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Ferdoush J, Kadir RA, Ogle M, Saha A. Regulation of eukaryotic transcription initiation in response to cellular stress. Gene 2024; 924:148616. [PMID: 38795856 DOI: 10.1016/j.gene.2024.148616] [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: 11/22/2023] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Transcription initiation is a vital step in the regulation of eukaryotic gene expression. It can be dysregulated in response to various cellular stressors which is associated with numerous human diseases including cancer. Transcription initiation is facilitated via many gene-specific trans-regulatory elements such as transcription factors, activators, and coactivators through their interactions with transcription pre-initiation complex (PIC). These trans-regulatory elements can uniquely facilitate PIC formation (hence, transcription initiation) in response to cellular nutrient stress. Cellular nutrient stress also regulates the activity of other pathways such as target of rapamycin (TOR) pathway. TOR pathway exhibits distinct regulatory mechanisms of transcriptional activation in response to stress. Like TOR pathway, the cell cycle regulatory pathway is also found to be linked to transcriptional regulation in response to cellular stress. Several transcription factors such as p53, C/EBP Homologous Protein (CHOP), activating transcription factor 6 (ATF6α), E2F, transforming growth factor (TGF)-β, Adenomatous polyposis coli (APC), SMAD, and MYC have been implicated in regulation of transcription of target genes involved in cell cycle progression, apoptosis, and DNA damage repair pathways. Additionally, cellular metabolic and oxidative stressors have been found to regulate the activity of long non-coding RNAs (lncRNA). LncRNA regulates transcription by upregulating or downregulating the transcription regulatory proteins involved in metabolic and cell signaling pathways. Numerous human diseases, triggered by chronic cellular stressors, are associated with abnormal regulation of transcription. Hence, understanding these mechanisms would help unravel the molecular regulatory insights with potential therapeutic interventions. Therefore, here we emphasize the recent advances of regulation of eukaryotic transcription initiation in response to cellular stress.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Matthew Ogle
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Ayan Saha
- Department of Bioinformatics and Biotechnology, Asian University for Women, Chattogram, Bangladesh
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2
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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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3
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Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components. EMBO J 2024; 43:1799-1821. [PMID: 38565951 PMCID: PMC11066129 DOI: 10.1038/s44318-024-00089-2] [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: 08/02/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
A great deal of work has revealed, in structural detail, the components of the preinitiation complex (PIC) machinery required for initiation of mRNA gene transcription by RNA polymerase II (Pol II). However, less-well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining how rates of in vivo RNA synthesis are established. We used competition ChIP in budding yeast to obtain genome-scale estimates of the residence times for five general transcription factors (GTFs): TBP, TFIIA, TFIIB, TFIIE and TFIIF. While many GTF-chromatin interactions were short-lived ( < 1 min), there were numerous interactions with residence times in the range of several minutes. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism, offering a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription.
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Elizabeth A Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
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Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ. DNA looping mediates cooperative transcription activation. Nat Struct Mol Biol 2024; 31:293-299. [PMID: 38177666 DOI: 10.1038/s41594-023-01149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.
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Affiliation(s)
- Shu-Jing Han
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
| | - Lin-Lin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Qiang Shen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Feng Yang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ning Cui
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui Sun
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ke Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui-Chao Meng
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Zhi-Peng Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Cong-Zhao Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
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Malik S, Roeder RG. Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genet 2023; 24:767-782. [PMID: 37532915 PMCID: PMC11088444 DOI: 10.1038/s41576-023-00630-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA
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6
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Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550532. [PMID: 37546819 PMCID: PMC10402067 DOI: 10.1101/2023.07.25.550532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. Results We used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. Conclusions The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA 22908
| | - Savera J. Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Elizabeth A. Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
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7
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Spreitzer E, Alderson TR, Bourgeois B, Eggenreich L, Habacher H, Brahmersdorfer G, Pritišanac I, Sánchez-Murcia PA, Madl T. FOXO transcription factors differ in their dynamics and intra/intermolecular interactions. Curr Res Struct Biol 2022; 4:118-133. [PMID: 35573459 PMCID: PMC9097636 DOI: 10.1016/j.crstbi.2022.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/19/2022] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - T. Reid Alderson
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Loretta Eggenreich
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Hermann Habacher
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Greta Brahmersdorfer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Iva Pritišanac
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Pedro A. Sánchez-Murcia
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Corresponding author. Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria.
