorly impact global gene expression but results in changes of alternative splicing events. Further, genome-wide binding analyses suggest that the TAF2 IDR impedes TAF2 promoter association by guiding TAF2 to nuclear speckles. This study demonstrates that an IDR within the large multiprotein complex TFIID controls nuclear compartmentalization and thus links distinct molecular processes, namely transcription initiation and RNA splicing.
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Affiliation(s)
- Tanja Bhuiyan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Strasse 66, 79106 Freiburg, Germany.
| | - Niccolò Arecco
- Genome Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Paulina Karen Mendoza Sanchez
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Strasse 66, 79106 Freiburg, Germany; German Cancer Consortium (DKTK) Partner Site Freiburg, 79106 Freiburg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Juhyeong Kim
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Sophie Weyrauch
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Alberstrasse 19A, 79104 Freiburg, Germany
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Strasse 66, 79106 Freiburg, Germany; German Cancer Consortium (DKTK) Partner Site Freiburg, 79106 Freiburg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andrea Prunotto
- Datenintegrationszentrum, Medical Center-University of Freiburg, Faculty of Medicine, Georges-Köhler-Allee 302, 79110 Freiburg, Germany
| | - Mehmet Tekman
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
| | - Bettina Knapp
- Institute for Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Stefanie Koidl
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Strasse 66, 79106 Freiburg, Germany; German Cancer Consortium (DKTK) Partner Site Freiburg, 79106 Freiburg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Friedel Drepper
- Institute for Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Pitter F Huesgen
- Institute for Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; BIOSS and CIBSS Signalling Research Centres, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; BIOSS and CIBSS Signalling Research Centres, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; BIOSS and CIBSS Signalling Research Centres, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; BIOSS and CIBSS Signalling Research Centres, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany.
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4
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Monté D, Lens Z, Dewitte F, Fislage M, Aumercier M, Verger A, Villeret V. Structural basis of human Mediator recruitment by the phosphorylated transcription factor Elk-1. Nat Commun 2025; 16:3772. [PMID: 40263353 PMCID: PMC12015215 DOI: 10.1038/s41467-025-59014-8] [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: 04/23/2024] [Accepted: 04/08/2025] [Indexed: 04/24/2025] Open
Abstract
One function of Mediator complex subunit MED23 is to mediate transcriptional activation by the phosphorylated transcription factor Elk-1, in response to the Ras-MAPK signaling pathway. Using cryogenic electron microscopy, we solve a 3.0 Å structure of human MED23 complexed with the phosphorylated activation domain of Elk-1. Elk-1 binds to MED23 via a hydrophobic sequence PSIHFWSTLSPP containing one phosphorylated residue (S383p), which forms a tight turn around the central Phenylalanine. Binding of Elk-1 induces allosteric changes in MED23 that propagate to the opposite face of the subunit, resulting in the dynamic behavior of a 19-residue segment, which alters the molecular surface of MED23. We design a specific MED23 mutation (G382F) that disrupts Elk--1 binding and consequently impairs Elk-1-dependent serum-induced activation of target genes in the Ras-Raf-MEK-ERK signaling pathway. The structure provides molecular details and insights into a Mediator subunit-transcription factor interface.
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Affiliation(s)
- Didier Monté
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France.
| | - Zoé Lens
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Frédérique Dewitte
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Marcus Fislage
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, Brussels, Belgium
| | - Marc Aumercier
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Alexis Verger
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France.
| | - Vincent Villeret
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France.
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5
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Huang Y, Xiang Z, Xiang Y, Pan H, He M, Guo Z, Kanca O, Liu C, Zhang Z, Zhan H, Wang Y, Bai QR, Bellen HJ, Wang H, Bian S, Mao X. Biallelic MED16 variants disrupt neural development and lead to an intellectual disability syndrome. J Genet Genomics 2025:S1673-8527(25)00113-4. [PMID: 40254158 DOI: 10.1016/j.jgg.2025.04.004] [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: 10/29/2024] [Revised: 04/03/2025] [Accepted: 04/06/2025] [Indexed: 04/22/2025]
Abstract
Mediator Complex Subunit 16 (MED16, MIM: 604062) is a member of the Mediator complex which controls many aspects of transcriptional activity in all eukaryotes. Here, we report two individuals from a non-consanguineous family with biallelic variants in MED16 identified by exome sequencing. The affected individuals present with global developmental delay, intellectual disability, and dysmorphisms. To assess the pathogenicity of the variants, functional studies were performed in Drosophila and patient-derived cells. The fly ortholog med16 is expressed in neurons and some glia of the developing central nervous system (CNS). Loss of med16 leads to a reduction in eclosion and lifespan, as well as impaired synaptic transmission. In neurons differentiated from the patient-derived induced pluripotent stem cells (iPSCs), the neurite outgrowth is impaired and rescued by expression of exogenous MED16. The patient-associated variants behave as loss-of-function (LoF) alleles in flies and iPSCs. Additionally, the transcription of genes related to neuronal maturation and function is preferentially altered in patient cells relative to differentiated H9 controls. In summary, our findings support that MED16 is important for appropriate development and function, and that biallelic MED16 variants cause a neurodevelopmental disease.
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Affiliation(s)
- Yan Huang
- Department of Medical Genetics & Pediatric Research Institute, The Affiliated Children's Hospital of Xiangya School of Medicine, Central South University, (Hunan Children's Hospital), Changsha, Hunan 410007, China
| | - Zhenglong Xiang
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yaqin Xiang
- Department of Medical Genetics, The Affiliated Children's Hospital of Xiangya School of Medicine, Central South University, (Hunan Children's Hospital), Changsha, Hunan 410007, China
| | - Hu Pan
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, University of South China, Changsha, Hunan 410008, China
| | - Mei He
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, University of South China, Changsha, Hunan 410008, China
| | - Zhenming Guo
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Chen Liu
- Neonatology, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China
| | - Zhao Zhang
- Department of Medical Genetics & Pediatric Research Institute, The Affiliated Children's Hospital of Xiangya School of Medicine, Central South University, (Hunan Children's Hospital), Changsha, Hunan 410007, China
| | - Huaizhe Zhan
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yuan Wang
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Qing-Ran Bai
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Medicine, Tongji University, 200065 Shanghai, China
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hua Wang
- Department of Medical Genetics, The Affiliated Children's Hospital of Xiangya School of Medicine, Central South University, (Hunan Children's Hospital), Changsha, Hunan 410007, China
| | - Shan Bian
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, University of South China, Changsha, Hunan 410008, China; China Regional Research Center, International Center for Genetic Engineering and Biotechnology, Taizhou, Jiangsu 225316,China.
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, University of South China, Changsha, Hunan 410008, China; Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China.
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6
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Guillouet C, Agostini V, Baujat G, Cocciadiferro D, Pippucci T, Lesieur-Sebellin M, Georget M, Schatz U, Fauth C, Louie RJ, Rogers C, Davis JM, Konstantopoulou V, Mayr JA, Bouman A, Wilke M, VanNoy GE, England EM, Park KL, Brown K, Saenz M, Novelli A, Digilio MC, Mastromoro G, Rongioletti MCA, Piacentini G, Kaiyrzhanov R, Guliyeva S, Hasanova L, Shears D, Bhatnagar I, Stals K, Klaas O, Horvath J, Bouvagnet P, Witmer PD, MacCarrick G, Cisarova K, Good JM, Gorokhova S, Boute O, Smol T, Bruel AL, Patat O, Broadbent JR, Tan TY, Tan NB, Lyonnet S, Busa T, Graziano C, Amiel J, Gordon CT. Bi-allelic MED16 variants cause a MEDopathy with intellectual disability, motor delay, and craniofacial, cardiac, and limb malformations. Am J Hum Genet 2025; 112:829-845. [PMID: 40081376 DOI: 10.1016/j.ajhg.2025.02.016] [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: 09/13/2024] [Revised: 02/14/2025] [Accepted: 02/14/2025] [Indexed: 03/16/2025] Open
Abstract
The Mediator complex regulates protein-coding gene transcription by coordinating the interaction of upstream enhancers with the basal transcription machinery at the promoter. Pathogenic variants in Mediator subunits typically lead to neurodevelopmental or neurodegenerative disorders with variable clinical presentations, designated as MEDopathies. Here, we report the identification of 25 individuals from 18 families with bi-allelic MED16 variants who have a multiple congenital anomalies (MCAs)-intellectual disability syndrome. Intellectual disability, speech delay, and/or motor delay of variable severity were constant and associated with variable combinations of craniofacial defects (micro/retrognathia, cleft palate, and preauricular tags), anomalies of the extremities, and heart defects (predominantly tetralogy of Fallot). Visual impairment, deafness, and magnetic resonance imaging (MRI) abnormalities were also frequent. The 26 variants identified were comprised of eight predicted protein-truncating (three intragenic deletions, two frameshifts, and one nonsense and two essential splice site variants) and 18 missense or in-frame duplication variants affecting conserved residues, without clear correlation between phenotypic severity and variant type combination. Three-dimensional modeling indicated that the missense and duplication variants likely have a destabilizing effect on the structural elements of the protein. Immunofluorescence assays demonstrated protein mislocalization from the nucleus to the cytoplasm for 16 of the 17 variants studied. Homozygous mutant med16 zebrafish presented growth delay and increased mortality compared with wild-type fish, and Med16 knockout mice are preweaning lethal, highlighting the conserved requirement of MED16 for development. Overall, we describe an autosomal recessive MCAs-intellectual disability MEDopathy, emphasizing the importance of Mediator during neurodevelopment and suggesting that some tissues are particularly sensitive to the loss of certain subunits.
