1
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Bernardini A, Tora L. Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription. J Mol Biol 2024; 436:168382. [PMID: 38061625 DOI: 10.1016/j.jmb.2023.168382] [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: 10/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Most factors that regulate gene transcription in eukaryotic cells are multimeric, often large, protein complexes. The understanding of the biogenesis pathways of such large and heterogeneous protein assemblies, as well as the dimerization partner choice among transcription factors, is crucial to interpret and control gene expression programs and consequent cell fate decisions. Co-translational assembly (Co-TA) is thought to play key roles in the biogenesis of protein complexes by directing complex formation during protein synthesis. In this review we discuss the principles of Co-TA with a special focus for the assembly of transcription regulatory complexes. We outline the expected molecular advantages of establishing co-translational interactions, pointing at the available, or missing, evidence for each of them. We hypothesize different molecular mechanisms based on Co-TA to explain the allocation "dilemma" of paralog proteins and subunits shared by different transcription complexes. By taking as a paradigm the different assembly pathways employed by three related transcription regulatory complexes (TFIID, SAGA and ATAC), we discuss alternative Co-TA strategies for nuclear multiprotein complexes and the widespread - yet specific - use of Co-TA for the formation of nuclear complexes involved in gene transcription. Ultimately, we outlined a series of open questions which demand well-defined lines of research to investigate the principles of gene regulation that rely on the coordinated assembly of protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
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2
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Das JK, Banskota N, Candia J, Griswold ME, Orenduff M, de Cabo R, Corcoran DL, Das SK, De S, Huffman KM, Kraus VB, Kraus WE, Martin C, Racette SB, Redman LM, Schilling B, Belsky D, Ferrucci L. Calorie restriction modulates the transcription of genes related to stress response and longevity in human muscle: The CALERIE study. Aging Cell 2023; 22:e13963. [PMID: 37823711 PMCID: PMC10726900 DOI: 10.1111/acel.13963] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 10/13/2023] Open
Abstract
The lifespan extension induced by 40% caloric restriction (CR) in rodents is accompanied by postponement of disease, preservation of function, and increased stress resistance. Whether CR elicits the same physiological and molecular responses in humans remains mostly unexplored. In the CALERIE study, 12% CR for 2 years in healthy humans induced minor losses of muscle mass (leg lean mass) without changes of muscle strength, but mechanisms for muscle quality preservation remained unclear. We performed high-depth RNA-Seq (387-618 million paired reads) on human vastus lateralis muscle biopsies collected from the CALERIE participants at baseline, 12- and 24-month follow-up from the 90 CALERIE participants randomized to CR and "ad libitum" control. Using linear mixed effect model, we identified protein-coding genes and splicing variants whose expression was significantly changed in the CR group compared to controls, including genes related to proteostasis, circadian rhythm regulation, DNA repair, mitochondrial biogenesis, mRNA processing/splicing, FOXO3 metabolism, apoptosis, and inflammation. Changes in some of these biological pathways mediated part of the positive effect of CR on muscle quality. Differentially expressed splicing variants were associated with change in pathways shown to be affected by CR in model organisms. Two years of sustained CR in humans positively affected skeletal muscle quality, and impacted gene expression and splicing profiles of biological pathways affected by CR in model organisms, suggesting that attainable levels of CR in a lifestyle intervention can benefit muscle health in humans.
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Affiliation(s)
- Jayanta Kumar Das
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Nirad Banskota
- Computational Biology and Genomics CoreNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Julián Candia
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | | | - Melissa Orenduff
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Rafael de Cabo
- Translation Gerontology Branch, National Institute on AgingNational Institutes of HealthBaltimoreMarylandUSA
| | - David L. Corcoran
- Department of GeneticsUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Sai Krupa Das
- Energy Metabolism, Jean Mayer USDA Human Nutrition Research Center on AgingTufts UniversityBostonMassachusettsUSA
| | - Supriyo De
- Computational Biology and Genomics CoreNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Kim Marie Huffman
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Virginia B. Kraus
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - William E. Kraus
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Corby K. Martin
- Pennington Biomedical Research CenterLouisiana State UniversityBaton RougeLouisianaUSA
| | - Susan B. Racette
- College of Health SolutionsArizona State UniversityPhoenixArizonaUSA
| | - Leanne M. Redman
- Pennington Biomedical Research CenterLouisiana State UniversityBaton RougeLouisianaUSA
| | | | - Daniel W. Belsky
- Department of Epidemiology & Butler Columbia Aging CenterColumbia University Mailman School of Public HealthNew York CityNew YorkUSA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
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3
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Heuts BMH, Martens JHA. Understanding blood development and leukemia using sequencing-based technologies and human cell systems. Front Mol Biosci 2023; 10:1266697. [PMID: 37886034 PMCID: PMC10598665 DOI: 10.3389/fmolb.2023.1266697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
Our current understanding of human hematopoiesis has undergone significant transformation throughout the years, challenging conventional views. The evolution of high-throughput technologies has enabled the accumulation of diverse data types, offering new avenues for investigating key regulatory processes in blood cell production and disease. In this review, we will explore the opportunities presented by these advancements for unraveling the molecular mechanisms underlying normal and abnormal hematopoiesis. Specifically, we will focus on the importance of enhancer-associated regulatory networks and highlight the crucial role of enhancer-derived transcription regulation. Additionally, we will discuss the unprecedented power of single-cell methods and the progression in using in vitro human blood differentiation system, in particular induced pluripotent stem cell models, in dissecting hematopoietic processes. Furthermore, we will explore the potential of ever more nuanced patient profiling to allow precision medicine approaches. Ultimately, we advocate for a multiparameter, regulatory network-based approach for providing a more holistic understanding of normal hematopoiesis and blood disorders.
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Affiliation(s)
- Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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4
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Lemma RB, Ledsaak M, Fuglerud BM, Rodríguez-Castañeda F, Eskeland R, Gabrielsen OS. MYB regulates the SUMO protease SENP1 and its novel interaction partner UXT, modulating MYB target genes and the SUMO landscape. J Biol Chem 2023; 299:105062. [PMID: 37468105 PMCID: PMC10463205 DOI: 10.1016/j.jbc.2023.105062] [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: 11/18/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
SUMOylation is a post-translational modification frequently found on nuclear proteins, including transcription factors (TFs) and coactivators. By controlling the activity of several TFs, SUMOylation may have far-reaching effects. MYB is an example of a developmental TF subjected to SUMO-mediated regulation, through both SUMO conjugation and SUMO binding. How SUMO affects MYB target genes is unknown. Here, we explored the global effect of reduced SUMOylation of MYB on its downstream gene programs. RNA-Seq in K562 cells after MYB knockdown and rescue with mutants having an altered SUMO status revealed a number of differentially regulated genes and distinct gene ontology term enrichments. Clearly, the SUMO status of MYB both quantitatively and qualitatively affects its regulome. The transcriptome data further revealed that MYB upregulates the SUMO protease SENP1, a key enzyme that removes SUMO conjugation from SUMOylated proteins. Given this role of SENP1 in the MYB regulome, we expanded the analysis, mapped interaction partners of SENP1, and identified UXT as a novel player affecting the SUMO system by acting as a repressor of SENP1. MYB inhibits the expression of UXT suggesting that MYB is able not only to control a specific gene program directly but also indirectly by affecting the SUMO landscape through SENP1 and UXT. These findings suggest an autoactivation loop whereby MYB, through enhancing SENP1 and reducing UXT, is itself being activated by a reduced level of repressive SUMOylation. We propose that overexpressed MYB, seen in multiple cancers, may drive this autoactivation loop and contribute to oncogenic activation of MYB.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
| | - Marit Ledsaak
- Department of Biosciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Faculty of Medicine, Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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5
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Mendoza Sanchez PK, Yayli G, Morlet B, Timmers HTM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. Nat Struct Mol Biol 2023; 30:1141-1152. [PMID: 37386215 PMCID: PMC10442232 DOI: 10.1038/s41594-023-01026-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates the RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that human TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1-the largest protein in the complex-as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Nature Protocols, London, UK
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
- Centre National de la Recherche Scientifique, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
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6
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Sanchez PKM, Yayli G, Morlet B, Timmers HM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535704. [PMID: 37066372 PMCID: PMC10104070 DOI: 10.1101/2023.04.05.535704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1 - the largest protein in the complex - as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H.T. Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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7
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Janssen BDE, van den Boogaard MJH, Lichtenbelt K, Seaby EG, Stals K, Ellard S, Newbury-Ecob R, Dixit A, Roht L, Pajusalu S, Õunap K, Firth HV, Buckley M, Wilson M, Roscioli T, Tidwell T, Mao R, Ennis S, Holwerda SJ, van Gassen K, van Jaarsveld RH. De novo putative loss-of-function variants in TAF4 are associated with a neuro-developmental disorder. Hum Mutat 2022; 43:1844-1851. [PMID: 35904126 PMCID: PMC10087332 DOI: 10.1002/humu.24444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 01/24/2023]
Abstract
TATA-binding protein associated factor 4 (TAF4) is a subunit of the Transcription Factor IID (TFIID) complex, a central player in transcription initiation. Other members of this multimeric complex have been implicated previously as monogenic disease genes in human developmental disorders. TAF4 has not been described to date as a monogenic disease gene. We here present a cohort of eight individuals, each carrying de novo putative loss-of-function (pLoF) variants in TAF4 and expressing phenotypes consistent with a neuro-developmental disorder (NDD). Common features include intellectual disability, abnormal behavior, and facial dysmorphisms. We propose TAF4 as a novel dominant disease gene for NDD, and coin this novel disorder "TAF4-related NDD" (T4NDD). We place T4NDD in the context of other disorders related to TFIID subunits, revealing shared features of T4NDD with other TAF-opathies.