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8
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Sloutskin A, Shir-Shapira H, Freiman RN, Juven-Gershon T. The Core Promoter Is a Regulatory Hub for Developmental Gene Expression. Front Cell Dev Biol 2021; 9:666508. [PMID: 34568311 PMCID: PMC8461331 DOI: 10.3389/fcell.2021.666508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
The development of multicellular organisms and the uniqueness of each cell are achieved by distinct transcriptional programs. Multiple processes that regulate gene expression converge at the core promoter region, an 80 bp region that directs accurate transcription initiation by RNA polymerase II (Pol II). In recent years, it has become apparent that the core promoter region is not a passive DNA component, but rather an active regulatory module of transcriptional programs. Distinct core promoter compositions were demonstrated to result in different transcriptional outputs. In this mini-review, we focus on the role of the core promoter, particularly its downstream region, as the regulatory hub for developmental genes. The downstream core promoter element (DPE) was implicated in the control of evolutionarily conserved developmental gene regulatory networks (GRNs) governing body plan in both the anterior-posterior and dorsal-ventral axes. Notably, the composition of the basal transcription machinery is not universal, but rather promoter-dependent, highlighting the importance of specialized transcription complexes and their core promoter target sequences as key hubs that drive embryonic development, differentiation and morphogenesis across metazoan species. The extent of transcriptional activation by a specific enhancer is dependent on its compatibility with the relevant core promoter. The core promoter content also regulates transcription burst size. Overall, while for many years it was thought that the specificity of gene expression is primarily determined by enhancers, it is now clear that the core promoter region comprises an important regulatory module in the intricate networks of developmental gene expression.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Richard N. Freiman
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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9
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Wu Y, Yang Q, Wang M, Chen S, Jia R, Yang Q, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. Multifaceted Roles of ICP22/ORF63 Proteins in the Life Cycle of Human Herpesviruses. Front Microbiol 2021; 12:668461. [PMID: 34163446 PMCID: PMC8215345 DOI: 10.3389/fmicb.2021.668461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/05/2021] [Indexed: 01/03/2023] Open
Abstract
Herpesviruses are extremely successful parasites that have evolved over millions of years to develop a variety of mechanisms to coexist with their hosts and to maintain host-to-host transmission and lifelong infection by regulating their life cycles. The life cycle of herpesviruses consists of two phases: lytic infection and latent infection. During lytic infection, active replication and the production of numerous progeny virions occur. Subsequent suppression of the host immune response leads to a lifetime latent infection of the host. During latent infection, the viral genome remains in an inactive state in the host cell to avoid host immune surveillance, but the virus can be reactivated and reenter the lytic cycle. The balance between these two phases of the herpesvirus life cycle is controlled by broad interactions among numerous viral and cellular factors. ICP22/ORF63 proteins are among these factors and are involved in transcription, nuclear budding, latency establishment, and reactivation. In this review, we summarized the various roles and complex mechanisms by which ICP22/ORF63 proteins regulate the life cycle of human herpesviruses and the complex relationships among host and viral factors. Elucidating the role and mechanism of ICP22/ORF63 in virus-host interactions will deepen our understanding of the viral life cycle. In addition, it will also help us to understand the pathogenesis of herpesvirus infections and provide new strategies for combating these infections.