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Affiliation(s)
- Charlotte Guillouet
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Valeria Agostini
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Geneviève Baujat
- Service de Médecine Génomique des Maladies Rares, Necker-Enfants Malades Hospital, AP-HP, Paris, France
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero, Universitaria di Bologna, Bologna, Italy
| | - Marion Lesieur-Sebellin
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Mathieu Georget
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Ulrich Schatz
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria; Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Christine Fauth
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | | | | | | | - Vassiliki Konstantopoulou
- Department of Pediatrics and Adolescent Medicine, Austrian Newborn Screening, Medical University of Vienna, 1090 Vienna, Austria
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University, 5020 Salzburg, Austria
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Grace E VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina M England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kathleen Brown
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Margarita Saenz
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics, Translational Pediatrics and Clinical Genetics Research Area, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Gioia Mastromoro
- Department of Laboratory Science, Ospedale Isola Tiberina - Gemelli Isola, Rome, Italy
| | | | - Gerardo Piacentini
- Fetal and Neonatal Cardiology Unit, Ospedale Isola Tiberina - Gemelli Isola, Rome, Italy
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Neurology, South Kazakhstan Medical Academy, Shymkent, Kazakhstan
| | | | | | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ishita Bhatnagar
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Patrice Bouvagnet
- Département de Génétique, Laboratoire Eurofins Biomnis, 69007 Lyon, France; Centre Pluridisciplinaire de Diagnostic Prénatal, Hôpital MFME, CHU Martinique, Fort de France, France
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Gretchen MacCarrick
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Katarina Cisarova
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Svetlana Gorokhova
- Aix Marseille University, INSERM, MMG, U 1251, 13005 Marseille, France; Department of Medical Genetics, Timone Children's Hospital, AP-HM, 13005 Marseille, France
| | - Odile Boute
- University Lille, CHU Lille, ULR 7364 - RADEME - Maladies Rares du Développement Embryonnaire et du Métabolisme, 59000 Lille, France
| | - Thomas Smol
- University Lille, CHU Lille, ULR 7364 - RADEME - Maladies Rares du Développement Embryonnaire et du Métabolisme, 59000 Lille, France
| | - Ange-Line Bruel
- INSERM UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000 Dijon, France; Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000 Dijon, France
| | - Olivier Patat
- Department of Medical Genetics, CHU Toulouse Purpan, Toulouse, France
| | - Julia R Broadbent
- Rare Disease Discovery Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Tiong Y Tan
- Rare Disease Discovery Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France; Service de Médecine Génomique des Maladies Rares, Necker-Enfants Malades Hospital, AP-HP, Paris, France
| | - Tiffany Busa
- Department of Medical Genetics, Timone Children's Hospital, AP-HM, 13005 Marseille, France
| | | | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France; Service de Médecine Génomique des Maladies Rares, Necker-Enfants Malades Hospital, AP-HP, Paris, France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, Institut Imagine, Université Paris Cité, Paris, France.
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7
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Gopi S, Brandani GB, Tan C, Jung J, Gu C, Mizutani A, Ochiai H, Sugita Y, Takada S. In silico nanoscope to study the interplay of genome organization and transcription regulation. Nucleic Acids Res 2025; 53:gkaf189. [PMID: 40114377 PMCID: PMC11925733 DOI: 10.1093/nar/gkaf189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 02/10/2025] [Accepted: 03/08/2025] [Indexed: 03/22/2025] Open
Abstract
In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kb Nanog gene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II-mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer-promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of ∼350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.
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Affiliation(s)
- Soundhararajan Gopi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Chenyang Gu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Azuki Mizutani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hiroshi Ochiai
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-0054, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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8
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Bhole R, Shinkar J, Labhade S, Karwa P, Kapare H. MED12 dysregulation: insights into cancer and therapeutic resistance. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-04006-0. [PMID: 40105922 DOI: 10.1007/s00210-025-04006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 02/28/2025] [Indexed: 03/21/2025]
Abstract
MED12, a critical subunit of the mediator (MED) complex, plays a central role in transcriptional regulation by bridging signal-dependent transcription factors and RNA polymerase II. Dysregulation of MED12, often through mutation, has emerged as a significant driver in various cancers, including uterine leiomyomas, breast cancer (B.C.), and prostate cancer (P.C.). These mutations disrupt normal transcriptional processes by impairing the mediator complex's ability to properly regulate gene expression, which activates oncogenic pathways such as Wnt/β-catenin and TGF-β signaling, promoting tumorigenesis and drug resistance. Specifically, mutations in the MED12 gene lead to altered interactions with the transcriptional machinery, fostering aberrant activation of oncogenic networks. MED12 alterations have also been implicated in chemoresistance, particularly to therapies targeting EGFR, ALK, and BRAF, highlighting its role as a barrier to effective treatment. This review explores the mechanisms underlying MED12 dysregulation, its impact on cancer progression, and its association with therapeutic resistance. By examining its potential as a predictive biomarker and a therapeutic target, the article underscores the importance of MED12 in advancing precision oncology. Understanding MED12-mediated mechanisms offers insights into overcoming therapeutic resistance and paves the way for innovative, personalized cancer treatments.
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Affiliation(s)
- Ritesh Bhole
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pune, 411018, Maharashtra, India.
- Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, India.
| | - Jagruti Shinkar
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pune, 411018, Maharashtra, India
| | - Sonali Labhade
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pune, 411018, Maharashtra, India
| | - Pawan Karwa
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pune, 411018, Maharashtra, India
| | - Harshad Kapare
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pune, 411018, Maharashtra, India
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9
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Zhang B, Zhu Y, Tang Y, Liu L, Liu Y, Li Y, Yu W, Lu L. The mediator subunit complex protein MED15 promotes lipid deposition and cancer progression during hypoxia. J Biol Chem 2025; 301:108296. [PMID: 39947475 PMCID: PMC11930138 DOI: 10.1016/j.jbc.2025.108296] [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: 11/28/2024] [Revised: 01/29/2025] [Accepted: 02/06/2025] [Indexed: 03/09/2025] Open
Abstract
Hypoxia, a hallmark of solid tumors, is associated with increased lipid droplet (LD) accumulation. However, the mechanisms underlying this remain elusive. Here, we identify Mediator complex subunit 15 (MED15) as a critical regulator of hypoxia-inducible factor (HIF) signaling, potentially impacting LD accumulation. In mammalian cells, we elucidated that MED15, as a HIF target gene, participates in promoting HIF transcriptional activity without affecting HIFα protein levels, creating a positive feedback loop. Furthermore, zebrafish deficiency in med15 displayed decreased HIF activity and impaired tolerance to hypoxic stress. Functionally, MED15 deficiency attenuated the proliferation of colon and renal cancer cells in vitro and tumor growth in vivo. Mechanistically, MED15 acts upstream of carnitine palmitoyltransferase 1A (CPT1A), a key enzyme in fatty acid oxidation, ultimately promoting HIF-mediated LD accumulation. Disrupting the MED15-CPT1A axis impairs this process. These findings reveal a novel MED15-HIF-CPT1A axis that promotes LD formation, potentially contributing to hypoxic tumor progression.
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Affiliation(s)
- Boqi Zhang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Yu Zhu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Yanfei Tang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Yunzhang Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Yun Li
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Wengong Yu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Ling Lu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, China.
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10
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Luyties O, Sanford L, Rodino J, Nagel M, Jones T, Rimel JK, Ebmeier CC, Shelby GS, Cozzolino K, Brennan F, Hartzog A, Saucedo MB, Watts LP, Spencer S, Kugel JF, Dowell RD, Taatjes DJ. Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3'-ends. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.632016. [PMID: 39829884 PMCID: PMC11741307 DOI: 10.1101/2025.01.08.632016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely understood mechanisms. Because contaminating kinases precluded CDK7 analysis with nuclear extracts, we completed biochemical assays with purified factors. Reconstitution of RNAPII transcription initiation showed CDK7 inhibition slowed and/or paused RNAPII promoter-proximal transcription, which reduced re-initiation. These CDK7-regulatory functions were Mediator- and TFIID-dependent. Similarly in human cells, CDK7 inhibition reduced transcription by suppressing RNAPII activity at promoters, consistent with reduced initiation and/or re-initiation. Moreover, widespread 3'-end readthrough transcription was observed in CDK7-inhibited cells; mechanistically, this occurred through rapid nuclear depletion of RNAPII elongation and termination factors, including high-confidence CDK7 targets. Collectively, these results define how CDK7 governs RNAPII function at gene 5'-ends and 3'-ends, and reveal that nuclear abundance of elongation and termination factors is kinase-dependent. Because 3'-readthrough transcription is commonly induced during stress, our results further suggest regulated suppression of CDK7 activity may enable this RNAPII transcriptional response.