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Affiliation(s)
- Beau D E Janssen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Klaske Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleanor G Seaby
- Genomic Informatics Group, University of Southampton, Southampton, UK
| | - Karen Stals
- Exeter Genomic Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Exeter Genomic Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Ruth Newbury-Ecob
- Clinical Genetics, St Michael's Hospital Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Abhijit Dixit
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Laura Roht
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | | | - Michael Buckley
- Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, and Discipline of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Tony Roscioli
- Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia.,Neurosciences Research Australia, University of NSW, Kensington, New South Wales, Australia.,Randwick Genomics laboratory, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | | | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Sarah Ennis
- Genomic Informatics Group, University of Southampton, Southampton, UK
| | - Sjoerd J Holwerda
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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8
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Santana JF, Collins GS, Parida M, Luse DS, Price D. Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB. Nucleic Acids Res 2022; 50:9127-9148. [PMID: 35947745 PMCID: PMC9458433 DOI: 10.1093/nar/gkac678] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
The effects of rapid acute depletion of components of RNA polymerase II (Pol II) general transcription factors (GTFs) that are thought to be critical for formation of preinitiation complexes (PICs) and initiation in vitro were quantified in HAP1 cells using precision nuclear run-on sequencing (PRO-Seq). The average dependencies for each factor across >70 000 promoters varied widely even though levels of depletions were similar. Some of the effects could be attributed to the presence or absence of core promoter elements such as the upstream TBP-specificity motif or downstream G-rich sequences, but some dependencies anti-correlated with such sequences. While depletion of TBP had a large effect on most Pol III promoters only a small fraction of Pol II promoters were similarly affected. TFIIB depletion had the largest general effect on Pol II and also correlated with apparent termination defects downstream of genes. Our results demonstrate that promoter activity is combinatorially influenced by recruitment of TFIID and sequence-specific transcription factors. They also suggest that interaction of the preinitiation complex (PIC) with nucleosomes can affect activity and that recruitment of TFIID containing TBP only plays a positive role at a subset of promoters.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Geoffrey S Collins
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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9
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Friis Theisen F, Salladini E, Davidsen R, Jo Rasmussen C, Staby L, Kragelund BB, Skriver K. αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes. J Biol Chem 2022; 298:101963. [PMID: 35452682 PMCID: PMC9127584 DOI: 10.1016/j.jbc.2022.101963] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Formation of transcription factor (TF)-coregulator complexes is a key step in transcriptional regulation, with coregulators having essential functions as hub nodes in molecular networks. How specificity and selectivity are maintained in these nodes remain open questions. In this work, we addressed specificity in transcriptional networks using complexes formed between TFs and αα-hubs, which are defined by a common αα-hairpin secondary structure motif, as a model. Using NMR spectroscopy and binding thermodynamics, we analyzed the structure, dynamics, stability, and ligand-binding properties of the Arabidopsis thaliana RST domains from TAF4 and known binding partner RCD1, and the TAFH domain from human TAF4, allowing comparison across species, functions, and architectural contexts. While these αα-hubs shared the αα-hairpin motif, they differed in length and orientation of accessory helices as well as in their thermodynamic profiles of ligand binding. Whereas biologically relevant RCD1-ligand pairs displayed high affinity driven by enthalpy, TAF4-ligand interactions were entropy driven and exhibited less binding-induced structuring. We in addition identified a thermal unfolding state with a structured core for all three domains, although the temperature sensitivity differed. Thermal stability studies suggested that initial unfolding of the RCD1-RST domain localized around helix 1, lending this region structural malleability, while effects in TAF4-RST were more stochastic, suggesting variability in structural adaptability upon binding. Collectively, our results support a model in which hub structure, flexibility, and binding thermodynamics contribute to αα-hub-TF binding specificity, a finding of general relevance to the understanding of coregulator-ligand interactions and interactome sizes.
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Affiliation(s)
- Frederik Friis Theisen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Davidsen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christina Jo Rasmussen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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10
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Kleiber T, Davidson G, Mengus G, Martianov I, Davidson I. Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4. Cell Death Dis 2021; 12:790. [PMID: 34385420 PMCID: PMC8361202 DOI: 10.1038/s41419-021-04067-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022]
Abstract
Regulation of gene expression involves a complex and dynamic dialogue between transcription factors, chromatin remodelling and modification complexes and the basal transcription machinery. To address the function of the Taf4 subunit of general transcription factor TFIID in the regulation of insulin signalling, it was inactivated in adult murine pancreatic beta cells. Taf4 inactivation impacted the expression of critical genes involved in beta-cell function leading to increased glycaemia, lowered plasma insulin levels and defective glucose-stimulated insulin secretion. One week after Taf4-loss, single-cell RNA-seq revealed cells with mixed beta cell, alpha and/or delta cell identities as well as a beta cell population trans-differentiating into alpha-like cells. Computational analysis of single-cell RNA-seq defines how known critical beta cell and alpha cell determinants may act in combination with additional transcription factors and the NuRF chromatin remodelling complex to promote beta cell trans-differentiation.
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Affiliation(s)
- Thomas Kleiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Orphazyme, Ole Malloes Vej 3, 2200, Copenhagen, Danmark
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Igor Martianov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire. BP 163, 67404 Illkirch Cedex, C.U, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Equipe Labélisée Ligue National contre le Cancer, Alsace, France.
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11
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Sun F, Sun T, Kronenberg M, Tan X, Huang C, Carey MF. The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter-enhancer looping. Genes Dev 2021; 35:1175-1189. [PMID: 34301767 PMCID: PMC8336890 DOI: 10.1101/gad.348471.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/24/2021] [Indexed: 02/05/2023]
Abstract
Knowledge of how Mediator and TFIID cross-talk contributes to promoter-enhancer (P-E) communication is important for elucidating the mechanism of enhancer function. We conducted an shRNA knockdown screen in murine embryonic stem cells to identify the functional overlap between Mediator and TFIID subunits on gene expression. Auxin-inducible degrons were constructed for TAF12 and MED4, the subunits eliciting the greatest overlap. Degradation of TAF12 led to a dramatic genome-wide decrease in gene expression accompanied by destruction of TFIID, loss of Pol II preinitiation complex (PIC) at promoters, and significantly decreased Mediator binding to promoters and enhancers. Interestingly, loss of the PIC elicited only a mild effect on P-E looping by promoter capture Hi-C (PCHi-C). Degradation of MED4 had a minor effect on Mediator integrity but led to a consistent twofold loss in gene expression, decreased binding of Pol II to Mediator, and decreased recruitment of Pol II to the promoters, but had no effect on the other PIC components. PCHi-C revealed no consistent effect of MED4 degradation on P-E looping. Collectively, our data show that TAF12 and MED4 contribute mechanistically in different ways to P-E communication but neither factor appears to directly control P-E looping, thereby dissociating P-E communication from physical looping.
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Affiliation(s)
- Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Terrence Sun
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Michael Kronenberg
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Xianglong Tan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Chengyang Huang
- Center for Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
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12
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Jia R, Song Z, Lin J, Li Z, Shan G, Huang C. Gawky modulates MTF-1-mediated transcription activation and metal discrimination. Nucleic Acids Res 2021; 49:6296-6314. [PMID: 34107019 PMCID: PMC8216474 DOI: 10.1093/nar/gkab474] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Metal-induced genes are usually transcribed at relatively low levels under normal conditions and are rapidly activated by heavy metal stress. Many of these genes respond preferentially to specific metal-stressed conditions. However, the mechanism by which the general transcription machinery discriminates metal stress from normal conditions and the regulation of MTF-1-meditated metal discrimination are poorly characterized. Using a focused RNAi screening in Drosophila Schneider 2 (S2) cells, we identified a novel activator, the Drosophila gawky, of metal-responsive genes. Depletion of gawky has almost no effect on the basal transcription of the metallothionein (MT) genes, but impairs the metal-induced transcription by inducing the dissociation of MTF-1 from the MT promoters and the deficient nuclear import of MTF-1 under metal-stressed conditions. This suggests that gawky serves as a 'checkpoint' for metal stress and metal-induced transcription. In fact, regular mRNAs are converted into gawky-controlled transcripts if expressed under the control of a metal-responsive promoter, suggesting that whether transcription undergoes gawky-mediated regulation is encrypted therein. Additionally, lack of gawky eliminates the DNA binding bias of MTF-1 and the transcription preference of metal-specific genes. This suggests a combinatorial control of metal discrimination by gawky, MTF-1, and MTF-1 binding sites.