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Affiliation(s)
- Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiqi Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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10
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Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription. Proc Natl Acad Sci U S A 2020; 117:32348-32357. [PMID: 33293419 DOI: 10.1073/pnas.2011224117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In eukaryotes, RNA polymerase II (RNApII) transcribes messenger RNA from template DNA. Decades of experiments have identified the proteins needed for transcription activation, initiation complex assembly, and productive elongation. However, the dynamics of recruitment of these proteins to transcription complexes, and of the transitions between these steps, are poorly understood. We used multiwavelength single-molecule fluorescence microscopy to directly image and quantitate these dynamics in a budding yeast nuclear extract that reconstitutes activator-dependent transcription in vitro. A strong activator (Gal4-VP16) greatly stimulated reversible binding of individual RNApII molecules to template DNA. Binding of labeled elongation factor Spt4/5 to DNA typically followed RNApII binding, was NTP dependent, and was correlated with association of mRNA binding protein Hek2, demonstrating specificity of Spt4/5 binding to elongation complexes. Quantitative kinetic modeling shows that only a fraction of RNApII binding events are productive and implies a rate-limiting step, probably associated with recruitment of general transcription factors, needed to assemble a transcription-competent preinitiation complex at the promoter. Spt4/5 association with transcription complexes was slowly reversible, with DNA-bound RNApII molecules sometimes binding and releasing Spt4/5 multiple times. The average Spt4/5 residence time was of similar magnitude to the time required to transcribe an average length yeast gene. These dynamics suggest that a single Spt4/5 molecule remains associated during a typical transcription event, yet can dissociate from RNApII to allow disassembly of abnormally long-lived (i.e., stalled) elongation complexes.
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11
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Depicting HIV-1 Transcriptional Mechanisms: A Summary of What We Know. Viruses 2020; 12:v12121385. [PMID: 33287435 PMCID: PMC7761857 DOI: 10.3390/v12121385] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022] Open
Abstract
Despite the introduction of combinatory antiretroviral therapy (cART), HIV-1 infection cannot be cured and is still one of the major health issues worldwide. Indeed, as soon as cART is interrupted, a rapid rebound of viremia is observed. The establishment of viral latency and the persistence of the virus in cellular reservoirs constitute the main barrier to HIV eradication. For this reason, new therapeutic approaches have emerged to purge or restrain the HIV-1 reservoirs in order to cure infected patients. However, the viral latency is a multifactorial process that depends on various cellular mechanisms. Since these new therapies mainly target viral transcription, their development requires a detailed and precise understanding of the regulatory mechanism underlying HIV-1 transcription. In this review, we discuss the complex molecular transcriptional network regulating HIV-1 gene expression by focusing on the involvement of host cell factors that could be used as potential drug targets to design new therapeutic strategies and, to a larger extent, to reach an HIV-1 functional cure.
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12
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Dual-Channel Stopped-Flow Apparatus for Simultaneous Fluorescence, Anisotropy, and FRET Kinetic Data Acquisition for Binary and Ternary Biological Complexes. BIOSENSORS 2020; 10:bios10110180. [PMID: 33227895 PMCID: PMC7699296 DOI: 10.3390/bios10110180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
The Stopped-Flow apparatus (SF) tracks molecular events by mixing the reactants in sub-millisecond regimes. The reaction of intrinsically or extrinsically labeled biomolecules can be monitored by recording the fluorescence, F(t), anisotropy, r(t), polarization, p(t), or FRET, F(t)FRET, traces at nanomolar concentrations. These kinetic measurements are critical to elucidate reaction mechanisms, structural information, and even thermodynamics. In a single detector SF, or L-configuration, the r(t), p(t), and F(t) traces are acquired by switching the orientation of the emission polarizer to collect the IVV and IVH signals however it requires two-shot experiments. In a two-detector SF, or T-configuration, these traces are collected in a single-shot experiment, but it increases the apparatus’ complexity and price. Herein, we present a single-detector dual-channel SF to obtain the F(t) and r(t) traces simultaneously, in which a photo-elastic modulator oscillates by 90° the excitation light plane at a 50 kHz frequency, and the emission signal is processed by a set of electronic filters that split it into the r(t) and F(t) analog signals that are digitized and stored into separated spreadsheets by a custom-tailored instrument control software. We evaluated the association kinetics of binary and ternary biological complexes acquired with our dual-channel SF and the traditional methods; such as a single polarizer at the magic angle to acquire F(t), a set of polarizers to track F(t), and r(t), and by energy transfer quenching, F(t)FRET. Our dual-channel SF economized labeled material and yielded rate constants in excellent agreement with the traditional methods.