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Affiliation(s)
- Olivia Luyties
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Lynn Sanford
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado; Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado; Boulder, CO, 80303, USA
| | - Jessica Rodino
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Michael Nagel
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Taylor Jones
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Jenna K. Rimel
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | | | - Grace S. Shelby
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Kira Cozzolino
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Finn Brennan
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Axel Hartzog
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Mirzam B. Saucedo
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Lotte P. Watts
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado; Boulder, CO, 80303, USA
| | - Sabrina Spencer
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado; Boulder, CO, 80303, USA
| | - Jennifer F. Kugel
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
| | - Robin D. Dowell
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado; Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado; Boulder, CO, 80303, USA
| | - Dylan J. Taatjes
- Dept. of Biochemistry, University of Colorado; Boulder, CO, 80303, USA
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11
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Palacio M, Taatjes DJ. Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.06.631569. [PMID: 39829877 PMCID: PMC11741285 DOI: 10.1101/2025.01.06.631569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Mediator. TFs and Mediator contain intrinsically-disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a Real-time In-vitro Fluorescence Transcription assay (RIFT) for second-by-second visualization of RNAPII transcription at hundreds of promoters simultaneously. We show rapid RNAPII activation is IDR-dependent, without condensate formation. For example, the MED1-IDR can functionally replace a native TF, activating RNAPII with similar (not identical) kinetics; however, MED1-IDR squelches transcription as a condensate, but activates as a single-protein. TFs and Mediator cooperatively activate RNAPII bursting and re-initiation and surprisingly, Mediator can drive TF-promoter recruitment, without TF-DNA binding. Collectively, RIFT addressed questions largely intractable with cell-based methods, yielding mechanistic insights about IDRs, condensates, enhancer-promoter communication, and RNAPII bursting that complement live-cell imaging data.
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Affiliation(s)
- Megan Palacio
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Dylan J. Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
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12
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Liu M, Xie XJ, Li X, Ren X, Sun JL, Lin Z, Hemba-Waduge RUS, Ji JY. Transcriptional coupling of telomeric retrotransposons with the cell cycle. SCIENCE ADVANCES 2025; 11:eadr2299. [PMID: 39752503 PMCID: PMC11698117 DOI: 10.1126/sciadv.adr2299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 11/27/2024] [Indexed: 01/06/2025]
Abstract
Unlike most species that use telomerase for telomere maintenance, many dipterans, including Drosophila, rely on three telomere-specific retrotransposons (TRs)-HeT-A, TART, and TAHRE-to form tandem repeats at chromosome ends. Although TR transcription is crucial in their life cycle, its regulation remains poorly understood. This study identifies the Mediator complex, E2F1-Dp, and Scalloped/dTEAD as key regulators of TR transcription. Reducing the activity of the Mediator or Sd/dTEAD increases TR expression and telomere length, while overexpressing E2F1-Dp or depleting Rbf1 stimulates TR transcription. The Mediator and Sd/dTEAD regulate this process through E2F1-Dp. CUT&RUN (Cleavage under targets and release using nuclease) analysis shows direct binding of CDK8, Dp, and Sd/dTEAD to telomeric repeats, with motif enrichment revealing E2F- and TEAD-binding sites. These findings uncover the Mediator complex's role in controlling TR transcription and telomere length through E2F1-Dp and Sd, coupling the transcriptional regulation of the TR life cycle with host cell-cycle machinery to protect chromosome ends in Drosophila.
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Affiliation(s)
- Mengmeng Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA 70112, USA
| | - Xiao-Jun Xie
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Xingjie Ren
- Institute for Human Genetics and Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jasmine L. Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA 70112, USA
| | - Zhen Lin
- Department of Pathology, Tulane University School of Medicine, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA 70112, USA
| | - Rajitha-Udakara-Sampath Hemba-Waduge
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA 70112, USA
| | - Jun-Yuan Ji
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA 70112, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
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13
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Kuldell JC, Kaplan CD. RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease. J Mol Biol 2025; 437:168770. [PMID: 39214283 PMCID: PMC11781076 DOI: 10.1016/j.jmb.2024.168770] [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: 07/23/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Gene expression is dependent on RNA Polymerase II (Pol II) activity in eukaryotes. In addition to determining the rate of RNA synthesis for all protein coding genes, Pol II serves as a platform for the recruitment of factors and regulation of co-transcriptional events, from RNA processing to chromatin modification and remodeling. The transcriptome can be shaped by changes in Pol II kinetics affecting RNA synthesis itself or because of alterations to co-transcriptional events that are responsive to or coupled with transcription. Genetic, biochemical, and structural approaches to Pol II in model organisms have revealed critical insights into how Pol II works and the types of factors that regulate it. The complexity of Pol II regulation generally increases with organismal complexity. In this review, we describe fundamental aspects of how Pol II activity can shape gene expression, discuss recent advances in how Pol II elongation is regulated on genes, and how altered Pol II function is linked to human disease and aging.
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Affiliation(s)
- James C Kuldell
- Department of Biological Sciences, 202A LSA, Fifth and Ruskin Avenues, University of Pittsburgh, Pittsburgh PA 15260, United States
| | - Craig D Kaplan
- Department of Biological Sciences, 202A LSA, Fifth and Ruskin Avenues, University of Pittsburgh, Pittsburgh PA 15260, United States.
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14
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Wang Z, Song A, Tao B, Miao M, Luo YQ, Wang J, Yin Z, Xiao R, Zhou X, Shang XY, Hu S, Liang K, Danko CG, Chen FX. The phosphatase PP1 sustains global transcription by promoting RNA polymerase II pause release. Mol Cell 2024; 84:4824-4842.e7. [PMID: 39603240 DOI: 10.1016/j.molcel.2024.10.046] [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: 01/24/2024] [Revised: 08/02/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024]
Abstract
RNA polymerase II progression from initiation to elongation is driven in part by a cascade of protein kinases acting on the core transcription machinery. Conversely, the corresponding phosphatases, notably PP2A and PP1-the most abundant serine-threonine phosphatases in cells-are thought to mainly impede polymerase progression, respectively restraining pause release at promoters and elongation at terminators. Here, we reveal an unexpected role of PP1, within the phosphatase 1 nuclear targeting subunit (PNUTS)-PP1 complex, in sustaining global transcriptional activation in human cells. Acute disruption of PNUTS-PP1 leads to severe defects in the release of paused polymerase and subsequent downregulation for the majority of transcribed genes. PNUTS-PP1 promotes pause release by dephosphorylating multiple substrates, including the 7SK small nuclear ribonucleoprotein particle (snRNP) subunit MEPCE, a known pausing regulator. PNUTS-PP1 exhibits antagonistic functions compared with Integrator-PP2A (INTAC) phosphatase, which generally inhibits pause release. Our research thus highlights opposing roles of PP1 and PP2A in modulating genome-wide transcriptional pausing and gene expression.
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Affiliation(s)
- Zhenning Wang
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Aixia Song
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bolin Tao
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Maojian Miao
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Qing Luo
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingwen Wang
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhinang Yin
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Ruijing Xiao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xinwen Zhou
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xue-Ying Shang
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shibin Hu
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kaiwei Liang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Fei Xavier Chen
- Cancer Institute & Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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15
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Yheskel M, Castiglione MA, Kelly RD, Sidoli S, Secombe J. The histone demethylase KDM5 has insulator activity in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.04.626780. [PMID: 39677601 PMCID: PMC11642926 DOI: 10.1101/2024.12.04.626780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
KDM5 family proteins are best known for their demethylation of the promoter proximal chromatin mark H3K4me3. KDM5-regulated transcription is critical in the brain, with variants in the X-linked paralog KDM5C causing the intellectual disability (ID) disorder Claes-Jensen syndrome. Although the demethylase activity of KDM5C is known to be important for neuronal function, the contribution of non-enzymatic activities remain less characterized. We therefore used Drosophila to model the ID variant Kdm5 L854F , which disrupts a C5HC2 zinc finger adjacent to the enzymatic JmjC domain. Kdm5 L854F causes similar transcriptional changes in the brain to a demethylase dead strain, Kdm5 J1310C * , despite having little effect on enzymatic activity. KDM5 L854F is also distinct from KDM5 J1310C * in its reduced interactions with insulator proteins and enhancement of position effect variegation. Instead, the common transcriptional deficits likely result from both the JmjC and C5HC2 domains driving proper genomic organization through their activity in promoting proper loop architecture.