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Affiliation(s)
- Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
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13
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Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD. Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. eLife 2021; 10:68068. [PMID: 33904398 PMCID: PMC8137143 DOI: 10.7554/elife.68068] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/25/2021] [Indexed: 01/07/2023] Open
Abstract
Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (‘fuzzy’ binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology. Cells adapt and respond to changes by regulating the activity of their genes. To turn genes on or off, they use a family of proteins called transcription factors. Transcription factors influence specific but overlapping groups of genes, so that each gene is controlled by several transcription factors that act together like a dimmer switch to regulate gene activity. The presence of transcription factors attracts proteins such as the Mediator complex, which activates genes by gathering the protein machines that read the genes. The more transcription factors are found near a specific gene, the more strongly they attract Mediator and the more active the gene is. A specific region on the transcription factor called the activation domain is necessary for this process. The biochemical sequences of these domains vary greatly between species, yet activation domains from, for example, yeast and human proteins are often interchangeable. To understand why this is the case, Sanborn et al. analyzed the genome of baker’s yeast and identified 150 activation domains, each very different in sequence. Three-quarters of them bound to a subunit of the Mediator complex called Med15. Sanborn et al. then developed a machine learning algorithm to predict activation domains in both yeast and humans. This algorithm also showed that negatively charged and greasy regions on the activation domains were essential to be activated by the Mediator complex. Further analyses revealed that activation domains used different poses to bind multiple sites on Med15, a behavior known as ‘fuzzy’ binding. This creates a high overall affinity even though the binding strength at each individual site is low, enabling the protein complexes to remain dynamic. These weak interactions together permit fine control over the activity of several genes, allowing cells to respond quickly and precisely to many changes. The computer algorithm used here provides a new way to identify activation domains across species and could improve our understanding of how living things grow, adapt and evolve. It could also give new insights into mechanisms of disease, particularly cancer, where transcription factors are often faulty.
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Affiliation(s)
- Adrian L Sanborn
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States.,Department of Computer Science, Stanford University, Stanford, United States
| | - Benjamin T Yeh
- Department of Computer Science, Stanford University, Stanford, United States
| | - Jordan T Feigerle
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Cynthia V Hao
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | | | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, United States.,Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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14
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Yundaeng C, Somta P, Chen J, Yuan X, Chankaew S, Chen X. Fine mapping of QTL conferring Cercospora leaf spot disease resistance in mungbean revealed TAF5 as candidate gene for the resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:701-714. [PMID: 33188437 DOI: 10.1007/s00122-020-03724-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
This paper reports fine mapping of qCLS for resistance to Cercospora leaf spot disease in mungbean and identified LOC106765332encoding TATA-binding-protein-associated factor 5 (TAF5) as the candidate gene for the resistance Cercospora leaf spot (CLS) caused by the fungus Cercospora canescens is an important disease of mungbean. A QTL mapping using mungbean F2 and BC1F1 populations developed from the "V4718" (resistant) and "Kamphaeng Saen 1" (KPS1; susceptible) has identified a major QTL controlling CLS resistance (qCLS). In this study, we finely mapped the qCLS and identified candidate genes at this locus. A BC8F2 [KPS1 × (KPS1 × V4718)] population developed in this study and the F2 (KPS1 × V4718) population used in a previous study were genotyped with 16 newly developed SSR markers. QTL analysis in the BC8F2 and F2 populations consistently showed that the qCLS was mapped to a genomic region of ~ 13 Kb on chromosome 6, which contains only one annotated gene, LOC106765332 (designated "VrTAF5"), encoding TATA-binding-protein-associated factor 5 (TAF5), a subunit of transcription initiation factor IID and Spt-Ada-Gcn5 acetyltransferase complexes. Sequence comparison of VrTAF5 between KPS1 and V4718 revealed many single nucleotide polymorphisms (SNPs) and inserts/deletions (InDels) in which eight SNPs presented in eight different exons, and an SNP (G4,932C) residing in exon 8 causes amino acid change (S250T) in V4718. An InDel marker was developed to detect a 24-bp InDel polymorphism in VrTAF5 between KPS1 and V4718. Analysis by RT-qPCR showed that expression levels of VrTAF5 in KPS1 and V4718 were not statistically different. These results indicated that mutation in VrTAF5 causing an amino acid change in the VrTAF5 protein is responsible for CLS resistance in V4718.
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Affiliation(s)
- Chutintorn Yundaeng
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, 73140, Nakhon Pathom, Thailand.
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Sompong Chankaew
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
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15
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Wang Z, Wang P, Li Y, Peng H, Zhu Y, Mohandas N, Liu J. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduct Target Ther 2021; 6:24. [PMID: 33468999 PMCID: PMC7815747 DOI: 10.1038/s41392-020-00422-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.
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Affiliation(s)
- Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
| | - Pan Wang
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Yanan Li
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY, USA
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
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16
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Bugge K, Staby L, Salladini E, Falbe-Hansen RG, Kragelund BB, Skriver K. αα-Hub domains and intrinsically disordered proteins: A decisive combo. J Biol Chem 2021; 296:100226. [PMID: 33361159 PMCID: PMC7948954 DOI: 10.1074/jbc.rev120.012928] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023] Open
Abstract
Hub proteins are central nodes in protein-protein interaction networks with critical importance to all living organisms. Recently, a new group of folded hub domains, the αα-hubs, was defined based on a shared αα-hairpin supersecondary structural foundation. The members PAH, RST, TAFH, NCBD, and HHD are found in large proteins such as Sin3, RCD1, TAF4, CBP, and harmonin, which organize disordered transcriptional regulators and membrane scaffolds in interactomes of importance to human diseases and plant quality. In this review, studies of structures, functions, and complexes across the αα-hubs are described and compared to provide a unified description of the group. This analysis expands the associated molecular concepts of "one domain-one binding site", motif-based ligand binding, and coupled folding and binding of intrinsically disordered ligands to additional concepts of importance to signal fidelity. These include context, motif reversibility, multivalency, complex heterogeneity, synergistic αα-hub:ligand folding, accessory binding sites, and supramodules. We propose that these multifaceted protein-protein interaction properties are made possible by the characteristics of the αα-hub fold, including supersite properties, dynamics, variable topologies, accessory helices, and malleability and abetted by adaptability of the disordered ligands. Critically, these features provide additional filters for specificity. With the presentations of new concepts, this review opens for new research questions addressing properties across the group, which are driven from concepts discovered in studies of the individual members. Combined, the members of the αα-hubs are ideal models for deconvoluting signal fidelity maintained by folded hubs and their interactions with intrinsically disordered ligands.
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Affiliation(s)
- Katrine Bugge
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus G Falbe-Hansen
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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17
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Abstract
Key discoveries in Drosophila have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in Drosophila has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these cis-regulatory elements operate in development and disease.
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Affiliation(s)
- Stephen Small
- Department of Biology, Developmental Systems Training Program, New York University, 10003 and
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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18
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LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia. Mol Cell Biol 2020; 40:MCB.00652-19. [PMID: 32229578 DOI: 10.1128/mcb.00652-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/14/2020] [Indexed: 12/22/2022] Open
Abstract
The LMO2/LDB1 macromolecular complex is critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as single-stranded DNA-binding protein (SSBP) cofactors and DNA-binding basic helix-loop-helix (bHLH) and GATA transcription factors. We analyzed the steady-state abundance and kinetic stability of LMO2 and its partners via Halo protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stabilities (with half-lives in descending order) as follows: LDB1 > SSBP > LMO2 > TAL1. Importantly, LDB1 is a remarkably stable protein that confers enhanced stability upon direct and indirect partners, thereby nucleating the formation of the multisubunit protein complex. The data imply that free subunits are more rapidly degraded than those incorporated within the LMO2/LDB1 complex. Our studies provided significant insights into LMO2/LDB1 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.
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19
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Fant CB, Levandowski CB, Gupta K, Maas ZL, Moir J, Rubin JD, Sawyer A, Esbin MN, Rimel JK, Luyties O, Marr MT, Berger I, Dowell RD, Taatjes DJ. TFIID Enables RNA Polymerase II Promoter-Proximal Pausing. Mol Cell 2020; 78:785-793.e8. [PMID: 32229306 DOI: 10.1016/j.molcel.2020.03.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/15/2019] [Accepted: 03/05/2020] [Indexed: 02/07/2023]
Abstract
RNA polymerase II (RNAPII) transcription is governed by the pre-initiation complex (PIC), which contains TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, RNAPII, and Mediator. After initiation, RNAPII enzymes pause after transcribing less than 100 bases; precisely how RNAPII pausing is enforced and regulated remains unclear. To address specific mechanistic questions, we reconstituted human RNAPII promoter-proximal pausing in vitro, entirely with purified factors (no extracts). As expected, NELF and DSIF increased pausing, and P-TEFb promoted pause release. Unexpectedly, the PIC alone was sufficient to reconstitute pausing, suggesting RNAPII pausing is an inherent PIC function. In agreement, pausing was lost upon replacement of the TFIID complex with TATA-binding protein (TBP), and PRO-seq experiments revealed widespread disruption of RNAPII pausing upon acute depletion (t = 60 min) of TFIID subunits in human or Drosophila cells. These results establish a TFIID requirement for RNAPII pausing and suggest pause regulatory factors may function directly or indirectly through TFIID.