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13
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Gene Transcription as a Limiting Factor in Protein Production and Cell Growth. G3-GENES GENOMES GENETICS 2020; 10:3229-3242. [PMID: 32694199 PMCID: PMC7466996 DOI: 10.1534/g3.120.401303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell growth is driven by the synthesis of proteins, genes, and other cellular components. Defining processes that limit biosynthesis rates is fundamental for understanding the determinants of cell physiology. Here, we analyze the consequences of engineering cells to express extremely high levels of mCherry proteins, as a tool to define limiting processes that fail to adapt upon increasing biosynthetic demands. Protein-burdened cells were transcriptionally and phenotypically similar to mutants of the Mediator, a transcription coactivator complex. However, our binding data suggest that the Mediator was not depleted from endogenous promoters. Burdened cells showed an overall increase in the abundance of the majority of endogenous transcripts, except for highly expressed genes. Our results, supported by mathematical modeling, suggest that wild-type cells transcribe highly expressed genes at the maximal possible rate, as defined by the transcription machinery’s physical properties. We discuss the possible cellular benefit of maximal transcription rates to allow a coordinated optimization of cell size and cell growth.
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14
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Steinhaus R, Gonzalez T, Seelow D, Robinson PN. Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers. Nucleic Acids Res 2020; 48:5306-5317. [PMID: 32338759 PMCID: PMC7261191 DOI: 10.1093/nar/gkaa223] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022] Open
Abstract
The temporal and spatial expression of genes is controlled by promoters and enhancers. Findings obtained over the last decade that not only promoters but also enhancers are characterized by bidirectional, divergent transcription have challenged the traditional notion that promoters and enhancers represent distinct classes of regulatory elements. Over half of human promoters are associated with CpG islands (CGIs), relatively CpG-rich stretches of generally several hundred nucleotides that are often associated with housekeeping genes. Only about 6% of transcribed enhancers defined by CAGE-tag analysis are associated with CGIs. Here, we present an analysis of enhancer and promoter characteristics and relate them to the presence or absence of CGIs. We show that transcribed enhancers share a number of CGI-dependent characteristics with promoters, including statistically significant local overrepresentation of core promoter elements. CGI-associated enhancers are longer, display higher directionality of transcription, greater expression, a lesser degree of tissue specificity, and a higher frequency of transcription-factor binding events than non-CGI-associated enhancers. Genes putatively regulated by CGI-associated enhancers are enriched for transcription regulator activity. Our findings show that CGI-associated transcribed enhancers display a series of characteristics related to sequence, expression and function that distinguish them from enhancers not associated with CGIs.