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16
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Tang Y, Tang S, Yang W, Zhang Z, Wang T, Wu Y, Xu J, Pilarsky C, Mazzone M, Wang LW, Sun Y, Tian R, Tang Y, Wang Y, Wang C, Xue J. MED12 loss activates endogenous retroelements to sensitise immunotherapy in pancreatic cancer. Gut 2024; 73:1999-2011. [PMID: 39216984 DOI: 10.1136/gutjnl-2024-332350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) stands as one of the most lethal cancers, marked by its lethality and limited treatment options, including the utilisation of checkpoint blockade (ICB) immunotherapy. Epigenetic dysregulation is a defining feature of tumourigenesis that is implicated in immune surveillance, but remains elusive in PDAC. DESIGN To identify the factors that modulate immune surveillance, we employed in vivo epigenetic-focused CRISPR-Cas9 screen in mouse PDAC tumour models engrafted in either immunocompetent or immunodeficient mice. RESULTS Here, we identified MED12 as a top hit, emerging as a potent negative modulator of immune tumour microenviroment (TME) in PDAC. Loss of Med12 significantly promoted infiltration and cytotoxicity of immune cells including CD8+ T cells, natural killer (NK) and NK1.1+ T cells in tumours, thereby heightening the sensitivity of ICB treatment in a mouse model of PDAC. Mechanistically, MED12 stabilised heterochromatin protein HP1A to repress H3K9me3-marked endogenous retroelements. The derepression of retrotransposons induced by MED12 loss triggered cytosolic nucleic acid sensing and subsequent activation of type I interferon pathways, ultimately leading to robust inflamed TME . Moreover, we uncovered a negative correlation between MED12 expression and immune resposne pathways, retrotransposon levels as well as the prognosis of patients with PDAC undergoing ICB therapy. CONCLUSION In summary, our findings underscore the pivotal role of MED12 in remodelling immnue TME through the epigenetic silencing of retrotransposons, offering a potential therapeutic target for enhancing tumour immunogenicity and overcoming immunotherapy resistance in PDAC.
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Affiliation(s)
- Yingying Tang
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shijie Tang
- Centre of Biomedical Systems and Informatics, ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, Zhejiang, China
| | - Wenjuan Yang
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengyan Zhang
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Teng Wang
- Centre of Biomedical Systems and Informatics, ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, Zhejiang, China
| | - Yuyun Wu
- Centre of Biomedical Systems and Informatics, ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, Zhejiang, China
| | - Junyi Xu
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Christian Pilarsky
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - Lei-Wei Wang
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongwei Sun
- Department of Biliary and Pancreatic Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China
| | - Ruijun Tian
- Shenzhen Key Laboratory of Functional Proteomics, Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Yujie Tang
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chaochen Wang
- Centre of Biomedical Systems and Informatics, ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, Zhejiang, China
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Hangzhou, China
- Biomedical and Health Translational Research Centre, Zhejiang University, Zhejiang, China
| | - Jing Xue
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Zhu S, Chen Z, Liu C, Duong J, Tran T, Liang Z, Fang X, Ouyang K. The essential role of MED27 in stabilizing the mediator complex for cardiac development and function. Life Sci 2024; 356:123020. [PMID: 39209248 DOI: 10.1016/j.lfs.2024.123020] [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: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
AIM Transcriptional regulation of gene expression plays a crucial role in orchestrating complex morphogenetic and molecular events during heart development and function. Mediator complex is an essential multi-subunit protein complex that governs gene expression in eukaryotic cells. Although Mediator subunits (MEDs) work integrally in the complex, individual MED component displays specialized functions. MED27, categorized as an Upper Tail subunit, possesses an as-yet-uncharacterized function. In this study, we aimed to investigate the physiological role of MED27 in cardiomyocytes. MATERIALS AND METHODS we generated a Med27 floxed mouse line, which was further used to generate constitutive (cKO) and inducible (icKO) cardiomyocyte-specific Med27 knockout mouse models. Morphological, histological analysis and cardiac physiological studies were performed in Med27 cKO and icKO mutants. Transcriptional profiles were determined by RNA sequencing (RNAseq) analysis. KEY FUNDINGS Ablation of MED27 in developing mouse cardiomyocytes results in embryonic lethality, while its deletion in adult cardiomyocytes leads to heart failure and mortality. Similar to the ablation of another Upper Tail subunit, MED30 in cardiomyocytes, deletion of MED27 leads to decreased protein levels of most MEDs in cardiomyocytes. Interestingly, overexpression of MED30 fails to restore the protein levels of Mediator subunits in MED27-deficient cardiomyocytes, demonstrating that the role of MED27 in maintaining the integrity and stability of the Mediator complex is independent of MED30. SIGNIFICANCE Our results revealed an essential role of MED27 in cardiac development and function by maintaining the stability of the Mediator core.
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Affiliation(s)
- Siting Zhu
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ze'e Chen
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Cardiovascular Medicine, Translational Medicine Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Janelle Duong
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Tiana Tran
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zhengyu Liang
- Department of Systems Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xi Fang
- Department of Medicine, University of California San Diego, La Jolla, California, USA.
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
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18
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Amith W, Chen VT, Dutagaci B. Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation. J Phys Chem B 2024; 128:10385-10396. [PMID: 39395159 PMCID: PMC11514005 DOI: 10.1021/acs.jpcb.4c04457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/23/2024] [Accepted: 10/01/2024] [Indexed: 10/14/2024]
Abstract
RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of the CTD affects clustering are not entirely known. In this work, we studied the concentrated solutions of two heptapeptide repeat (2CTD) models at different phosphorylation patterns and protein and ion concentrations using all-atom molecular dynamics simulations to investigate clustering behavior and molecular interactions driving the cluster formation. Our results show that salt concentration and phosphorylation patterns play an important role in determining the clustering pattern, specifically at low protein concentrations. The balance between inter- and intrapeptide interactions and counterion coordination together impact the clustering behavior upon phosphorylation.
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Affiliation(s)
- Weththasinghage
D. Amith
- Department
of Molecular and Cell Biology, University
of California, Merced, California 95343, United States
| | - Vincent T. Chen
- Department
of Molecular and Cell Biology, University
of California, Merced, California 95343, United States
| | - Bercem Dutagaci
- Department
of Molecular and Cell Biology, University
of California, Merced, California 95343, United States
- Health
Sciences Research Institute, University
of California, Merced, California 95343, United States
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19
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Chao TC, Chen SF, Kim HJ, Tang HC, Tseng HC, Xu A, Palao L, Khadka S, Li T, Huang MF, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module. Mol Cell 2024; 84:3932-3949.e10. [PMID: 39321804 PMCID: PMC11832219 DOI: 10.1016/j.molcel.2024.09.001] [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: 03/28/2023] [Revised: 01/05/2024] [Accepted: 09/03/2024] [Indexed: 09/27/2024]
Abstract
The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex formation in a manner repressed by the CKM through mechanisms presently unknown. Herein, we report cryoelectron microscopy structures of the complete human Mediator and its CKM. The CKM binds to multiple regions on cMED through both MED12 and MED13, including a large intrinsically disordered region (IDR) in the latter. MED12 and MED13 together anchor the CKM to the cMED hook, positioning CDK8 downstream and proximal to the transcription start site. Notably, the MED13 IDR obstructs the recruitment of RNA Pol II/MED26 onto cMED by direct occlusion of their respective binding sites, leading to functional repression of cMED-dependent transcription. Combined with biochemical and functional analyses, these structures provide a conserved mechanistic framework to explain the basis for CKM-mediated repression of cMED function.
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Affiliation(s)
- Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui-Chi Tang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hsiang-Ching Tseng
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Subash Khadka
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA; Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, 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; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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20
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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 PMCID: PMC11779508 DOI: 10.1016/j.sbi.2024.102892] [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: 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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21
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Li Z, Sun M, Yang R, Wang Z, Zhu Q, Zhang Y, Yang H, Meng Z, Hu L, Sui L. Mediator complex subunit 1 promotes oral squamous cell carcinoma progression by activating MMP9 transcription and suppressing CD8 + T cell antitumor immunity. J Exp Clin Cancer Res 2024; 43:270. [PMID: 39343952 PMCID: PMC11440895 DOI: 10.1186/s13046-024-03191-9] [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: 06/06/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND The role of Mediator complex subunit 1 (MED1), a pivotal transcriptional coactivator implicated in diverse biological pathways, remains unexplored in the context of oral squamous cell carcinoma (OSCC). This study aims to elucidate the contributory mechanisms and potential impact of MED1 on the progression of OSCC. METHODS The expression and clinical significance of MED1 in OSCC tissues were evaluated through the bioinformatics analyses. The effects of MED1 on the biological behavior of OSCC cancer cells were assessed both in vitro and in vivo. Dual-luciferase reporter assay, chromatin immunoprecipitation (ChIP) assay, bioinformatic analysis, CD8+ T cell isolation experiment, coculture experiment, enzyme-linked immunosorbent assay (ELISA), and flow cytometric analysis were employed to elucidate the underlying mechanism through which MED1 operates in the progression of OSCC. RESULTS MED1 exhibited upregulation in both OSCC tissues and multiple OSCC cell lines, which correlated with decreased overall survival in patients. In vitro experiments demonstrated that knockdown of MED1 in metastatic OSCC cell lines SCC-9 and UPCI-SCC-154 hindered cell migration and invasion, while overexpression of MED1 promoted these processes. Whereas, MED1 knockdown had no impact on proliferation of cell lines mentioned above. In vivo studies further revealed that downregulation of MED1 effectively suppressed distant metastasis in OSCC. Mechanistically, MED1 enhanced the binding of transcription factors c-Jun and c-Fos to the matrix metalloprotein 9 (MMP9) promoters, resulting in a significant upregulation of MMP9 transcription. This process contributes to the migration and invasion of SCC-9 and UPCI-SCC-154 cells. Furthermore, MED1 modulated the expression of programmed death-ligand 1 (PD-L1) through the Notch signaling pathway, consequently impacting the tumor-killing capacity of CD8+ T cells in the tumor microenvironment. CONCLUSIONS Our findings indicate that MED1 plays a pivotal role in OSCC progression through the activation of MMP9 transcription and suppression of CD8+ T cell antitumor immunity, suggesting that MED1 may serve as a novel prognostic marker and therapeutic target in OSCC.
