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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [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: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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Recktenwald M, Hutt E, Davis L, MacAulay J, Daringer NM, Galie PA, Staehle MM, Vega SL. Engineering transcriptional regulation for cell-based therapies. SLAS Technol 2024; 29:100121. [PMID: 38340892 DOI: 10.1016/j.slast.2024.100121] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
A major aim in the field of synthetic biology is developing tools capable of responding to user-defined inputs by activating therapeutically relevant cellular functions. Gene transcription and regulation in response to external stimuli are some of the most powerful and versatile of these cellular functions being explored. Motivated by the success of chimeric antigen receptor (CAR) T-cell therapies, transmembrane receptor-based platforms have been embraced for their ability to sense extracellular ligands and to subsequently activate intracellular signal transduction. The integration of transmembrane receptors with transcriptional activation platforms has not yet achieved its full potential. Transient expression of plasmid DNA is often used to explore gene regulation platforms in vitro. However, applications capable of targeting therapeutically relevant endogenous or stably integrated genes are more clinically relevant. Gene regulation may allow for engineered cells to traffic into tissues of interest and secrete functional proteins into the extracellular space or to differentiate into functional cells. Transmembrane receptors that regulate transcription have the potential to revolutionize cell therapies in a myriad of applications, including cancer treatment and regenerative medicine. In this review, we will examine current engineering approaches to control transcription in mammalian cells with an emphasis on systems that can be selectively activated in response to extracellular signals. We will also speculate on the potential therapeutic applications of these technologies and examine promising approaches to expand their capabilities and tighten the control of gene regulation in cellular therapies.
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Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Evan Hutt
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Leah Davis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - James MacAulay
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Peter A Galie
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Mary M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; Department of Orthopaedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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Turner DL, Fritzlar S, Sadeghipour S, Barugahare AA, Russ BE, Turner SJ, Mathias RA. UL49 is an essential subunit of the viral pre-initiation complex that regulates human cytomegalovirus gene transcription. iScience 2022; 25:105168. [PMID: 36204275 PMCID: PMC9530030 DOI: 10.1016/j.isci.2022.105168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/25/2022] [Accepted: 09/16/2022] [Indexed: 11/03/2022] Open
Abstract
More than half the world’s population is infected with human cytomegalovirus (HCMV), causing congenital birth defects and impacting the immuno-compromised. Many of the >170 HCMV genes remain uncharacterized, and this gap in knowledge limits the development of novel antivirals. In this study, we investigated the essential viral protein UL49 and found it displayed leaky late expression kinetics, and localized to nuclear replication compartments. Cells infected with mutant UL49 virus were unable to produce infectious virions and phenocopied other beta-gamma viral pre-initiation complex (vPIC) subunit (UL79, UL87, UL91, UL92, and UL95) mutant infections. RNA-seq analysis of vPIC mutant infections revealed a consistent diminution of genes encoding capsid subunits, including TRX2/UL85 and MCP/UL86, envelope glycoproteins gM, gL and gO, and egress-associated tegument proteins UL99 and UL103. Therefore, as a member of the vPIC, UL49 serves as a fundamental HCMV effector that governs viral gene transcription required to complete the replication cycle. Beta- and gamma-herpes viruses encode a viral pre-initiation complex (vPIC) UL49, together with UL79, UL87, UL91, UL92, and UL95 Comprise the HCMV vPIC UL49 is essential for HCMV replication and orchestrates late viral gene expression Mutation of vPIC subunits reduces the transcription of structural virion components
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Zhang L, Wang R, Xing Y, Xu Y, Xiong D, Wang Y, Yao S. Separable regulation of POW1 in grain size and leaf angle development in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2517-2531. [PMID: 34343399 PMCID: PMC8633490 DOI: 10.1111/pbi.13677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/27/2023]
Abstract
Leaf angle is one of the key factors that determines rice plant architecture. However, the improvement of leaf angle erectness is often accompanied by unfavourable changes in other traits, especially grain size reduction. In this study, we identified the pow1 (put on weight 1) mutant that leads to increased grain size and leaf angle, typical brassinosteroid (BR)-related phenotypes caused by excessive cell proliferation and cell expansion. We show that modulation of the BR biosynthesis genes OsDWARF4 (D4) and D11 and the BR signalling gene D61 could rescue the phenotype of leaf angle but not grain size in the pow1 mutant. We further demonstrated that POW1 functions in grain size regulation by repressing the transactivation activity of the interacting protein TAF2, a highly conserved member of the TFIID transcription initiation complex. Down-regulation of TAF2 rescued the enlarged grain size of pow1 but had little effect on the increased leaf angle phenotype of the mutant. The separable functions of the POW1-TAF2 and POW1-BR modules in grain size and leaf angle control provide a promising strategy for designing varieties with compact plant architecture and increased grain size, thus promoting high-yield breeding in rice.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Ruci Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yide Xing