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Affiliation(s)
- Robin Steinhaus
- Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tonatiuh Gonzalez
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.,Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA
| | - Dominik Seelow
- Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.,Institute for Systems Genomics, University of Connecticut, 263 Farmington Avenue, Farmington, CT 06030, USA
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15
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Hu B, Zhou Y, Sun D, Yang Y, Liu Y, Li X, Li H, Chen L. PROTACs: New method to degrade transcription regulating proteins. Eur J Med Chem 2020; 207:112698. [PMID: 32858471 DOI: 10.1016/j.ejmech.2020.112698] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 01/03/2023]
Abstract
Transcription is the fundamental process in all living organisms. A variety of important proteins, such as NRs, BETs, HDACs and many others are involved in transcription process. In general, overexpression of these proteins would cause many diseases. Some approved therapeutics employed inhibitors to regulate the transcription process, however, the results are far from satisfying. Therefore, it is in high demand to develop new technology to improve the therapeutic effects. In recent years, proteolysis-targeting chimaera (PROTAC) turned out to be a novel efficient therapeutic method to treat various diseases which were caused by proteins overexpression. PROTAC molecules are bifunctional small molecules that simultaneously bind a target protein and an E3-ubiquitin ligase, thus causing ubiquitination and subsequent degradation of the target protein by the proteasome. In contrast to traditional inhibitors, PROTACs showed higher efficiency to tackle the diseases which were caused by protein overexpression due to their excellent performance for degrading target proteins in transcription regulation. In this review, 29 kinds of PROTACs targeting transcription regulator proteins are summarized, and meanwhile the advantages of PROTACs are highlighted. Furthermore, several examples of PROTACs regulating the transcription for the treatment of diseases and functioning as tools for biological research are also disscussed.
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Affiliation(s)
- Beichen Hu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yirong Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yueying Yang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xingzhou Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China.
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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16
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Harden TT, Herlambang KS, Chamberlain M, Lalanne JB, Wells CD, Li GW, Landick R, Hochschild A, Kondev J, Gelles J. Alternative transcription cycle for bacterial RNA polymerase. Nat Commun 2020; 11:448. [PMID: 31974358 PMCID: PMC6978322 DOI: 10.1038/s41467-019-14208-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/10/2019] [Indexed: 11/18/2022] Open
Abstract
RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. Here we use single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remains bound to DNA and sometimes exhibits one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarts transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this secondary initiation in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.
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Affiliation(s)
- Timothy T Harden
- Department of Physics, Brandeis University, Waltham, MA, 02454, USA
| | | | | | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christopher D Wells
- Department of Microbiology, Blavatnick Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ann Hochschild
- Department of Microbiology, Blavatnick Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA, 02454, USA.
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA, 02454, USA.
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17
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Wang Y, Liang H, Chen G, Liao C, Wang Y, Hu Z, Xie Q. Molecular and Phylogenetic Analyses of the Mediator Subunit Genes in Solanum lycopersicum. Front Genet 2019; 10:1222. [PMID: 31827491 PMCID: PMC6892441 DOI: 10.3389/fgene.2019.01222] [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: 09/03/2019] [Accepted: 11/05/2019] [Indexed: 11/19/2022] Open
Abstract
The Mediator complex is a multi-subunit protein assembly that serves as a central scaffold to help regulate DNA-binding transcription factors (TFs) and RNA polymerase II (Pol II) activity controlled gene expression programmed in response to developmental or environmental factors. However, litter information about Mediator complex subunit (MED) genes in tomato is available, although it is an essential model plant. In this study, we retrieved 46 candidate SlMED genes from the genome of tomato, and a comprehensive analysis was conducted, including their phylogenetic relationship, chromosomal locations, gene structure, cis-regulatory elements prediction, as well as gene expression. The expression profiling of 46 SlMED genes was analyzed using publicly available RNA-seq data. Furthermore, we selected some SlMED genes to evaluate their expression patterns in various tissues and under different abiotic stress treatments by quantitative reverse transcription PCR experiments. This is the first detailed report to elucidate the molecular and phylogenetic features of the MED genes in tomato, and it provides valuable clues for further functional analysis in order to clarify the role of the SlMED genes in diverse plant growth, development and abiotic stress response.