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Affiliation(s)
- Zhe Li
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institute of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China
| | - Mengke Sun
- Immunology Department, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 22 Qixiangtai Road, Tianjin, 300070, China
| | - Ruimeng Yang
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institute of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China
| | - Zheng Wang
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institute of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China
| | - Qianyu Zhu
- Immunology Department, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 22 Qixiangtai Road, Tianjin, 300070, China
| | - Yue Zhang
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institute of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China
| | - Haosun Yang
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institute of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China
| | - Zhaosong Meng
- Department of Oral and Maxillofacial Surgery, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institue of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China.
| | - Lizhi Hu
- Immunology Department, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 22 Qixiangtai Road, Tianjin, 300070, China.
| | - Lei Sui
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University Institute of Stomatology, 12 Qixiangtai Road, Tianjin, 300070, China.
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22
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Zhang Q, Kim W, Panina SB, Mayfield JE, Portz B, Zhang YJ. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. Nat Commun 2024; 15:7985. [PMID: 39266551 PMCID: PMC11393077 DOI: 10.1038/s41467-024-52391-6] [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: 01/11/2024] [Accepted: 09/04/2024] [Indexed: 09/14/2024] Open
Abstract
The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. With CTD driving condensate formation on gene loci, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulators, forms distinct condensates from unphosphorylated CTD. Functional studies demonstrate CTD variants with diverse condensation properties exhibit differences in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths influence the assembly of RNA processing machinery and alternative splicing outcomes, which in turn affects cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
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Affiliation(s)
- Qian Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, USA
| | - Svetlana B Panina
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Joshua E Mayfield
- Department of Pharmacology, Pathology, Chemistry, and Biochemistry, and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Y Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA.
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23
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Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R, Asturias FJ. An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Mol Cell 2024; 84:2648-2664.e10. [PMID: 38955181 PMCID: PMC11283359 DOI: 10.1016/j.molcel.2024.06.006] [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: 06/28/2023] [Revised: 02/29/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
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Affiliation(s)
- Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Jiaqin Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | | | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - McKayla Riney
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | | | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Seol Kyoung Jung
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA.
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24
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Chen SF, Chao TC, Kim HJ, Tang HC, Khadka S, Li T, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator complex modulated by its dissociable Kinase module. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601608. [PMID: 39005267 PMCID: PMC11244988 DOI: 10.1101/2024.07.01.601608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), regulates RNA Polymerase II (Pol II)-dependent transcription. cMED recruits Pol II and promotes pre-initiation complex (PIC) formation in a manner inhibited by the CKM, which is also implicated in post-initiation control of gene expression. Herein we report cryo-electron microscopy structures of the human complete Mediator and its CKM, which explains the basis for CKM inhibition of cMED-activated transcription. The CKM binds to cMED through an intrinsically disordered region (IDR) in MED13 and HEAT repeats in MED12. The CKM inhibits transcription by allocating its MED13 IDR to occlude binding of Pol II and MED26 to cMED and further obstructing cMED-PIC assembly through steric hindrance with TFIIH and the +1 nucleosome. Notably, MED12 binds to the cMED Hook, positioning CDK8 downstream of the transcription start site, which sheds new light on its stimulatory function in post-initiation events.
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25
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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 PMCID: PMC11574175 DOI: 10.1038/s41580-024-00710-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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26
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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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27
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Velychko T, Mohammad E, Ferrer-Vicens I, Parfentev I, Werner M, Studniarek C, Schwalb B, Urlaub H, Murphy S, Cramer P, Lidschreiber M. CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release. Mol Cell 2024; 84:2287-2303.e10. [PMID: 38821049 DOI: 10.1016/j.molcel.2024.05.007] [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: 12/02/2022] [Revised: 02/01/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]
Abstract
Cyclin-dependent kinase 7 (CDK7), part of the general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (RNA Pol II). Here, we combine rapid CDK7 kinase inhibition with multi-omics analysis to unravel the direct functions of CDK7 in human cells. CDK7 inhibition causes RNA Pol II retention at promoters, leading to decreased RNA Pol II initiation and immediate global downregulation of transcript synthesis. Elongation, termination, and recruitment of co-transcriptional factors are not directly affected. Although RNA Pol II, initiation factors, and Mediator accumulate at promoters, RNA Pol II complexes can also proceed into gene bodies without promoter-proximal pausing while retaining initiation factors and Mediator. Further downstream, RNA Pol II phosphorylation increases and initiation factors and Mediator are released, allowing recruitment of elongation factors and an increase in RNA Pol II elongation velocity. Collectively, CDK7 kinase activity promotes the release of initiation factors and Mediator from RNA Pol II, facilitating RNA Pol II escape from the promoter.
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Affiliation(s)
- Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eusra Mohammad
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ivan Ferrer-Vicens
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marcel Werner
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cecilia Studniarek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
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Wang L, Zang P, Li J, Zhang Z, Li C, Zheng A, Zhao S, Yao J, Li C, Guo Z, Zhang W, Zhou L. Single Effective Complex Loading into Zero-Mode Waveguides Optimized with Fluorescence Evaluation at Quenching and Accumulation Checkpoints. ACS APPLIED MATERIALS & INTERFACES 2024; 16:25676-25685. [PMID: 38742765 DOI: 10.1021/acsami.4c01836] [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: 05/16/2024]
Abstract
Single-molecule detection with high accuracy and specialty plays an important role in biomedical diagnosis and screening. Zero-mode waveguides (ZMWs) enable the possibility of single biological molecule detection in real time. Nevertheless, the absence of a reliable assessment for single effective complex loading has constrained further applications of ZMWs in complex interaction. Both the quantity and activity of the complex loaded into ZMWs have a critical effect on the efficiency of detection. Herein, a fluorescence evaluation at quenching and accumulation checkpoints was established to assess and optimize single effective complex loading into ZMWs. A primer-template-enzyme ternary complex was designed, and then an evaluation for quantity statistics at the quenching checkpoint and functional activity at the accumulation checkpoint was used to validate the effectiveness of complexes loaded into ZMWs. By optimizing the parameters such as loading time, procedures, and enzyme amount, the single-molecule effective occupancy was increased to 25.48%, achieving 68.86% of the theoretical maximum value (37%) according to Poisson statistics. It is of great significance to provide effective complex-loading validation for improving the sample-loading efficiency of single-molecule assays or sequencing in the future.
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Affiliation(s)
- Lu Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Peilin Zang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Jinze Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Zhiqi Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Chao Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Anran Zheng
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Shasha Zhao
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Jia Yao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Chuanyu Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Zhen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Wei Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
- Ji Hua Laboratory, 528200 Foshan, China
| | - Lianqun Zhou
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
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Cheng IH, Pi WC, Hsu CH, Guo Y, Lai JL, Wang GG, Chung BC, Roeder RG, Chen WY. TAF2, within the TFIID complex, regulates the expression of a subset of protein-coding genes. Cell Death Discov 2024; 10:244. [PMID: 38773077 PMCID: PMC11109217 DOI: 10.1038/s41420-024-02017-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
TFIID, one of the general transcription factor (GTF), regulates transcriptional initiation of protein-coding genes through direct binding to promoter elements and subsequent recruitment of other GTFs and RNA polymerase II. Although generally required for most protein-coding genes, accumulated studies have also demonstrated promoter-specific functions for several TFIID subunits in gene activation. Here, we report that TBP-associated factor 2 (TAF2) specifically regulates TFIID binding to a small subset of protein-coding genes and is essential for cell growth of multiple cancer lines. Co-immunoprecipitation assays revealed that TAF2 may be sub-stoichiometrically associated with the TFIID complex, thus indicating a minor fraction of TAF2-containing TFIID in cells. Consistently, integrated genome-wide profiles show that TAF2 binds to and regulates only a small subset of protein-coding genes. Furthermore, through the use of an inducible TAF2 degradation system, our results reveal a reduction of TBP/TFIID binding to several ribosomal genes upon selective ablation of TAF2. In addition, depletion of TAF2, as well as the TAF2-regulated ribosomal protein genes RPL30 and RPL39, decreases ribosome assembly and global protein translation. Collectively, this study suggests that TAF2 within the TFIID complex is of functional importance for TBP/TFIID binding to and expression of a small subset of protein-coding genes, thus establishing a previously unappreciated promoter-selective function for TAF2.