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yufang Xu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
- College of Life ScienceHenan Agricultural UniversityZhengzhouChina
| | - Dunping Xiong
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yueming Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Shanguo Yao
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
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Lourenco C, Resetca D, Redel C, Lin P, MacDonald AS, Ciaccio R, Kenney TMG, Wei Y, Andrews DW, Sunnerhagen M, Arrowsmith CH, Raught B, Penn LZ. MYC protein interactors in gene transcription and cancer. Nat Rev Cancer 2021; 21:579-591. [PMID: 34188192 DOI: 10.1038/s41568-021-00367-9] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
The transcription factor and oncoprotein MYC is a potent driver of many human cancers and can regulate numerous biological activities that contribute to tumorigenesis. How a single transcription factor can regulate such a diverse set of biological programmes is central to the understanding of MYC function in cancer. In this Perspective, we highlight how multiple proteins that interact with MYC enable MYC to regulate several central control points of gene transcription. These include promoter binding, epigenetic modifications, initiation, elongation and post-transcriptional processes. Evidence shows that a combination of multiple protein interactions enables MYC to function as a potent oncoprotein, working together in a 'coalition model', as presented here. Moreover, as MYC depends on its protein interactome for function, we discuss recent research that emphasizes an unprecedented opportunity to target protein interactors to directly impede MYC oncogenesis.
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Affiliation(s)
| | - Diana Resetca
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Cornelia Redel
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Peter Lin
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Alannah S MacDonald
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Roberto Ciaccio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Tristan M G Kenney
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Yong Wei
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - David W Andrews
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, Toronto, ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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6
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Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194749. [PMID: 34425241 PMCID: PMC10359485 DOI: 10.1016/j.bbagrm.2021.194749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022]
Abstract
The domain of transcription regulation has been notoriously difficult to annotate in the Gene Ontology, partly because of the intricacies of gene regulation which involve molecular interactions with DNA as well as amongst protein complexes. The molecular function 'transcription coregulator activity' is a part of the biological process 'regulation of transcription, DNA-templated' that occurs in the cellular component 'chromatin'. It can mechanistically link sequence-specific DNA-binding transcription factor (dbTF) regulatory DNA target sites to coactivator and corepressor target sites through the molecular function 'cis-regulatory region sequence-specific DNA binding'. Many questions arise about transcription coregulators (coTF). Here, we asked how many unannotated, putative coregulators can be identified in protein complexes? Therefore, we mined the CORUM and hu.MAP protein complex databases with known and strongly presumed human transcription coregulators. In addition, we trawled the BioGRID and IntAct molecular interaction databases for interactors of the known 1457 human dbTFs annotated by the GREEKC and GO consortia. This yielded 1093 putative transcription factor coregulator complex subunits, of which 954 interact directly with a dbTF. This substantially expands the set of coTFs that could be annotated to 'transcription coregulator activity' and sets the stage for renewed annotation and wet-lab research efforts. To this end, we devised a prioritisation score based on existing GO annotations of already curated transcription coregulators as well as interactome representation. Since all the proteins that we mined are parts of protein complexes, we propose to concomitantly engage in annotation of the putative transcription coregulator-containing complexes in the Complex Portal database.
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7
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Cazier AP, Blazeck J. Advances in promoter engineering: novel applications and predefined transcriptional control. Biotechnol J 2021; 16:e2100239. [PMID: 34351706 DOI: 10.1002/biot.202100239] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew P Cazier
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
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8
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Pimmett VL, Dejean M, Fernandez C, Trullo A, Bertrand E, Radulescu O, Lagha M. Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics. Nat Commun 2021; 12:4504. [PMID: 34301936 PMCID: PMC8302612 DOI: 10.1038/s41467-021-24461-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge in transcription is understanding how promoter composition dictates bursting, particularly in multicellular organisms. We investigate two key Drosophila developmental promoter motifs, the TATA box (TATA) and the Initiator (INR). Using live imaging in Drosophila embryos and new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds to minutes. TATA-containing promoters and INR-containing promoters exhibit distinct dynamics, with one or two separate rate-limiting steps respectively. A TATA box is associated with long active states, high rates of polymerase initiation, and short-lived, infrequent inactive states. In contrast, the INR motif leads to two inactive states, one of which relates to promoter-proximal polymerase pausing. Surprisingly, the model suggests pausing is not obligatory, but occurs stochastically for a subset of polymerases. Overall, our results provide a rationale for promoter switching during zygotic genome activation.