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Affiliation(s)
- Yunshu Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Honglian Liang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Yicong Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, China
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18
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Xu Y, Man N, Karl D, Martinez C, Liu F, Sun J, Martinez CJ, Martin GM, Beckedorff F, Lai F, Yue J, Roisman A, Greenblatt S, Duffort S, Wang L, Sun X, Figueroa M, Shiekhattar R, Nimer S. TAF1 plays a critical role in AML1-ETO driven leukemogenesis. Nat Commun 2019. [PMID: 31664040 DOI: 10.1038/s41467-019-12735-z.pmid:31664040;pmcid:pmc6820555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
AML1-ETO (AE) is a fusion transcription factor, generated by the t(8;21) translocation, that functions as a leukemia promoting oncogene. Here, we demonstrate that TATA-Box Binding Protein Associated Factor 1 (TAF1) associates with K43 acetylated AE and this association plays a pivotal role in the proliferation of AE-expressing acute myeloid leukemia (AML) cells. ChIP-sequencing indicates significant overlap of the TAF1 and AE binding sites. Knockdown of TAF1 alters the association of AE with chromatin, affecting of the expression of genes that are activated or repressed by AE. Furthermore, TAF1 is required for leukemic cell self-renewal and its reduction promotes the differentiation and apoptosis of AE+ AML cells, thereby impairing AE driven leukemogenesis. Together, our findings reveal a role of TAF1 in leukemogenesis and identify TAF1 as a potential therapeutic target for AE-expressing leukemia.
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Affiliation(s)
- Ye Xu
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Medicine, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Na Man
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Daniel Karl
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Concepcion Martinez
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Fan Liu
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Jun Sun
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Camilo Jose Martinez
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Gloria Mas Martin
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Fan Lai
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Jingyin Yue
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Alejandro Roisman
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Sarah Greenblatt
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Stephanie Duffort
- Department of Medicine, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Lan Wang
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA.,Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojian Sun
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA.,State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Maria Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Stephen Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA. .,Department of Medicine, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA. .,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA.
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19
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Xu Y, Man N, Karl D, Martinez C, Liu F, Sun J, Martinez CJ, Martin GM, Beckedorff F, Lai F, Yue J, Roisman A, Greenblatt S, Duffort S, Wang L, Sun X, Figueroa M, Shiekhattar R, Nimer S. TAF1 plays a critical role in AML1-ETO driven leukemogenesis. Nat Commun 2019; 10:4925. [PMID: 31664040 PMCID: PMC6820555 DOI: 10.1038/s41467-019-12735-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
AML1-ETO (AE) is a fusion transcription factor, generated by the t(8;21) translocation, that functions as a leukemia promoting oncogene. Here, we demonstrate that TATA-Box Binding Protein Associated Factor 1 (TAF1) associates with K43 acetylated AE and this association plays a pivotal role in the proliferation of AE-expressing acute myeloid leukemia (AML) cells. ChIP-sequencing indicates significant overlap of the TAF1 and AE binding sites. Knockdown of TAF1 alters the association of AE with chromatin, affecting of the expression of genes that are activated or repressed by AE. Furthermore, TAF1 is required for leukemic cell self-renewal and its reduction promotes the differentiation and apoptosis of AE+ AML cells, thereby impairing AE driven leukemogenesis. Together, our findings reveal a role of TAF1 in leukemogenesis and identify TAF1 as a potential therapeutic target for AE-expressing leukemia. AML1-ETO is a fusion protein in which acetylation of lysine-43 is critical to leukemogenesis. Here, they show that TAF1 is required for AML1-ETO mediated gene expression such that it binds to acetylated AML1-ETO to facilitate the association of AML1-ETO with chromatin, and consequently, promotes leukemic self-renewal.
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Affiliation(s)
- Ye Xu
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Medicine, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Na Man
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Daniel Karl
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Concepcion Martinez
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Fan Liu
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Jun Sun
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Camilo Jose Martinez
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Gloria Mas Martin
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Fan Lai
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Jingyin Yue
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Alejandro Roisman
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Sarah Greenblatt
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Stephanie Duffort
- Department of Medicine, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Lan Wang
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA.,Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojian Sun
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA.,State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Maria Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA.,Department of Human Genetics, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA
| | - Stephen Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA. .,Department of Medicine, Miller School of Medicine, University of Miami, 1120 NW 14th St, Miami, FL, 33136, USA. .,Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL, 33136, USA.