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Affiliation(s)
- I-Hsin Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Hao Hsu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Durham, NC, 27710, USA
| | - Jun-Lin Lai
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Gang G Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Durham, NC, 27710, USA
| | - Bon-Chu Chung
- Insitute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biomedical Sciences, Neuroscience and Brain Disease Center, China Medical University, Taichung, Taiwan
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei, Taiwan
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan.
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Kolonay DW, Sattler KM, Strawser C, Rafael-Fortney J, Mihaylova MM, Miller KE, Lepper C, Baskin KK. Temporal regulation of the Mediator complex during muscle proliferation, differentiation, regeneration, aging, and disease. Front Cell Dev Biol 2024; 12:1331563. [PMID: 38690566 PMCID: PMC11058648 DOI: 10.3389/fcell.2024.1331563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Genesis of skeletal muscle relies on the differentiation and fusion of mono-nucleated muscle progenitor cells into the multi-nucleated muscle fiber syncytium. The temporally-controlled cellular and morphogenetic changes underlying this process are initiated by a series of highly coordinated transcription programs. At the core, the myogenic differentiation cascade is driven by muscle-specific transcription factors, i.e., the Myogenic Regulatory Factors (MRFs). Despite extensive knowledge on the function of individual MRFs, very little is known about how they are coordinated. Ultimately, highly specific coordination of these transcription programs is critical for their masterfully timed transitions, which in turn facilitates the intricate generation of skeletal muscle fibers from a naïve pool of progenitor cells. The Mediator complex links basal transcriptional machinery and transcription factors to regulate transcription and could be the integral component that coordinates transcription factor function during muscle differentiation, growth, and maturation. In this study, we systematically deciphered the changes in Mediator complex subunit expression in skeletal muscle development, regeneration, aging, and disease. We incorporated our in vitro and in vivo experimental results with analysis of publicly available RNA-seq and single nuclei RNA-seq datasets and uncovered the regulation of Mediator subunits in different physiological and temporal contexts. Our experimental results revealed that Mediator subunit expression during myogenesis is highly dynamic. We also discovered unique temporal patterns of Mediator expression in muscle stem cells after injury and during the early regeneration period, suggesting that Mediator subunits may have unique contributions to directing muscle stem cell fate. Although we observed few changes in Mediator subunit expression in aging muscles compared to younger muscles, we uncovered extensive heterogeneity of Mediator subunit expression in dystrophic muscle nuclei, characteristic of chronic muscle degeneration and regeneration cycles. Taken together, our study provides a glimpse of the complex regulation of Mediator subunit expression in the skeletal muscle cell lineage and serves as a springboard for mechanistic studies into the function of individual Mediator subunits in skeletal muscle.
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Affiliation(s)
- Dominic W. Kolonay
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Kristina M. Sattler
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Corinne Strawser
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Jill Rafael-Fortney
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Maria M. Mihaylova
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Katherine E. Miller
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Christoph Lepper
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Kedryn K. Baskin
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Shang XY, Xu C, Chen FX. From snapshots to a movie: Capturing eukaryotic transcription initiation at single-nucleotide resolution. Sci Bull (Beijing) 2024; 69:853-855. [PMID: 38320900 DOI: 10.1016/j.scib.2024.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Affiliation(s)
- Xue-Ying Shang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Radiation Oncology, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Congling Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Radiation Oncology, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Radiation Oncology, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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32
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Konuma T, Zhou MM. Distinct Histone H3 Lysine 27 Modifications Dictate Different Outcomes of Gene Transcription. J Mol Biol 2024; 436:168376. [PMID: 38056822 DOI: 10.1016/j.jmb.2023.168376] [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: 09/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Site-specific histone modifications have long been recognized to play an important role in directing gene transcription in chromatin in biology of health and disease. However, concrete illustration of how different histone modifications in a site-specific manner dictate gene transcription outcomes, as postulated in the influential "Histone code hypothesis", introduced by Allis and colleagues in 2000, has been lacking. In this review, we summarize our latest understanding of the dynamic regulation of gene transcriptional activation, silence, and repression in chromatin that is directed distinctively by histone H3 lysine 27 acetylation, methylation, and crotonylation, respectively. This represents a special example of a long-anticipated verification of the "Histone code hypothesis."
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Affiliation(s)
- Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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33
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Wu Y, Fu Y, Zhu Z, Hu Q, Sheng F, Du X. The Mediator Subunit OsMED16 Interacts with the WRKY Transcription Factor OsWRKY45 to Enhance Rice Resistance Against Magnaporthe oryzae. RICE (NEW YORK, N.Y.) 2024; 17:23. [PMID: 38558163 PMCID: PMC10984912 DOI: 10.1186/s12284-024-00698-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/03/2024] [Indexed: 04/04/2024]
Abstract
Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most common and damaging diseases of rice that limits rice yield and quality. The mediator complex plays a vital role in promoting transcription by bridging specific transcription factors and RNA polymerase II. Here, we show that the rice mediator subunit OsMED16 is essential for full induction of the diterpenoid phytoalexin biosynthesis genes and resistance to the ascomycetous fungus M. oryzae. Mutants of Osmed16 show reduced expression of the DP biosynthesis genes and are markedly more susceptible to M. oryzae, while transgenic plants overexpressing OsMED16 increased the expression of the DP biosynthesis genes and significantly enhanced resistance to M. oryzae. Interestingly, OsMED16 is physically associated with the WRKY family transcription factor OsWRKY45, which interacts with the phytoalexin synthesis key regulator transcription factor OsWRKY62. Further, OsMED16-OsWRKY45-OsWRKY62 complex could bind to the promoter regions of phytoalexin synthesis-related genes and activate their gene expression. Our results show that OsMED16 may enhance rice tolerance to M. oryzae via directly manipulating phytoalexin de novo biosynthesis.
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Affiliation(s)
- Yanfei Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yuquan Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Zhonglin Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Qin Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China.
| | - Feng Sheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Xuezhu Du
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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34
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Greber BJ. High-resolution cryo-EM of a small protein complex: The structure of the human CDK-activating kinase. Structure 2024:S0969-2126(24)00085-6. [PMID: 38565138 DOI: 10.1016/j.str.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/27/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
The human CDK-activating kinase (CAK) is a multifunctional protein complex and key regulator of cell growth and division. Because of its critical functions in regulating the cell cycle and transcription initiation, it is a key target for multiple cancer drug discovery programs. However, the structure of the active human CAK, insights into its regulation, and its interactions with cellular substrates and inhibitors remained elusive until recently due to the lack of high-resolution structures of the intact complex. This review covers the progress in structure determination of the human CAK by cryogenic electron microscopy (cryo-EM), from early efforts to recent near-atomic resolution maps routinely resolved at 2Å or better. These results were enabled by the latest cryo-EM technologies introduced after the initial phase of the "resolution revolution" and allowed the application of high-resolution methods to new classes of molecular targets, including small protein complexes that were intractable using earlier technology.
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Affiliation(s)
- Basil J Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK.
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35
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Wang L, Qiao C, Han L, Wang X, Miao J, Cao L, Huang C, Wang J. HOXD3 promotes the migration and angiogenesis of hepatocellular carcinoma via modifying hepatocellular carcinoma cells exosome-delivered CCR6 and regulating chromatin conformation of CCL20. Cell Death Dis 2024; 15:221. [PMID: 38493218 PMCID: PMC10944507 DOI: 10.1038/s41419-024-06593-x] [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: 12/05/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Angiogenesis plays an essential role in the microenvironment of hepatocellular carcinoma (HCC). HOXD3 is involved in the metastasis and invasion of HCC cells; Whereas the underlying molecular mechanisms in the microenvironment of HCC remain unknown. Wound healing, transwell invasion, tube formation and spheroid sprouting assays were carried out to identify the effects of HCC-HOXD3-exosomes and genes on the migration of HCC cells. ChIP-PCR was applied to test the binding region of HOXD3 on CCR6, Med15, and CREBBP promoter. Exosome isolation and mRNA-seq were applied to examine the morphological characteristics of exosomes and the contained mRNA in exosomes. Co-IP and Immunofluorescence assays were used to demonstrate the role of CREBBP in the chromatin conformation of CCL20. The nude mice were used to identify the function of genes in regulating migration of HCC in vivo. In this study, integrated cellular and bioinformatic analyses revealed that HOXD3 targeted the promoter region of CCR6 and induced its transcription. CCR6 was delivered by exosomes to endothelial cells and promoted tumour migration. Overexpression of CCR6 promoted metastasis, invasion in HCCs and angiogenesis in endothelial cells (ECs), whereas its downregulation suppressed these functions. The role of HOXD3 in the metastasis and invasion of HCC cells was reversed after the suppression of CCR6. Furthermore, CCL20 was demonstrated as the ligand of CCR6, and its high expression was found in HCC tissues and cells, which was clinically associated with the poor prognosis of HCC. Mechanistically, HOXD3 targets the promoter regions of CREBBP and Med15, which affect CCL20 chromatin conformation by regulating histone acetylation and expression of Pol II to enhance the migration of HCCs. This study demonstrated the function of the HOXD3-CREBBP/Med15-CCL20-CCR6 axis in regulating invasion and migration in HCC, thus providing new therapeutic targets for HCC.