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Affiliation(s)
- Charli B Fant
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | | | - Kapil Gupta
- School of Biochemistry, Bristol Research Centre for Synthetic Biology, University of Bristol, Bristol, UK
| | - Zachary L Maas
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - John Moir
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jonathan D Rubin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Andrew Sawyer
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Meagan N Esbin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jenna K Rimel
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Olivia Luyties
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Michael T Marr
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Imre Berger
- School of Biochemistry, Bristol Research Centre for Synthetic Biology, University of Bristol, Bristol, UK
| | - Robin D Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA; BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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20
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Multivalent Role of Human TFIID in Recruiting Elongation Components at the Promoter-Proximal Region for Transcriptional Control. Cell Rep 2020; 26:1303-1317.e7. [PMID: 30699356 DOI: 10.1016/j.celrep.2019.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/05/2018] [Accepted: 01/02/2019] [Indexed: 01/08/2023] Open
Abstract
Despite substantial progress in our understanding of the players involved and the regulatory mechanisms controlling the initiation and elongation steps of transcription, little is known about the recruitment of elongation factors at promoter-proximal regions for the initiation-to-elongation transition. Here, we show evidence that human TFIID, which initiates pre-initiation complex (PIC) assembly, contributes to regulating the recruitment of super-elongation complex (SEC) components at the promoter-proximal region through interactions among selective TAF and SEC components. In vitro direct interactions, coupled with cell-based assays, identified an important poly-Ser domain within SEC components that are involved in their interaction with TFIID. DNA template-based recruitment assays, using purified components, further show a direct role for poly-Ser domain-dependent TFIID interaction in recruiting SEC components on target DNA. Consistently, ChIP and RNA analyses have shown the importance of this mechanism in TFIID-dependent SEC recruitment and target gene expression within mammalian cells.
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21
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DBC1, p300, HDAC3, and Siah1 coordinately regulate ELL stability and function for expression of its target genes. Proc Natl Acad Sci U S A 2020; 117:6509-6520. [PMID: 32152128 PMCID: PMC7104407 DOI: 10.1073/pnas.1912375117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Among all of the Super Elongation Complex (SEC) components, ELL1 (also known as ELL) is the only bona fide elongation factor that directly stimulates transcription elongation by RNA polymerase II. However, the mechanism(s) of functional regulation of ELL1 (referred to as ELL hereafter), through its stabilization, is completely unknown. Here, we report a function of human DBC1 in regulating ELL stability involving HDAC3, p300, and Siah1. Mechanistically, we show that p300-mediated site-specific acetylation increases, whereas HDAC3-mediated deacetylation decreases, ELL stability through polyubiquitylation by the E3 ubiquitin ligase Siah1. DBC1 competes with HDAC3 for the same binding sites on ELL and thus increases its acetylation and stability. Knockdown of DBC1 reduces ELL levels and expression of a significant number of genes, including those involved in glucose metabolism. Consistently, Type 2 diabetes patient-derived peripheral blood mononuclear cells show reduced expression of DBC1 and ELL and associated key target genes required for glucose homeostasis. Thus, we describe a pathway of regulating stability and functions of key elongation factor ELL for expression of diverse sets of genes, including ones that are linked to Type 2 diabetes pathogenesis.
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22
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Li P, Meng Y, Wang Y, Li J, Lam M, Wang L, Di LJ. Nuclear localization of Desmoplakin and its involvement in telomere maintenance. Int J Biol Sci 2019; 15:2350-2362. [PMID: 31595153 PMCID: PMC6775319 DOI: 10.7150/ijbs.34450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/28/2019] [Indexed: 12/21/2022] Open
Abstract
The interaction between genomic DNA and protein fundamentally determines the activity and the function of DNA elements. Capturing the protein complex and identifying the proteins associated with a specific DNA locus is difficult. Herein, we employed CRISPR, the well-known gene-targeting tool in combination with the proximity-dependent labeling tool BioID to capture a specific genome locus associated proteins and to uncover the novel functions of these proteins. By applying this research tool on telomeres, we identified DSP, out of many others, as a convincing telomere binding protein validated by both biochemical and cell-biological approaches. We also provide evidence to demonstrate that the C-terminal domain of DSP is required for its binding to telomere after translocating to the nucleus mediated by NLS sequence of DSP. In addition, we found that the telomere binding of DSP is telomere length dependent as hTERT inhibition or knockdown caused a decrease of telomere length and diminished DSP binding to the telomere. Knockdown of TRF2 also negatively influenced DSP binding to the telomere. Functionally, loss of DSP resulted in the shortened telomere DNA and induced the DNA damage response and cell apoptosis. In conclusion, our studies identified DSP as a novel potential telomere binding protein and highlighted its role in protecting against telomere DNA damage and resultant cell apoptosis.
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Affiliation(s)
- Peipei Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Yuan Meng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Yuan Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Jingjing Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Manting Lam
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Li Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
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23
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Bhuiyan T, Timmers HTM. Promoter Recognition: Putting TFIID on the Spot. Trends Cell Biol 2019; 29:752-763. [PMID: 31300188 DOI: 10.1016/j.tcb.2019.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 11/18/2022]
Abstract
Basal transcription factor TFIID connects transcription activation to the assembly of the RNA polymerase II preinitiation complex at the core promoter of genes. The mechanistic understanding of TFIID function and dynamics has been limited by the lack of high-resolution structures of the holo-TFIID complex. Recent cryo-electron microscopy studies of yeast and human TFIID complexes provide insight into the molecular organization and structural dynamics of this highly conserved transcription factor. Here, we discuss how these TFIID structures provide new paradigms for: (i) the dynamic recruitment of TFIID; (ii) the binding of TATA-binding protein (TBP) to promoter DNA; (iii) the multivalency of TFIID interactions with (co)activators, nucleosomes, or promoter DNA; and (iv) the opportunities for regulation of TBP turnover and promoter dynamics.
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Affiliation(s)
- Tanja Bhuiyan
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; German Cancer Consortium (DKTK) partner site Freiburg, 79106, Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Medical Faculty, Breisacher Straße 66, 79106, Freiburg, Germany
| | - H Th Marc Timmers
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; German Cancer Consortium (DKTK) partner site Freiburg, 79106, Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Medical Faculty, Breisacher Straße 66, 79106, Freiburg, Germany. @dkfz-heidelberg.de
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24
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Patel AB, Louder RK, Greber BJ, Grünberg S, Luo J, Fang J, Liu Y, Ranish J, Hahn S, Nogales E. Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Science 2018; 362:eaau8872. [PMID: 30442764 PMCID: PMC6446905 DOI: 10.1126/science.aau8872] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022]
Abstract
The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box-binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
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Affiliation(s)
- Avinash B Patel
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert K Louder
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Basil J Greber
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720, USA
| | - Sebastian Grünberg
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jie Fang
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Yutong Liu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Steve Hahn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eva Nogales
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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25
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Avendaño-Borromeo B, Narayanasamy RK, García-Rivera G, Labra-Barrios ML, Lagunes-Guillén AE, Munguía-Chávez B, Castañón-Sánchez CA, Orozco E, Luna-Arias JP. Identification of the gene encoding the TATA box-binding protein-associated factor 1 (TAF1) and its putative role in the heat shock response in the protozoan parasite Entamoeba histolytica. Parasitol Res 2018; 118:517-538. [PMID: 30552577 DOI: 10.1007/s00436-018-6170-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/29/2018] [Indexed: 11/26/2022]
Abstract
Transcription factor IID (TFIID) is a cornerstone in the transcription initiation in eukaryotes. It is composed of TBP and approximately 14 different subunits named TBP-associated factors (TAFs). TFIID has a key role in transcription of many genes involved in cell proliferation, cell growth, cell cycle, cell cycle checkpoint, and various other processes as well. Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, represents a major global health concern. Our research group has previously reported the genes coding the TATA box-binding protein (EhTBP) and TBP-related factor 1 (EhTRF1), which displayed different mRNA levels in trophozoites under different stress conditions. In this work, we identified the TBP-associated factor 1 (Ehtaf1) gene in the E. histolytica genome, which possess a well-conserved DUF domain and a Bromo domain located in the middle and C-terminus of the protein, respectively. The EhTAF1-DUF domain tertiary structure is similar to the corresponding HsTAF1 DUF domain. RT-qPCR experiments with RNA isolated from trophozoites harvested at different time points of the growth curve and under different stress conditions revealed that the Ehtaf1 gene was found slightly upregulated in the death phase of growth curve, but under heat shock stress, it was found upregulated 10 times, suggesting that Ehtaf1 might have an important role in the heat shock stress response. We also found that EhTAF1 is expressed in the nucleus and cytoplasm at 37 °C, but under heat shock stress, it is overexpressed in both the nucleus and cytoplasm, and partially colocalized with EhHSP70 in cytoplasm.
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Affiliation(s)
- Bartolo Avendaño-Borromeo
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Ravi Kumar Narayanasamy
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - María Luisa Labra-Barrios
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Anel E Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Bibiana Munguía-Chávez
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Carlos Alberto Castañón-Sánchez
- Laboratorio de Investigación Biomédica, Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Aldama S/N, San Bartolo Coyotepec, 71256, Oaxaca, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Juan Pedro Luna-Arias
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico.