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Affiliation(s)
- Virginia L Pimmett
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Matthieu Dejean
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Carola Fernandez
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Antonio Trullo
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France
| | - Ovidiu Radulescu
- Laboratory of Pathogen Host Interactions, Univ Montpellier, CNRS, Montpellier, France
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
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Krischuns T, Lukarska M, Naffakh N, Cusack S. Influenza Virus RNA-Dependent RNA Polymerase and the Host Transcriptional Apparatus. Annu Rev Biochem 2021; 90:321-348. [PMID: 33770447 DOI: 10.1146/annurev-biochem-072820-100645] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza virus RNA-dependent RNA polymerase (FluPol) transcribes the viral RNA genome in the infected cell nucleus. In the 1970s, researchers showed that viral transcription depends on host RNA polymerase II (RNAP II) activity and subsequently that FluPol snatches capped oligomers from nascent RNAP II transcripts to prime its own transcription. Exactly how this occurs remains elusive. Here, we review recent advances in the mechanistic understanding of FluPol transcription and early events in RNAP II transcription that are relevant to cap-snatching. We describe the known direct interactions between FluPol and the RNAP II C-terminal domain and summarize the transcription-related host factors that have been found to interact with FluPol. We also discuss open questions regarding how FluPol may be targeted to actively transcribing RNAP II and the exact context and timing of cap-snatching, which is presumed to occur after cap completion but before the cap is sequestered by the nuclear cap-binding complex.
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Affiliation(s)
- Tim Krischuns
- Unité Biologie des ARN et Virus Influenza, Département de Virologie, Institut Pasteur, CNRS UMR 3569, F-75015 Paris, France; ,
| | - Maria Lukarska
- European Molecular Biology Laboratory, 38042 Grenoble CEDEX 9, France; .,Current affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA;
| | - Nadia Naffakh
- Unité Biologie des ARN et Virus Influenza, Département de Virologie, Institut Pasteur, CNRS UMR 3569, F-75015 Paris, France; ,
| | - Stephen Cusack
- European Molecular Biology Laboratory, 38042 Grenoble CEDEX 9, France;
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Wang P, Yang W, Zhao S, Nashun B. Regulation of chromatin structure and function: insights into the histone chaperone FACT. Cell Cycle 2021; 20:465-479. [PMID: 33590780 DOI: 10.1080/15384101.2021.1881726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, changes in chromatin accessibility are necessary for chromatin to maintain its highly dynamic nature at different times during the cell cycle. Histone chaperones interact with histones and regulate chromatin dynamics. Facilitates chromatin transcription (FACT) is an important histone chaperone that plays crucial roles during various cellular processes. Here, we analyze the structural characteristics of FACT, discuss how FACT regulates nucleosome/chromatin reorganization and summarize possible functions of FACT in transcription, replication, and DNA repair. The possible involvement of FACT in cell fate determination is also discussed.Abbreviations: FACT: facilitates chromatin transcription, Spt16: suppressor of Ty16, SSRP1: structure-specific recognition protein-1, NTD: N-terminal domain, DD: dimerization domain, MD: middle domain, CTD: C-terminus domain, IDD: internal intrinsically disordered domain, HMG: high mobility group, CID: C-terminal intrinsically disordered domain, Nhp6: non-histone chromosomal protein 6, RNAPII: RNA polymerase II, CK2: casein kinase 2, AID: acidic inner disorder, PIC: pre-initiation complex, IR: ionizing radiation, DDSB: DNA double-strand break, PARlation: poly ADP-ribosylation, BER: base-excision repair, UVSSA: UV-stimulated scaffold protein A, HR: homologous recombination, CAF-1: chromatin assembly factor 1, Asf1: anti-silencing factor 1, Rtt106: regulator of Ty1 transposition protein 106, H3K56ac: H3K56 acetylation, KD: knock down, SETD2: SET domain containing 2, H3K36me3: trimethylation of lysine36 in histone H3, H2Bub: H2B ubiquitination, iPSCs: induced pluripotent stem cells, ESC: embryonic stem cell, H3K4me3: trimethylation of lysine 4 on histone H3 protein subunit, CHD1: chromodomain protein.