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Affiliation(s)
- Lumin Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, P. R. China.
| | - Chenyang Qiao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, P. R. China
| | - Lili Han
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, P. R. China
| | - Xiaofei Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, P. R. China
| | - Jiyu Miao
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, P. R. China
| | - Li Cao
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, P. R. China
| | - Chen Huang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, P. R. China.
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, P. R. China.
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Russo M, Gualdrini F, Vallelonga V, Prosperini E, Noberini R, Pedretti S, Borriero C, Di Chiaro P, Polletti S, Imperato G, Marenda M, Ghirardi C, Bedin F, Cuomo A, Rodighiero S, Bonaldi T, Mitro N, Ghisletti S, Natoli G. Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide. Mol Cell 2024; 84:967-980.e10. [PMID: 38242130 PMCID: PMC7615796 DOI: 10.1016/j.molcel.2023.12.033] [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: 03/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Histone-modifying enzymes depend on the availability of cofactors, with acetyl-coenzyme A (CoA) being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA-producing enzymes translocate to the nucleus suggests that high concentrations of locally synthesized metabolites may impact acylation of histones and other nuclear substrates, thereby controlling gene expression. Here, we show that 2-ketoacid dehydrogenases are stably associated with the Mediator complex, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in lipopolysaccharide-stimulated macrophages, inhibited the activity of Mediator-associated 2-ketoacid dehydrogenases. Elevation of NO levels and the disruption of Mediator complex integrity both affected de novo histone acetylation within a shared set of genomic regions. Our findings indicate that the local supply of acetyl-CoA generated by 2-ketoacid dehydrogenases bound to Mediator is required to maximize acetylation of histone tails at sites of elevated HAT activity.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Gabriele Imperato
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; Department of Hematology and Hematology-Oncology (DIPO), Università degli Studi di Milano, Milano 20122, Italy
| | - Nico Mitro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
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Chen X, Xu Y. Interplay between the transcription preinitiation complex and the +1 nucleosome. Trends Biochem Sci 2024; 49:145-155. [PMID: 38218671 DOI: 10.1016/j.tibs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
Eukaryotic transcription starts with the assembly of a preinitiation complex (PIC) on core promoters. Flanking this region is the +1 nucleosome, the first nucleosome downstream of the core promoter. While this nucleosome is rich in epigenetic marks and plays a key role in transcription regulation, how the +1 nucleosome interacts with the transcription machinery has been a long-standing question. Here, we summarize recent structural and functional studies of the +1 nucleosome in complex with the PIC. We specifically focus on how differently organized promoter-nucleosome templates affect the assembly of the PIC and PIC-Mediator on chromatin and result in distinct transcription initiation.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, 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, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ. DNA looping mediates cooperative transcription activation. Nat Struct Mol Biol 2024; 31:293-299. [PMID: 38177666 DOI: 10.1038/s41594-023-01149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.
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Affiliation(s)
- Shu-Jing Han
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
| | - Lin-Lin You
- 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, China
| | - Li-Qiang Shen
- 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, China
| | - Xiaoxian Wu
- 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, China
| | - Feng Yang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ning Cui
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui Sun
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ke Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui-Chao Meng
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Zhi-Peng Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, 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, China.
| | - Cong-Zhao Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
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Crawford T, Siebler L, Sulkowska A, Nowack B, Jiang L, Pan Y, Lämke J, Kappel C, Bäurle I. The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis. EMBO J 2024; 43:437-461. [PMID: 38228917 PMCID: PMC10897291 DOI: 10.1038/s44318-023-00024-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation to high temperatures entails transcriptional responses, which prime plants to better withstand subsequent stress events. Heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurrence of heat stress. Here, we identified CDK8 and MED12, two subunits of the kinase module of the transcription co-regulator complex, Mediator, as promoters of heat stress memory and associated histone modifications in Arabidopsis. CDK8 is recruited to heat-stress memory genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, CDK8 is largely dispensable for the initial gene induction upon HS, and its function in transcriptional memory is thus independent of primary gene activation. In addition to the promoter and transcriptional start region of target genes, CDK8 also binds their 3'-region, where it may promote elongation, termination, or rapid re-initiation of RNA polymerase II (Pol II) complexes during transcriptional memory bursts. Our work presents a complex role for the Mediator kinase module during transcriptional memory in multicellular eukaryotes, through interactions with transcription factors, chromatin modifications, and promotion of Pol II efficiency.
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Affiliation(s)
- Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Lara Siebler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bryan Nowack
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Yufeng Pan
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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40
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Dunn LEM, Birkenheuer CH, Baines JD. A Revision of Herpes Simplex Virus Type 1 Transcription: First, Repress; Then, Express. Microorganisms 2024; 12:262. [PMID: 38399666 PMCID: PMC10892140 DOI: 10.3390/microorganisms12020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The herpes virus genome bears more than 80 strong transcriptional promoters. Upon entry into the host cell nucleus, these genes are transcribed in an orderly manner, producing five immediate-early (IE) gene products, including ICP0, ICP4, and ICP22, while non-IE genes are mostly silent. The IE gene products are necessary for the transcription of temporal classes following sequentially as early, leaky late, and true late. A recent analysis using precision nuclear run-on followed by deep sequencing (PRO-seq) has revealed an important step preceding all HSV-1 transcription. Specifically, the immediate-early proteins ICP4 and ICP0 enter the cell with the incoming genome to help preclude the nascent antisense, intergenic, and sense transcription of all viral genes. VP16, which is also delivered into the nucleus upon entry, almost immediately reverses this repression on IE genes. The resulting de novo expression of ICP4 and ICP22 further repress antisense, intergenic, and early and late viral gene transcription through different mechanisms before the sequential de-repression of these gene classes later in infection. This early repression, termed transient immediate-early protein-mediated repression (TIEMR), precludes unproductive, antisense, intergenic, and late gene transcription early in infection to ensure the efficient and orderly progression of the viral cascade.
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Affiliation(s)
- Laura E M Dunn
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Claire H Birkenheuer
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Joel D Baines
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
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41
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Zhang Q, Kim W, Panina S, Mayfield JE, Portz B, Zhang YJ. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573828. [PMID: 38260389 PMCID: PMC10802280 DOI: 10.1101/2024.01.01.573828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight the pivotal role of CTD in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
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Affiliation(s)
- Qian Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
| | - Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas, Austin, Texas, 78712
| | - Svetlana Panina
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
| | - Joshua E. Mayfield
- Department of Pharmacology, Chemistry, and Biochemistry, and Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093
| | - Bede Portz
- Dewpoint Therapeutics, 451 D Street, Boston, Massachusetts 02210
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
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Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y. Structural visualization of transcription initiation in action. Science 2023; 382:eadi5120. [PMID: 38127763 DOI: 10.1126/science.adi5120] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
Abstract
Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The 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
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, 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, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuechun Qu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, 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, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The 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
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Dominguez EC, Roleder C, Ball B, Danilov AV. Cyclin-dependent kinase-9 in B-cell malignancies: pathogenic role and therapeutic implications. Leuk Lymphoma 2023; 64:1893-1904. [PMID: 37552126 DOI: 10.1080/10428194.2023.2244102] [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: 06/02/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Cyclin-dependent kinases (CDK) regulate cell cycle and transcriptional activity. Pan-CDK inhibitors demonstrated early efficacy in lymphoid malignancies, but also have been associated with narrow therapeutic index. Among transcriptional CDKs, CDK7 and CDK9 emerged as promising targets. CDK9 serves as a component of P-TEFb elongation complex and thus is indispensable in mRNA transcription. Selective CDK9 inhibitors demonstrated pre-clinical efficacy in in vitro and in vivo models of B-cell non-Hodgkin lymphoma. CDK9 inhibition results in transcriptional pausing with rapid downmodulation of short-lived oncogenic proteins, e.g. Myc and Mcl-1, followed by cell apoptosis. Early phase clinical trials established safety of CDK9 inhibitors, with manageable neutropenia, infections and gastrointestinal toxicities. In this review, we summarize the rationale of targeting CDK9 in lymphoid malignancies, as well as pre-clinical and early clinical data with pan-CDK and selective CDK9 inhibitors.