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26
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Chaperonin CCT checkpoint function in basal transcription factor TFIID assembly. Nat Struct Mol Biol 2018; 25:1119-1127. [PMID: 30510221 PMCID: PMC6292499 DOI: 10.1038/s41594-018-0156-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/25/2018] [Indexed: 12/12/2022]
Abstract
TFIID is a cornerstone of eukaryotic gene regulation. Distinct TFIID
complexes with unique subunit composition exist and several TFIID subunits are
shared with other complexes, conveying intricate cellular decision making to
control subunit allocation and functional assembly of this essential
transcription factor. However, the underlying molecular mechanisms remain poorly
understood. Here, we used quantitative proteomics to examine TFIID submodules
and assembly mechanisms in human cells. Structural and mutational analysis of
the cytoplasmic TAF5-TAF6-TAF9 submodule identified novel interactions crucial
for TFIID integrity, and for allocating TAF9 to TFIID or the SAGA co-activator
complex. We discover a key checkpoint function for the chaperonin CCT, which
specifically associates with nascent TAF5 for subsequent handover to TAF6-TAF9
and ultimate holo-TFIID formation. Our findings illustrate at the molecular
level how multisubunit complexes are crafted in the cell, involving checkpoint
decisions facilitated by a chaperone machine.
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27
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Lebedeva LA, Yakovlev KV, Kozlov EN, Schedl P, Deshpande G, Shidlovskii YV. Transcriptional quiescence in primordial germ cells. Crit Rev Biochem Mol Biol 2018; 53:579-595. [PMID: 30280955 PMCID: PMC8729227 DOI: 10.1080/10409238.2018.1506733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/09/2018] [Accepted: 07/27/2018] [Indexed: 12/31/2022]
Abstract
In most animal species, newly formed primordial germ cells (PGCs) acquire the special characteristics that distinguish them from the surrounding somatic cells. Proper fate specification of the PGCs is coupled with transcriptional quiescence, whether they are segregated by determinative or inductive mechanisms. Inappropriate differentiation of PGCs into somatic cells is thought to be prevented due to repression of RNA polymerase (Pol) II-dependent transcription. In the case of a determinative mode of PGC formation (Drosophila, Caenorhabditis elegans, etc.), there is a broad downregulation of Pol II activity. By contrast, PGCs display only gene-specific repression in organisms that rely on inductive signaling-based mechanism (e.g., mice). In addition to the global block of Pol II activity in PGCs, gene expression can be suppressed in other ways, such as chromatin remodeling and Piwi-mediated RNAi. Here, we discuss the mechanisms responsible for the transcriptionally silent state of PGCs in common experimental animals, such as Drosophila, C. elegans, Danio rerio, Xenopus, and mouse. While a PGC-specific downregulation of transcription is a common feature among these organisms, the diverse nature of underlying mechanisms suggests that this functional trait likely evolved independently on several instances. We discuss the possible biological relevance of these silencing mechanisms vis-a-vis fate determination of PGCs.
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Affiliation(s)
| | - Konstantin V. Yakovlev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Eugene N. Kozlov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, USA
| | - Girish Deshpande
- Department of Molecular Biology, Princeton University, Princeton, USA
| | - Yulii V. Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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28
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Kolesnikova O, Ben-Shem A, Luo J, Ranish J, Schultz P, Papai G. Molecular structure of promoter-bound yeast TFIID. Nat Commun 2018; 9:4666. [PMID: 30405110 PMCID: PMC6220335 DOI: 10.1038/s41467-018-07096-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/09/2018] [Indexed: 01/29/2023] Open
Abstract
Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe. Transcription preinitiation complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID complex, providing a detailed view of its subunit organization and promoter DNA contacts.
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Affiliation(s)
- Olga Kolesnikova
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, 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, Illkirch, 67404, France
| | - Adam Ben-Shem
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, 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, Illkirch, 67404, France
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Patrick Schultz
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, 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, Illkirch, 67404, France.
| | - Gabor Papai
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, 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, Illkirch, 67404, France.
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29
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Rodríguez-Castañeda F, Lemma RB, Cuervo I, Bengtsen M, Moen LM, Ledsaak M, Eskeland R, Gabrielsen OS. The SUMO protease SENP1 and the chromatin remodeler CHD3 interact and jointly affect chromatin accessibility and gene expression. J Biol Chem 2018; 293:15439-15454. [PMID: 30082317 DOI: 10.1074/jbc.ra118.002844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/12/2018] [Indexed: 01/22/2023] Open
Abstract
The small ubiquitin-like modifier (SUMO) post-translationally modifies lysine residues of transcription factors and co-regulators and thereby contributes to an important layer of control of the activities of these transcriptional regulators. Likewise, deSUMOylation of these factors by the sentrin-specific proteases (SENPs) also plays a role in gene regulation, but whether SENPs functionally interact with other regulatory factors that control gene expression is unclear. In the present work, we focused on SENP1, specifically, on its role in activation of gene expression investigated through analysis of the SENP1 interactome, which revealed that SENP1 physically interacts with the chromatin remodeler chromodomain helicase DNA-binding protein 3 (CHD3). Using several additional methods, including GST pulldown and co-immunoprecipitation assays, we validated and mapped this interaction, and using CRISPR-Cas9-generated CHD3- and SENP1-KO cells (in the haploid HAP1 cell line), we investigated whether these two proteins are functionally linked in regulating chromatin remodeling and gene expression. Genome-wide ATAC-Seq analysis of the CHD3- and SENP1-KO cells revealed a large degree of overlap in differential chromatin openness between these two mutant cell lines. Moreover, motif analysis and comparison with ChIP-Seq profiles in K562 cells pointed to an association of CHD3 and SENP1 with CCCTC-binding factor (CTCF) and SUMOylated chromatin-associated factors. Lastly, genome-wide RNA-Seq also indicated that these two proteins co-regulate the expression of several genes. We propose that the functional link between chromatin remodeling by CHD3 and deSUMOylation by SENP1 uncovered here provides another level of control of gene expression.
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Affiliation(s)
| | - Roza Berhanu Lemma
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Ignacio Cuervo
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Mads Bengtsen
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Lisa Marie Moen
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Marit Ledsaak
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
| | - Ragnhild Eskeland
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and.,the Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, P.O. Box 1112 Blindern, N-0317 Oslo, Norway
| | - Odd Stokke Gabrielsen
- From the Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, N-0316 Oslo and
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30
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Hoff FW, Hu CW, Qiu Y, Ligeralde A, Yoo SY, Scheurer ME, de Bont ESJM, Qutub AA, Kornblau SM, Horton TM. Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance. Mol Cancer Res 2018; 16:1263-1274. [PMID: 29669823 DOI: 10.1158/1541-7786.mcr-17-0730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/21/2018] [Accepted: 03/30/2018] [Indexed: 12/13/2022]
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, and the second leading cause of pediatric cancer-related death in developed countries. While the cure rate for newly diagnosed ALL is excellent, the genetic heterogeneity and chemoresistance of leukemia cells at relapse makes individualized curative treatment plans difficult. We hypothesize that genetic events would coalesce into a finite number of protein signatures that could guide the design of individualized therapy. Custom reverse-phase protein arrays were produced from pediatric ALL (n = 73) and normal CD34+ (n = 10) samples with 194 validated antibodies. Proteins were allocated into 31 protein functional groups (PFG) to analyze them in the context of other proteins, based on known associations from the literature. The optimal number of protein clusters was determined for each PFG. Protein networks showed distinct transition states, revealing "normal-like" and "leukemia-specific" protein patterns. Block clustering identified strong correlation between various protein clusters that formed 10 protein constellations. Patients that expressed similar recurrent combinations of constellations comprised 7 distinct signatures, correlating with risk stratification, cytogenetics, and laboratory features. Most constellations and signatures were specific for T-cell ALL or pre-B-cell ALL; however, some constellations showed significant overlap. Several signatures were associated with Hispanic ethnicity, suggesting that ethnic pathophysiologic differences likely exist. In addition, some constellations were enriched for "normal-like" protein clusters, whereas others had exclusively "leukemia-specific" patterns.Implications: Recognition of proteins that have universally altered expression, together with proteins that are specific for a given signature, suggests targets for directed combinatorial inhibition or replacement to enable personalized therapy. Mol Cancer Res; 16(8); 1263-74. ©2018 AACRSee related article by Hoff et al., p. 1275.
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Affiliation(s)
- Fieke W Hoff
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.,Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Chenyue W Hu
- Department of Bioengineering, Rice University, Houston, Texas
| | - Yihua Qiu
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Suk-Young Yoo
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael E Scheurer
- Department of Pediatrics and Department of Epidemiology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston TX
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Amina A Qutub
- Department of Bioengineering, Rice University, Houston, Texas
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.
| | - Terzah M Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children's Cancer Center, Houston, Texas
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31
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Dahiya R, Natarajan K. Mutational analysis of TAF6 revealed the essential requirement of the histone-fold domain and the HEAT repeat domain for transcriptional activation. FEBS J 2018; 285:1491-1510. [PMID: 29485702 DOI: 10.1111/febs.14423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 12/31/2022]
Abstract
TAF6, bearing the histone H4-like histone-fold domain (HFD), is a subunit of the core TAF module in TFIID and SAGA transcriptional regulatory complexes. We isolated and characterized several yeast TAF6 mutants bearing amino acid substitutions in the HFD, the middle region or the HEAT repeat domain. The TAF6 mutants were highly defective for transcriptional activation by the Gcn4 and Gal4 activators. CHIP assays showed that the TAF6-HFD and the TAF6-HEAT domain mutations independently abrogated the promoter occupancy of TFIID and SAGA complex in vivo. We employed genetic and biochemical assays to identify the relative contributions of the TAF6 HFD and HEAT domains. First, the temperature-sensitive phenotype of the HEAT domain mutant was suppressed by overexpression of the core TAF subunits TAF9 and TAF12, as well as TBP. The HFD mutant defect, however, was suppressed by TAF5 but not by TAF9, TAF12 or TBP. Second, the HEAT mutant but not the HFD mutant was defective for growth in the presence of transcription elongation inhibitors. Third, coimmunoprecipitation assays using yeast cell extracts indicated that the specific TAF6 HEAT domain residues are critical for the interaction of core TAF subunits with the SAGA complex but not with TFIID. The specific HFD residues in TAF6, although required for heterodimerization between TAF6 and TAF9 recombinant proteins, were dispensable for association of the core TAF subunits with TFIID and SAGA in yeast cell extracts. Taken together, the results of our studies have uncovered the non-overlapping requirement of the evolutionarily conserved HEAT domain and the HFD in TAF6 for transcriptional activation.