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Affiliation(s)
- Peijun Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wanting Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Shuxin Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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11
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Makashov AA, Myasnikova EM, Spirov AV. Fuzzy Linguistic Modeling of the Regulation of Drosophila Segmentation Genes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Luse DS, Parida M, Spector BM, Nilson KA, Price DH. A unified view of the sequence and functional organization of the human RNA polymerase II promoter. Nucleic Acids Res 2020; 48:7767-7785. [PMID: 32597978 PMCID: PMC7641323 DOI: 10.1093/nar/gkaa531] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location.
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Affiliation(s)
- Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Benjamin M Spector
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Kyle A Nilson
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
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14
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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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15
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Dvorak P, Leupen S, Soucek P. Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. Cells 2019; 8:cells8060623. [PMID: 31234415 PMCID: PMC6627321 DOI: 10.3390/cells8060623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023] Open
Abstract
Single nucleotide polymorphisms located in 5′ untranslated regions (5′UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5′UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5′UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5′UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5′UTRs, such as GC content variation, hairpin structure conservation or 5′UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Sarah Leupen
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42 Prague 10, Czech Republic.
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16
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Feigerle JT, Kornberg RD. IID in 3D: Improved Resolution of Transcription Factor Structure by Cryo-Electron Microscopy. Biochemistry 2019; 58:2653-2654. [PMID: 31150224 DOI: 10.1021/acs.biochem.9b00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jordan T Feigerle
- Department of Structural Biology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Roger D Kornberg
- Department of Structural Biology , Stanford University School of Medicine , Stanford , California 94305 , United States
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17
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Antonova SV, Boeren J, Timmers HTM, Snel B. Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID. Genes Dev 2019; 33:888-902. [PMID: 31123066 PMCID: PMC6672047 DOI: 10.1101/gad.300475.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this perspective, Antonova et al. determine the evolutionary history of all TFIID subunits and place them in a functional context to understand their diversification. This analysis of TFIID evolution exemplifies how phylogenetic protein interrogation aids in uncovering existing structures, drawing parallels between related complexes and challenges offered by genome expansions that can be countered by exploiting chromatin modifications. The basal transcription factor TFIID is central for RNA polymerase II-dependent transcription. Human TFIID is endowed with chromatin reader and DNA-binding domains and protein interaction surfaces. Fourteen TFIID TATA-binding protein (TBP)-associated factor (TAF) subunits assemble into the holocomplex, which shares subunits with the Spt–Ada–Gcn5–acetyltransferase (SAGA) coactivator. Here, we discuss the structural and functional evolution of TFIID and its divergence from SAGA. Our orthologous tree and domain analyses reveal dynamic gains and losses of epigenetic readers, plant-specific functions of TAF1 and TAF4, the HEAT2-like repeat in TAF2, and, importantly, the pre-LECA origin of TFIID and SAGA. TFIID evolution exemplifies the dynamic plasticity in transcription complexes in the eukaryotic lineage.
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Affiliation(s)
- Simona V Antonova
- Molecular Cancer Research and Regenerative Medicine, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands
| | - Jeffrey Boeren
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, The Netherlands
| | - H T Marc Timmers
- Molecular Cancer Research and Regenerative Medicine, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands.,Department of Urology, Medical Centre-University of Freiburg, 79106 Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) Standort Freiburg, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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18
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Gupta K, Tölzer C, Sari-Ak D, Fitzgerald DJ, Schaffitzel C, Berger I. MultiBac: Baculovirus-Mediated Multigene DNA Cargo Delivery in Insect and Mammalian Cells. Viruses 2019; 11:E198. [PMID: 30813511 PMCID: PMC6466381 DOI: 10.3390/v11030198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 12/22/2022] Open
Abstract
The baculovirus/insect cell system (BICS) is widely used in academia and industry to produce eukaryotic proteins for many applications, ranging from structure analysis to drug screening and the provision of protein biologics and therapeutics. Multi-protein complexes have emerged as vital catalysts of cellular function. In order to unlock the structure and mechanism of these essential molecular machines and decipher their function, we developed MultiBac, a BICS particularly tailored for heterologous multigene transfer and multi-protein complex production. Baculovirus is unique among common viral vectors in its capacity to accommodate very large quantities of heterologous DNA and to faithfully deliver this cargo to a host cell of choice. We exploited this beneficial feature to outfit insect cells with synthetic DNA circuitry conferring new functionality during heterologous protein expression, and developing customized MultiBac baculovirus variants in the process. By altering its tropism, recombinant baculovirions can be used for the highly efficient delivery of a customized DNA cargo in mammalian cells and tissues. Current advances in synthetic biology greatly facilitate the construction or recombinant baculoviral genomes for gene editing and genome engineering, mediated by a MultiBac baculovirus tailored to this purpose. Here, recent developments and exploits of the MultiBac system are presented and discussed.