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Affiliation(s)
| | - Carly Roleder
- City of Hope National Medical Center, Duarte, CA, USA
| | - Brian Ball
- City of Hope National Medical Center, Duarte, CA, USA
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Huang L, Yang H, Chen K, Yuan J, Li J, Dai G, Gu M, Shi Y. The suppressive efficacy of THZ1 depends on KRAS mutation subtype and is associated with super-enhancer activity and the PI3K/AKT/mTOR signalling in pancreatic ductal adenocarcinoma: A hypothesis-generating study. Clin Transl Med 2023; 13:e1500. [PMID: 38037549 PMCID: PMC10689978 DOI: 10.1002/ctm2.1500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 10/24/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Inhibition of CDK7, a potent transcription regulator, may bring new hope for treating pancreatic ductal adenocarcinoma (PDAC), which is featured by large genetic heterogeneity and abundant KRAS mutations. This investigation aimed at exploring the discrepant efficacies of THZ1, a small-molecule covalent CDK7 inhibitor, on PDACs with different KRAS mutations and the underlying mechanisms. METHODS Associations of CDK7 expression with survival by KRAS mutations were first assessed. Effects of THZ1 on PDAC by different KRAS mutations were then investigated in vitro and in vivo. Moreover, the effects of THZ1 on gene transcription and phosphorylation of RNA polymerase II (RNAPOLII) in different KRAS mutant PDACs were assessed, and the effect of THZ1 on super-enhancer activity was evaluated using chromatin immunoprecipitation sequencing. Lastly, the effects of THZ1 on the binding of H3K27ac to PIK3CA and on the PI3K/AKT/mTOR signalling were analysed. RESULTS High CDK7 expression was significantly linked to worse survival within PDAC patients carrying KRAS-G12V mutation but not in those with KRAS-G12D mutation. The apoptosis-inducing effect of THZ1 was markedly stronger in KRAS-G12V PDAC than KRAS-G12D cancer. THZ1 significantly inhibited the growth of xenograft tumour with KRAS-G12V mutation, and the inhibition was markedly stronger than for KRAS-G12D tumour. In mini-cell-derived xenograft (CDX) models, THZ1 significantly suppressed KRAS-G12V PDAC but not KRAS-G12D cancer. THZ1 significantly suppressed the phosphorylation of RNAPOLII, and this effect was stronger in KRAS-G12V PDAC (especially at ser5). KRAS-G12V PDAC had more H3K27ac-binding super-enhancers, and the inhibition of THZ1 on super-enhancer activity was also stronger in KRAS-G12V PDAC. Furthermore, THZ1 significantly weakened the binding of H3K27ac to PIK3CA in KRAS-G12V PDAC. THZ1 significantly suppressed the PI3K/AKT/mTOR pathway and its downstream markers, and this effect was stronger in KRAS-G12V cells. CONCLUSIONS In this hypothesis-generating study, THZ1 might selectively inhibit certain PDACs with KRAS-G12V mutation more potently compared with some other PDACs with KRAS-G12D mutation, which might be associated with its effect on super-enhancer activity and the PI3K/AKT/mTOR signalling. Our findings might offer novel key clues for the precise management of PDAC and important evidence for future targeted trial design. HIGHLIGHTS THZ1 had a stronger effect on PDAC-bearing KRAS-G12V mutation than G12D mutation. Suppressive effect of THZ1 on phosphorylation of RNAPOLII was stronger in KRAS-G12V than KRAS-G12D PDAC. Inhibition of THZ1 on super-enhancer activity and H3K27ac binding to PIK3CA was stronger in KRAS-G12V PDAC. Suppressive effect of THZ1 on PI3K/AKT/mTOR pathway was stronger in KRAS-G12V PDAC.
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Affiliation(s)
- Lei Huang
- Department of OncologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hui Yang
- Department of OncologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kaidi Chen
- School of Pharmaceutical ScienceZhejiang Chinese Medical UniversityHangzhouChina
| | - Jing Yuan
- Department of PathologyChinese PLA General HospitalBeijingChina
| | - Jie Li
- Department of PathologyChinese PLA General HospitalBeijingChina
| | - Guanghai Dai
- Department of Medical OncologyChinese PLA General HospitalBeijingChina
| | - Mancang Gu
- School of Pharmaceutical ScienceZhejiang Chinese Medical UniversityHangzhouChina
- Academy of Chinese Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Yan Shi
- Department of General SurgeryShanghai Seventh People's HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
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45
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Huang J, Ji X. Never a dull enzyme, RNA polymerase II. Transcription 2023; 14:49-67. [PMID: 37132022 PMCID: PMC10353340 DOI: 10.1080/21541264.2023.2208023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
RNA polymerase II (Pol II) is composed of 12 subunits that collaborate to synthesize mRNA within the nucleus. Pol II is widely recognized as a passive holoenzyme, with the molecular functions of its subunits largely ignored. Recent studies employing auxin-inducible degron (AID) and multi-omics techniques have revealed that the functional diversity of Pol II is achieved through the differential contributions of its subunits to various transcriptional and post-transcriptional processes. By regulating these processes in a coordinated manner through its subunits, Pol II can optimize its activity for diverse biological functions. Here, we review recent progress in understanding Pol II subunits and their dysregulation in diseases, Pol II heterogeneity, Pol II clusters and the regulatory roles of RNA polymerases.
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Affiliation(s)
- Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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46
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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: 36] [Impact Index Per Article: 18.0] [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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47
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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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Bernardini A, Hollinger C, Willgenss D, Müller F, Devys D, Tora L. Transcription factor IID parks and drives preinitiation complexes at sharp or broad promoters. Trends Biochem Sci 2023; 48:839-848. [PMID: 37574371 PMCID: PMC10529448 DOI: 10.1016/j.tibs.2023.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Core promoters are sites where transcriptional regulatory inputs of a gene are integrated to direct the assembly of the preinitiation complex (PIC) and RNA polymerase II (Pol II) transcription output. Until now, core promoter functions have been investigated by distinct methods, including Pol II transcription initiation site mappings and structural characterization of PICs on distinct promoters. Here, we bring together these previously unconnected observations and hypothesize how, on metazoan TATA promoters, the precisely structured building up of transcription factor (TF) IID-based PICs results in sharp transcription start site (TSS) selection; or, in contrast, how the less strictly controlled positioning of the TATA-less promoter DNA relative to TFIID-core PIC components results in alternative broad TSS selections by Pol II.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | | | | | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
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Kassouf M, Ford S, Blayney J, Higgs D. Understanding fundamental principles of enhancer biology at a model locus: Analysing the structure and function of an enhancer cluster at the α-globin locus. Bioessays 2023; 45:e2300047. [PMID: 37404089 PMCID: PMC11414744 DOI: 10.1002/bies.202300047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 07/06/2023]
Abstract
Despite ever-increasing accumulation of genomic data, the fundamental question of how individual genes are switched on during development, lineage-specification and differentiation is not fully answered. It is widely accepted that this involves the interaction between at least three fundamental regulatory elements: enhancers, promoters and insulators. Enhancers contain transcription factor binding sites which are bound by transcription factors (TFs) and co-factors expressed during cell fate decisions and maintain imposed patterns of activation, at least in part, via their epigenetic modification. This information is transferred from enhancers to their cognate promoters often by coming into close physical proximity to form a 'transcriptional hub' containing a high concentration of TFs and co-factors. The mechanisms underlying these stages of transcriptional activation are not fully explained. This review focuses on how enhancers and promoters are activated during differentiation and how multiple enhancers work together to regulate gene expression. We illustrate the currently understood principles of how mammalian enhancers work and how they may be perturbed in enhanceropathies using expression of the α-globin gene cluster during erythropoiesis, as a model.
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Affiliation(s)
- Mira Kassouf
- Laboratory of Gene RegulationMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Seren Ford
- Laboratory of Gene RegulationMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Joseph Blayney
- Laboratory of Gene RegulationMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Doug Higgs
- Laboratory of Gene RegulationMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
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Liu M, Xie XJ, Li X, Ren X, Sun J, Lin Z, Hemba-Waduge RUS, Ji JY. Transcriptional coupling of telomeric retrotransposons with the cell cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560321. [PMID: 37808851 PMCID: PMC10557779 DOI: 10.1101/2023.09.30.560321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Instead of employing telomerases to safeguard chromosome ends, dipteran species maintain their telomeres by transposition of telomeric-specific retrotransposons (TRs): in Drosophila , these are HeT-A , TART , and TAHRE . Previous studies have shown how these TRs create tandem repeats at chromosome ends, but the exact mechanism controlling TR transcription has remained unclear. Here we report the identification of multiple subunits of the transcription cofactor Mediator complex and transcriptional factors Scalloped (Sd, the TEAD homolog in flies) and E2F1-Dp as novel regulators of TR transcription and telomere length in Drosophila . Depletion of multiple Mediator subunits, Dp, or Sd increased TR expression and telomere length, while over-expressing E2F1-Dp or knocking down the E2F1 regulator Rbf1 (Retinoblastoma-family protein 1) stimulated TR transcription, with Mediator and Sd affecting TR expression through E2F1-Dp. The CUT&RUN analysis revealed direct binding of CDK8, Dp, and Sd to telomeric repeats. These findings highlight the essential role of the Mediator complex in maintaining telomere homeostasis by regulating TR transcription through E2F1-Dp and Sd, revealing the intricate coupling of TR transcription with the host cell-cycle machinery, thereby ensuring chromosome end protection and genomic stability during cell division.
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