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Affiliation(s)
- Rashmi Dahiya
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Krishnamurthy Natarajan
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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32
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Xu Y, Milazzo JP, Somerville TDD, Tarumoto Y, Huang YH, Ostrander EL, Wilkinson JE, Challen GA, Vakoc CR. A TFIID-SAGA Perturbation that Targets MYB and Suppresses Acute Myeloid Leukemia. Cancer Cell 2018; 33:13-28.e8. [PMID: 29316427 PMCID: PMC5764110 DOI: 10.1016/j.ccell.2017.12.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/22/2017] [Accepted: 12/05/2017] [Indexed: 01/08/2023]
Abstract
Targeting of general coactivators is an emerging strategy to interfere with oncogenic transcription factors (TFs). However, coactivator perturbations often lead to pleiotropic effects by influencing numerous TFs. Here we identify TAF12, a subunit of TFIID and SAGA coactivator complexes, as a selective requirement for acute myeloid leukemia (AML) progression. We trace this dependency to a direct interaction between the TAF12/TAF4 histone-fold heterodimer and the transactivation domain of MYB, a TF with established roles in leukemogenesis. Ectopic expression of the TAF4 histone-fold fragment can efficiently squelch TAF12 in cells, suppress MYB, and regress AML in mice. Our study reveals a strategy for potent MYB inhibition in AML and highlights how an oncogenic TF can be selectively neutralized by targeting a general coactivator complex.
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Affiliation(s)
- Yali Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, New York, NY 11794, USA
| | - Joseph P Milazzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Elizabeth L Ostrander
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John E Wilkinson
- ULAM/Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Grant A Challen
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
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33
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A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster. PLoS Genet 2017; 13:e1007120. [PMID: 29261646 PMCID: PMC5752043 DOI: 10.1371/journal.pgen.1007120] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/03/2018] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
In nearly all metazoans, the earliest stages of development are controlled by maternally deposited mRNAs and proteins. The zygotic genome becomes transcriptionally active hours after fertilization. Transcriptional activation during this maternal-to-zygotic transition (MZT) is tightly coordinated with the degradation of maternally provided mRNAs. In Drosophila melanogaster, the transcription factor Zelda plays an essential role in widespread activation of the zygotic genome. While Zelda expression is required both maternally and zygotically, the mechanisms by which it functions to remodel the embryonic genome and prepare the embryo for development remain unclear. Using Cas9-mediated genome editing to generate targeted mutations in the endogenous zelda locus, we determined the functional relevance of protein domains conserved amongst Zelda orthologs. We showed that neither a conserved N-terminal zinc finger nor an acidic patch were required for activity. Similarly, a previously identified splice isoform of zelda is dispensable for viability. By contrast, we identified a highly conserved zinc-finger domain that is essential for the maternal, but not zygotic functions of Zelda. Animals homozygous for mutations in this domain survived to adulthood, but embryos inheriting these loss-of-function alleles from their mothers died late in embryogenesis. These mutations did not interfere with the capacity of Zelda to activate transcription in cell culture. Unexpectedly, these mutations generated a hyperactive form of the protein and enhanced Zelda-dependent gene expression. These data have defined a protein domain critical for controlling Zelda activity during the MZT, but dispensable for its roles later in development, for the first time separating the maternal and zygotic requirements for Zelda. This demonstrates that highly regulated levels of Zelda activity are required for establishing the developmental program during the MZT. We propose that tightly regulated gene expression is essential to navigate the MZT and that failure to precisely execute this developmental program leads to embryonic lethality. Following fertilization, the one-celled zygote must be rapidly reprogrammed to enable the development of a new, unique organism. During these initial stages of development there is little or no transcription of the zygotic genome, and maternally deposited products control this process. Among the essential maternal products are mRNAs that encode transcription factors required for preparing the zygotic genome for transcriptional activation. This ensures that there is a precisely coordinated hand-off from maternal to zygotic control. In Drosophila melanogaster, the transcription factor Zelda is essential for activating the zygotic genome and coupling this activation to the degradation of the maternally deposited products. Nonetheless, the mechanism by which Zelda functions remains unclear. Here we used Cas9-mediated genome engineering to determine the functional requirements for highly conserved domains within Zelda. We identified a domain required specifically for Zelda’s role in reprogramming the early embryonic genome, but not essential for its functions later in development. Surprisingly, this domain restricts the ability of Zelda to activate transcription. These data demonstrate that Zelda activity is tightly regulated, and we propose that precise regulation of both the timing and levels of genome activation is required for the embryo to successfully transition from maternal to zygotic control.
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34
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Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife 2017; 6:e30395. [PMID: 29111974 PMCID: PMC5690282 DOI: 10.7554/elife.30395] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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Affiliation(s)
- Kapil Gupta
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
- European Molecular Biology LaboratoryGrenobleFrance
| | | | - Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Anna L Chambers
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | | | - Juan Zou
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Ima Obong-Ebong
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Eaazhisai Kandiah
- European Molecular Biology LaboratoryGrenobleFrance
- Institut de Biologie Structurale IBSGrenobleFrance
| | | | - Adam Round
- European Molecular Biology LaboratoryGrenobleFrance
| | - Eric Forest
- Institut de Biologie Structurale IBSGrenobleFrance
| | - Petr Man
- Institute of MicrobiologyThe Czech Academy of SciencesVestecCzech Republic
- BioCeV - Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Ernest D Laue
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Juri Rappsilber
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Carol V Robinson
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Làszlò Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Imre Berger
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
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35
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Hibino E, Inoue R, Sugiyama M, Kuwahara J, Matsuzaki K, Hoshino M. Identification of heteromolecular binding sites in transcription factors Sp1 and TAF4 using high-resolution nuclear magnetic resonance spectroscopy. Protein Sci 2017; 26:2280-2290. [PMID: 28857320 PMCID: PMC5654864 DOI: 10.1002/pro.3287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 01/17/2023]
Abstract
The expression of eukaryotic genes is precisely controlled by interactions between general transcriptional factors and promoter-specific transcriptional activators. The fourth element of TATA-box binding protein-associated factor (TAF4), an essential subunit of the general transcription factor TFIID, serves as a coactivator for various promoter-specific transcriptional regulators. Interactions between TAF4 and site-specific transcriptional activators, such as Sp1, are important for regulating the expression levels of genes of interest. However, only limited information is available on the molecular mechanisms underlying the interactions between these transcriptional regulatory proteins. We herein analyzed the interaction between the transcriptional factors Sp1 and TAF4 using high-resolution solution nuclear magnetic resonance spectroscopy. We found that four glutamine-rich (Q-rich) regions in TAF4 were largely disordered under nearly physiological conditions. Among them, the first Q-rich region in TAF4 was essential for the interaction with another Q-rich region in the Sp1 molecule, most of which was largely disordered. The residues responsible for this interaction were specific and highly localized in a defined region within a range of 20-30 residues. Nevertheless, a detailed analysis of 13 C-chemical shift values suggested that no significant conformational change occurred upon binding. These results indicate a prominent and exceptional binding mode for intrinsically disordered proteins other than the well-accepted concept of "coupled folding and binding."
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Affiliation(s)
- Emi Hibino
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
| | - Rintaro Inoue
- Research Reactor Institute, Kyoto UniversitySennan‐gunOsaka590‐0494Japan
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto UniversitySennan‐gunOsaka590‐0494Japan
| | - Jun Kuwahara
- Faculty of Pharmaceutical SciencesDoshisha Women's UniversityKyotanabe cityKyoto610‐0395Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
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36
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Warfield L, Ramachandran S, Baptista T, Devys D, Tora L, Hahn S. Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID. Mol Cell 2017; 68:118-129.e5. [PMID: 28918900 DOI: 10.1016/j.molcel.2017.08.014] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/28/2017] [Accepted: 08/18/2017] [Indexed: 11/17/2022]
Abstract
Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We re-examined the role of TFIID by rapid depletion of S. cerevisiae TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Taf1, Taf2, Taf7, Taf11, and Taf13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing, and TATA-less gene classes. The magnitude of TFIID dependence varies with growth conditions, although this variation is similar genome-wide. Many studies have suggested differences in gene-regulatory mechanisms between TATA and TATA-less genes, and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID participates in expression of nearly all yeast mRNAs and that differences in regulation between these two gene categories is due to other properties.