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Affiliation(s)
- Kapil Gupta
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol BS8 1TQ, UK.
| | - Christine Tölzer
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol BS8 1TQ, UK.
| | - Duygu Sari-Ak
- European Molecular Biology Laboratory EMBL, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | | | - Christiane Schaffitzel
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol BS8 1TQ, UK.
| | - Imre Berger
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol BS8 1TQ, UK.
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19
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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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20
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Ali R, Ramadurai S, Barry F, Nasheuer HP. Optimizing fluorescent protein expression for quantitative fluorescence microscopy and spectroscopy using herpes simplex thymidine kinase promoter sequences. FEBS Open Bio 2018; 8:1043-1060. [PMID: 29928582 PMCID: PMC5985997 DOI: 10.1002/2211-5463.12432] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/19/2018] [Accepted: 04/10/2018] [Indexed: 12/22/2022] Open
Abstract
The modulation of expression levels of fluorescent fusion proteins (FFPs) is central for recombinant DNA technologies in modern biology as overexpression of proteins contributes to artifacts in biological experiments. In addition, some microscopy techniques such as fluorescence correlation spectroscopy (FCS) and single-molecule-based techniques are very sensitive to high expression levels of FFPs. To reduce the levels of recombinant protein expression in comparison with the commonly used, very strong CMV promoter, the herpes simplex virus thymidine kinase (TK) gene promoter, and mutants thereof were analyzed. Deletion mutants of the TK promoter were constructed and introduced into the Gateway® system for ectopic expression of enhanced green fluorescent protein (eGFP), monomeric cherry (mCherry), and FFPs containing these FPs. Two promoter constructs, TK2ST and TKTSC, were established, which have optimal low expression levels suitable for FCS studies in U2OS, HeLa CCL2, NIH 3T3, and BALB/c cells. Interestingly, when tested in these four cell lines, promoter constructs having a deletion within TK gene 5'-UTR showed significantly higher protein expression levels than the equivalent constructs lacking this deletion. This suggests that a negative regulatory element is localized within the TK gene 5'-UTR.
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Affiliation(s)
- Rizwan Ali
- Systems Biology IrelandNUI GalwayIreland
- BiochemistrySchool of Natural Sciences and Centre for Chromosome BiologyNational University of Ireland GalwayIreland
- Present address:
Medical Core Facility & Research PlatformsKing Abdullah International Medical Research CenterNational Guard Health AffairsP.O. Box 3660Riyadh11481 Mail Code 1515Saudi Arabia
| | - Sivaramakrishnan Ramadurai
- Systems Biology IrelandNUI GalwayIreland
- BiochemistrySchool of Natural Sciences and Centre for Chromosome BiologyNational University of Ireland GalwayIreland
- Present address:
School of Chemical SciencesDublin City UniversityDublin‐9Ireland
| | - Frank Barry
- Systems Biology IrelandNUI GalwayIreland
- Regenerative Medicine InstituteNational University of Ireland GalwayIreland
| | - Heinz Peter Nasheuer
- Systems Biology IrelandNUI GalwayIreland
- BiochemistrySchool of Natural Sciences and Centre for Chromosome BiologyNational University of Ireland GalwayIreland
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21
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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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22
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Mechanistic Differences in Transcription Initiation at TATA-Less and TATA-Containing Promoters. Mol Cell Biol 2017; 38:MCB.00448-17. [PMID: 29038161 DOI: 10.1128/mcb.00448-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/06/2017] [Indexed: 12/14/2022] Open
Abstract
A yeast in vitro system was developed that is active for transcription at both TATA-containing and TATA-less promoters. Transcription with extracts made from cells depleted of TFIID subunit Taf1 demonstrated that promoters of both classes are TFIID dependent, in agreement with recent in vivo findings. TFIID depletion can be complemented in vitro by additional recombinant TATA binding protein (TBP) at only the TATA-containing promoters. In contrast, high levels of TBP did not complement Taf1 depletion in vivo and instead repressed transcription from both promoter types. We also demonstrate the importance of the TATA-like sequence found at many TATA-less promoters and describe how the presence or absence of the TATA element is likely not the only feature that distinguishes these two types of promoters.
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23
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24
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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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25
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Pelosse M, Crocker H, Gorda B, Lemaire P, Rauch J, Berger I. MultiBac: from protein complex structures to synthetic viral nanosystems. BMC Biol 2017; 15:99. [PMID: 29084535 PMCID: PMC5661938 DOI: 10.1186/s12915-017-0447-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. We review some of these developments, including the ongoing rewiring of the MultiBac system for mammalian applications, notably CRISPR/Cas9-mediated gene editing.
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Affiliation(s)
- Martin Pelosse
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK
| | - Hannah Crocker
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK
| | - Barbara Gorda
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK
| | - Paul Lemaire
- Geneva Biotech SARL, Avenue de la Roseraie 64, 1205, Genève, Switzerland
| | - Jens Rauch
- Systems Biology Ireland, University College Dublin, Belfield Dublin 4, Republic of Ireland
| | - Imre Berger
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK.
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26
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Abstract
Over the past two decades there has been a great deal of interest in the development of inhibitors of the cyclin-dependent kinases (CDKs). This attention initially stemmed from observations that different CDK isoforms have key roles in cancer cell proliferation through loss of regulation of the cell cycle, a hallmark feature of cancer. CDKs have now been shown to regulate other processes, particularly various aspects of transcription. The early non-selective CDK inhibitors exhibited considerable toxicity and proved to be insufficiently active in most cancers. The lack of patient selection biomarkers and an absence of understanding of the inhibitory profile required for efficacy hampered the development of these inhibitors. However, the advent of potent isoform-selective inhibitors with accompanying biomarkers has re-ignited interest. Palbociclib, a selective CDK4/6 inhibitor, is now approved for the treatment of ER+/HER2- advanced breast cancer. Current developments in the field include the identification of potent and selective inhibitors of the transcriptional CDKs; these include tool compounds that have allowed exploration of individual CDKs as cancer targets and the determination of their potential therapeutic windows. Biomarkers that allow the selection of patients likely to respond are now being discovered. Drug resistance has emerged as a major hurdle in the clinic for most protein kinase inhibitors and resistance mechanism are beginning to be identified for CDK inhibitors. This suggests that the selective inhibitors may be best used combined with standard of care or other molecularly targeted agents now in development rather than in isolation as monotherapies.
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Affiliation(s)
- Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Aurélie Mallinger
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul A Clarke
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom.
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27
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Songock WK, Kim SM, Bodily JM. The human papillomavirus E7 oncoprotein as a regulator of transcription. Virus Res 2016; 231:56-75. [PMID: 27818212 DOI: 10.1016/j.virusres.2016.10.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022]
Abstract
High-risk human papillomaviruses (HPVs) encode oncoproteins which manipulate gene expression patterns in the host keratinocytes to facilitate viral replication, regulate viral transcription, and promote immune evasion and persistence. In some cases, oncoprotein-induced changes in host cell behavior can cause progression to cancer, but a complete picture of the functions of the viral oncoproteins in the productive HPV life cycle remains elusive. E7 is the HPV-encoded factor most responsible for maintaining cell cycle competence in differentiating keratinocytes. Through interactions with dozens of host factors, E7 has an enormous impact on host gene expression patterns. In this review, we will examine the role of E7 specifically as a regulator of transcription. We will discuss mechanisms of regulation of cell cycle-related genes by E7 as well as genes involved in immune regulation, growth factor signaling, DNA damage responses, microRNAs, and others pathways. We will also discuss some unanswered questions about how transcriptional regulation by E7 impacts the biology of HPV in both benign and malignant conditions.
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Affiliation(s)
- William K Songock
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Seong-Man Kim
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Jason M Bodily
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA.
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28
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Eukaryotic Transcription Regulation: Getting to the Heart of the Matter: Commentary on Mediator Architecture and RNA Polymerase II Function by Plaschka et al. J Mol Biol 2016; 428:2575-2580. [DOI: 10.1016/j.jmb.2016.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/18/2022]
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Passmore LA, Taatjes DJ. Macromolecular Complexes in Transcription and Co-Transcriptional RNA Processing. J Mol Biol 2016; 428:2539-2541. [PMID: 27155574 DOI: 10.1016/j.jmb.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Lori A Passmore
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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