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Affiliation(s)
- Linda Warfield
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Srinivas Ramachandran
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Steven Hahn
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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37
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MacLennan M, García-Cañadas M, Reichmann J, Khazina E, Wagner G, Playfoot CJ, Salvador-Palomeque C, Mann AR, Peressini P, Sanchez L, Dobie K, Read D, Hung CC, Eskeland R, Meehan RR, Weichenrieder O, García-Pérez JL, Adams IR. Mobilization of LINE-1 retrotransposons is restricted by Tex19.1 in mouse embryonic stem cells. eLife 2017; 6:e26152. [PMID: 28806172 PMCID: PMC5570191 DOI: 10.7554/elife.26152] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Mobilization of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events can also cause genetic disorders. In humans, retrotransposon mobilization is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilize in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilization. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, loss of Tex19.1 increases L1-ORF1p levels and L1 mobilization in pluripotent mouse embryonic stem cells, implying that Tex19.1 prevents de novo retrotransposition in the pluripotent phase of the germline cycle. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in mammals.
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Affiliation(s)
- Marie MacLennan
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Marta García-Cañadas
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Judith Reichmann
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Elena Khazina
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Gabriele Wagner
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Christopher J Playfoot
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Carmen Salvador-Palomeque
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Abigail R Mann
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Paula Peressini
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Laura Sanchez
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Karen Dobie
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - David Read
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Chao-Chun Hung
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Ragnhild Eskeland
- Department of
Biosciences, University of Oslo,
Oslo,
Norway
- Norwegian Center for
Stem Cell Research, Department of Immunology, Oslo
University Hospital, Oslo, Norway
| | - Richard R Meehan
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Oliver Weichenrieder
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Jose Luis García-Pérez
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Ian R Adams
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
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38
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Jian W, Yan B, Huang S, Qiu Y. Histone deacetylase 1 activates PU.1 gene transcription through regulating TAF9 deacetylation and transcription factor IID assembly. FASEB J 2017; 31:4104-4116. [PMID: 28572446 DOI: 10.1096/fj.201700022r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/15/2017] [Indexed: 11/11/2022]
Abstract
Histone acetyltransferases and histone deacetylases (HDACs) are important epigenetic coregulators. It has been thought that HDACs associate with corepressor complexes and repress gene transcription; however, in this study, we have found that PU.1-a key master regulator for hematopoietic self-renewal and lineage specification-requires HDAC activity for gene activation. Deregulated PU.1 gene expression is linked to dysregulated hematopoiesis and the development of leukemia. In this study, we used erythroid differentiation as a model to analyze how the PU.1 gene is regulated. We found that active HDAC1 is directly recruited to active PU.1 promoter in progenitor cells, whereas acetylated HDAC1, which is inactive, is on the silenced PU.1 promoter in differentiated erythroid cells. We then studied the mechanism of HDAC1-mediated activation. We discovered that HDAC1 activates PU.1 gene transcription via deacetylation of TATA-binding protein-associated factor 9 (TAF9), a component in the transcription factor IID (TFIID) complex. Treatment with HDAC inhibitor results in an increase in TAF9 acetylation. Acetylated TAF9 does not bind to the PU.1 gene promoter and subsequently leads to the disassociation of the TFIID complex and transcription repression. Thus, these results demonstrate a key role for HDAC1 in PU.1 gene transcription and, more importantly, uncover a novel mechanism of TFIID recruitment and gene activation.-Jian, W., Yan, B., Huang, S., Qiu, Y. Histone deacetylase 1 activates PU.1 gene transcription through regulating TAF9 deacetylation and transcription factor IID assembly.
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Affiliation(s)
- Wei Jian
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Bowen Yan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Suming Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA; and.,Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau
| | - Yi Qiu
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA;
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39
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Sinha I, Kumar S, Poonia P, Sawhney S, Natarajan K. Functional specialization of two paralogous TAF12 variants by their selective association with SAGA and TFIID transcriptional regulatory complexes. J Biol Chem 2017; 292:6047-6055. [PMID: 28275052 PMCID: PMC5391738 DOI: 10.1074/jbc.c116.768549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
TATA box-binding protein (TBP)-associated factors (TAFs), evolutionarily conserved from yeast to humans, play a central role during transcription initiation. A subset of TAF proteins is shared in transcription factor II D (TFIID) and SAGA transcription regulatory complexes. Although higher eukaryotes contain multiple TAF variants that specify tissue- and developmental stage-specific organization of TFIID or SAGA complexes, in unicellular genomes, however, each TAF is encoded by a single gene. Surprisingly, we found that the genome of Candida albicans, the predominant human fungal pathogen, contains two paralogous TAF12 genes, CaTAF12L and CaTAF12, encoding H2B-like histone-fold domain-containing variants. Of the available fungal genome sequences, only seven other closely related diploid pathogenic Candida genomes encode the two TAF12 paralogs. Using affinity purifications from C. albicans cell extracts, we demonstrate that CaTAF12L uniquely associates with the SAGA complex and CaTAF12 associates with the TFIID complex. We further show that CaTAF12, but not CaTAF12L, is essential for C. albicans growth. Conditional depletion of the two TAF12 variant proteins caused distinct cellular and colony phenotypes. Together our results define a specialized organization of the TAF12 variants and non-redundant roles for the two TAF12 variants in the unicellular C. albicans genome.
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Affiliation(s)
- Ishani Sinha
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shambhu Kumar
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Poonia
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonal Sawhney
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishnamurthy Natarajan
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition. PLoS Genet 2017; 13:e1006664. [PMID: 28273089 PMCID: PMC5362240 DOI: 10.1371/journal.pgen.1006664] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/22/2017] [Accepted: 02/28/2017] [Indexed: 11/19/2022] Open
Abstract
The general transcription factor TBP (TATA-box binding protein) and its associated factors (TAFs) together form the TFIID complex, which directs transcription initiation. Through RNAi and mutant analysis, we identified a specific TBP family protein, TRF2, and a set of TAFs that regulate lipid droplet (LD) size in the Drosophila larval fat body. Among the three Drosophila TBP genes, trf2, tbp and trf1, only loss of function of trf2 results in increased LD size. Moreover, TRF2 and TAF9 regulate fatty acid composition of several classes of phospholipids. Through RNA profiling, we found that TRF2 and TAF9 affects the transcription of a common set of genes, including peroxisomal fatty acid β-oxidation-related genes that affect phospholipid fatty acid composition. We also found that knockdown of several TRF2 and TAF9 target genes results in large LDs, a phenotype which is similar to that of trf2 mutants. Together, these findings provide new insights into the specific role of the general transcription machinery in lipid homeostasis. Lipid droplets (LD) are main lipid storage structures in most cells. The size of LDs varies greatly in different cell types or different metabolic states to accommodate cellular functions and metabolism demands. How cells regulate the lipid storage and LD dynamics is not fully understood. Here, we identified that general transcription factors, including a specific TBP (TATA-box binding protein) family protein TRF2 (TBP-related factor 2) and several TAFs (TBP-associated factors), regulate LD size in the fruitfly larval fat body. Moreover, quantitated lipid analysis reveals that TRF2 and TAF9 affect the fatty acid composition of several classes of phospholipids. We showed that TRF2 and TAF9 regulate transcription of several target genes, including peroxisomal fatty acid β-oxidation-related genes which likely mediate the effect of TRF2 and TAF9 on phospholipid fatty acid composition. We also found that overexpression of some target genes restores the LD phenotype in trf2 mutants. Our findings therefore reveal specific roles of general transcription factors in lipid homeostasis.
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Zabidi MA, Stark A. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet 2016; 32:801-814. [PMID: 27816209 DOI: 10.1016/j.tig.2016.10.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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Nardone V, Chaves-Sanjuan A, Nardini M. Structural determinants for NF-Y/DNA interaction at the CCAAT box. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:571-580. [PMID: 27677949 DOI: 10.1016/j.bbagrm.2016.09.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 12/26/2022]
Abstract
The recently determined crystal structures of the sequence-specific transcription factor NF-Y have illuminated the structural mechanism underlying transcription at the CCAAT box. NF-Y is a trimeric protein complex composed by the NF-YA, NF-YB, and NF-YC subunits. NF-YB and NF-YC contain a histone-like domain and assemble on a head-to-tail fashion to form a dimer, which provides the structural scaffold for the DNA sugar-phosphate backbone binding (mimicking the nucleosome H2A/H2B-DNA assembly) and for the interaction with NF-YA. The NF-YA subunit hosts two structurally extended α-helices; one is involved in NF-YB/NF-YC binding and the other inserts deeply into the DNA minor groove, providing exquisite sequence-specificity for recognition and binding of the CCAAT box. The analysis of these structural data is expected to serve as a powerful guide for future experiments aimed at understanding the role of post-translational modification at NF-Y regulation sites and to unravel the three-dimensional architecture of higher order complexes formed between NF-Y and other transcription factors that act synergistically for transcription activation. Moreover, these structures represent an excellent starting point to challenge the formation of a stable hybrid nucleosome between NF-Y and core histone proteins, and to rationalize the fine molecular details associated with the wide combinatorial association of plant NF-Y subunits. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Valentina Nardone
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Antonio Chaves-Sanjuan
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marco Nardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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Gupta K, Sari-Ak D, Haffke M, Trowitzsch S, Berger I. Zooming in on Transcription Preinitiation. J Mol Biol 2016; 428:2581-2591. [PMID: 27067110 PMCID: PMC4906157 DOI: 10.1016/j.jmb.2016.04.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 02/08/2023]
Abstract
Class II gene transcription commences with the assembly of the Preinitiation Complex (PIC) from a plethora of proteins and protein assemblies in the nucleus, including the General Transcription Factors (GTFs), RNA polymerase II (RNA pol II), co-activators, co-repressors, and more. TFIID, a megadalton-sized multiprotein complex comprising 20 subunits, is among the first GTFs to bind the core promoter. TFIID assists in nucleating PIC formation, completed by binding of further factors in a highly regulated stepwise fashion. Recent results indicate that TFIID itself is built from distinct preformed submodules, which reside in the nucleus but also in the cytosol of cells. Here, we highlight recent insights in transcription factor assembly and the regulation of transcription preinitiation. Architectural models of human and yeast PIC were proposed. Mediator core–ITC complex structure reveals novel interactions. TFIID submodule residing in the cytoplasm has been discovered. Complex assembly emerges as key concept in transcription regulation.
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Affiliation(s)
- Kapil Gupta
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France; Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Duygu Sari-Ak
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France; Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Matthias Haffke
- Center for Proteomic Chemistry, Structural Biophysics, Novartis Institute for Biomedical Research NIBR, Fabrikstrasse 2, 4056 Basel, Switzerland
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main Germany
| | - Imre Berger
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France; Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France; The School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
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Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature 2016; 531:604-9. [PMID: 27007846 PMCID: PMC4856295 DOI: 10.1038/nature17394] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 02/03/2016] [Indexed: 12/11/2022]
Abstract
The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.
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Langer D, Martianov I, Alpern D, Rhinn M, Keime C, Dollé P, Mengus G, Davidson I. Essential role of the TFIID subunit TAF4 in murine embryogenesis and embryonic stem cell differentiation. Nat Commun 2016; 7:11063. [PMID: 27026076 PMCID: PMC4820908 DOI: 10.1038/ncomms11063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/17/2016] [Indexed: 12/15/2022] Open
Abstract
TAF4 (TATA-binding protein-associated factor 4) and its paralogue TAF4b are components of the TFIID core module. We inactivated the murine Taf4a gene to address Taf4 function during embryogenesis. Here we show that Taf4a−/− embryos survive until E9.5 where primary germ layers and many embryonic structures are identified showing Taf4 is dispensable for their specification. In contrast, Taf4 is required for correct patterning of the trunk and anterior structures, ventral morphogenesis and proper heart positioning. Overlapping expression of Taf4a and Taf4b during embryogenesis suggests their redundancy at early stages. In agreement with this, Taf4a−/− embryonic stem cells (ESCs) are viable and comprise Taf4b-containing TFIID. Nevertheless, Taf4a−/− ESCs do not complete differentiation into glutamatergic neurons and cardiomyocytes in vitro due to impaired preinitiation complex formation at the promoters of critical differentiation genes. We define an essential role of a core TFIID TAF in differentiation events during mammalian embryogenesis. The role of TFIID core module TAFs (TATA-binding protein-associated factors) in embryogenesis is unknown. Here, the authors show that Taf4 is essential at mid-gestation and for complete neuronal differentiation of embryonic stem cells, but that Taf4a and Taf4b are redundant at early embryonic stages.
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Affiliation(s)
- Diana Langer
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Igor Martianov
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Daniel Alpern
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France.,L'École polytechnique fédérale de Lausanne, Route Cantonale, 1015 Lausanne, Switzerland
| | - Muriel Rhinn
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Pascal Dollé
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch, France
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LMO2 Oncoprotein Stability in T-Cell Leukemia Requires Direct LDB1 Binding. Mol Cell Biol 2015; 36:488-506. [PMID: 26598604 DOI: 10.1128/mcb.00901-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/16/2015] [Indexed: 12/24/2022] Open
Abstract
LMO2 is a component of multisubunit DNA-binding transcription factor complexes that regulate gene expression in hematopoietic stem and progenitor cell development. Enforced expression of LMO2 causes leukemia by inducing hematopoietic stem cell-like features in T-cell progenitor cells, but the biochemical mechanisms of LMO2 function have not been fully elucidated. In this study, we systematically dissected the LMO2/LDB1-binding interface to investigate the role of this interaction in T-cell leukemia. Alanine scanning mutagenesis of the LIM interaction domain of LDB1 revealed a discrete motif, R(320)LITR, required for LMO2 binding. Most strikingly, coexpression of full-length, wild-type LDB1 increased LMO2 steady-state abundance, whereas coexpression of mutant proteins deficient in LMO2 binding compromised LMO2 stability. These mutant LDB1 proteins also exerted dominant negative effects on growth and transcription in diverse leukemic cell lines. Mass spectrometric analysis of LDB1 binding partners in leukemic lines supports the notion that LMO2/LDB1 function in leukemia occurs in the context of multisubunit complexes, which also protect the LMO2 oncoprotein from degradation. Collectively, these data suggest that the assembly of LMO2 into complexes, via direct LDB1 interaction, is a potential molecular target that could be exploited in LMO2-driven leukemias resistant to existing chemotherapy regimens.
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Pahi Z, Kiss Z, Komonyi O, Borsos BN, Tora L, Boros IM, Pankotai T. dTAF10- and dTAF10b-Containing Complexes Are Required for Ecdysone-Driven Larval-Pupal Morphogenesis in Drosophila melanogaster. PLoS One 2015; 10:e0142226. [PMID: 26556600 PMCID: PMC4640578 DOI: 10.1371/journal.pone.0142226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/18/2015] [Indexed: 12/23/2022] Open
Abstract
In eukaryotes the TFIID complex is required for preinitiation complex assembly which positions RNA polymerase II around transcription start sites. On the other hand, histone acetyltransferase complexes including SAGA and ATAC, modulate transcription at several steps through modification of specific core histone residues. In this study we investigated the function of Drosophila melanogaster proteins TAF10 and TAF10b, which are subunits of dTFIID and dSAGA, respectively. We generated a mutation which eliminated the production of both Drosophila TAF10 orthologues. The simultaneous deletion of both dTaf10 genes impaired the recruitment of the dTFIID subunit dTAF5 to polytene chromosomes, while binding of other TFIID subunits, dTAF1 and RNAPII was not affected. The lack of both dTAF10 proteins resulted in failures in the larval-pupal transition during metamorphosis and in transcriptional reprogramming at this developmental stage. Surprisingly, unlike dSAGA mutations, dATAC subunit mutations resulted in very similar changes in the steady state mRNA levels of approximately 5000 genes as did ablation of both dTaf10 genes, indicating that dTAF10- and/or dTAF10b-containing complexes and dATAC affect similar pathways. Importantly, the phenotype resulting from dTaf10+dTaf10b mutation could be rescued by ectopically added ecdysone, suggesting that dTAF10- and/or dTAF10b-containing complexes are involved in the expression of ecdysone biosynthetic genes. Indeed, in dTaf10+dTaf10b mutants, cytochrome genes, which regulate ecdysone synthesis in the ring gland, were underrepresented. Therefore our data support the idea that the presence of dTAF10 proteins in dTFIID and/or dSAGA is required only at specific developmental steps. We propose that distinct forms of dTFIID and/or dSAGA exist during Drosophila metamorphosis, wherein different TAF compositions serve to target RNAPII at different developmental stages and tissues.
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Affiliation(s)
- Zoltan Pahi
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Zsuzsanna Kiss
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Orbán Komonyi
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Barbara N. Borsos
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Laszlo Tora
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France
| | - Imre M. Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Tibor Pankotai
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Center, Szeged, Hungary
- * E-mail:
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Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A. Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature 2015; 528:147-51. [PMID: 26550828 DOI: 10.1038/nature15545] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/02/2015] [Indexed: 12/25/2022]
Abstract
One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.
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Affiliation(s)
- Gerald Stampfel
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Tomáš Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Olga Frank
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Sebastian Wienerroither
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Franziska Reiter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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50
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Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules. Nat Commun 2015; 6:6011. [PMID: 25586196 PMCID: PMC4309443 DOI: 10.1038/ncomms7011] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/02/2014] [Indexed: 01/27/2023] Open
Abstract
General transcription factor TFIID is a cornerstone of RNA polymerase II transcription initiation in eukaryotic cells. How human TFIID-a megadalton-sized multiprotein complex composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs)-assembles into a functional transcription factor is poorly understood. Here we describe a heterotrimeric TFIID subcomplex consisting of the TAF2, TAF8 and TAF10 proteins, which assembles in the cytoplasm. Using native mass spectrometry, we define the interactions between the TAFs and uncover a central role for TAF8 in nucleating the complex. X-ray crystallography reveals a non-canonical arrangement of the TAF8-TAF10 histone fold domains. TAF2 binds to multiple motifs within the TAF8 C-terminal region, and these interactions dictate TAF2 incorporation into a core-TFIID complex that exists in the nucleus. Our results provide evidence for a stepwise assembly pathway of nuclear holo-TFIID, regulated by nuclear import of preformed cytoplasmic submodules.
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