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20
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Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
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Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
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21
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Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
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22
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Venters BJ. Insights from resolving protein-DNA interactions at near base-pair resolution. Brief Funct Genomics 2019; 17:80-88. [PMID: 29211822 DOI: 10.1093/bfgp/elx043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task. Since its introduction in 1985, chromatin immunoprecipitation (ChIP) has remained a key tool for investigating protein-DNA contacts in vivo. Over 30 years of intensive research using ChIP have provided numerous insights into mechanisms of gene regulation. As functional genomic technologies improve, they present new opportunities to address key biological questions. ChIP-exo is a refined version of ChIP-seq that significantly reduces background signal, while providing near base-pair mapping resolution for protein-DNA interactions. This review discusses the evolution of the ChIP assay over the years; the methodological differences between ChIP-seq, ChIP-exo and ChIP-nexus; and highlight new insights into epigenetic and transcriptional mechanisms that were uniquely enabled with the near base-pair resolution of ChIP-exo.
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Transcription initiation factor TBP: old friend new questions. Biochem Soc Trans 2019; 47:411-423. [DOI: 10.1042/bst20180623] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/14/2022]
Abstract
Abstract
In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.
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Abstract
A wide variety of factors are required for the conversion of pre-tRNA molecules into the mature tRNAs that function in translation. To identify factors influencing tRNA biogenesis, we previously performed a screen for strains carrying mutations that induce lethality when combined with a sup61-T47:2C allele, encoding a mutant form of [Formula: see text]. Analyzes of two complementation groups led to the identification of Tan1 as a protein involved in formation of the modified nucleoside N4-acetylcytidine (ac4C) in tRNA and Bud13 as a factor controlling the levels of ac4C by promoting TAN1 pre-mRNA splicing. Here, we describe the remaining complementation groups and show that they include strains with mutations in genes for known tRNA biogenesis factors that modify (DUS2, MOD5 and TRM1), transport (LOS1), or aminoacylate (SES1) [Formula: see text]. Other strains carried mutations in genes for factors involved in rRNA/mRNA synthesis (RPA49, RRN3 and MOT1) or magnesium uptake (ALR1). We show that mutations in not only DUS2, LOS1 and SES1 but also in RPA49, RRN3 and MOT1 cause a reduction in the levels of the altered [Formula: see text]. These results indicate that Rpa49, Rrn3 and Mot1 directly or indirectly influence [Formula: see text] biogenesis.
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Affiliation(s)
- Fu Xu
- a Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Yang Zhou
- a Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Anders S Byström
- a Department of Molecular Biology , Umeå University , Umeå , Sweden
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25
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Watanabe K, Kokubo T. SAGA mediates transcription from the TATA-like element independently of Taf1p/TFIID but dependent on core promoter structures in Saccharomyces cerevisiae. PLoS One 2017; 12:e0188435. [PMID: 29176831 PMCID: PMC5703507 DOI: 10.1371/journal.pone.0188435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/07/2017] [Indexed: 11/21/2022] Open
Abstract
In Saccharomyces cerevisiae, core promoters of class II genes contain a TATA element, either a TATA box (TATA[A/T]A[A/T][A/G]) or TATA-like element (1 or 2 bp mismatched version of the TATA box). The TATA element directs the assembly of the preinitiation complex (PIC) to ensure accurate transcriptional initiation. It has been proposed the PIC is assembled by two distinct pathways in which TBP is delivered by TFIID or SAGA, leading to the widely accepted model that these complexes mediate transcription mainly from TATA-like element- or TATA box-containing promoters, respectively. Although both complexes are involved in transcription of nearly all class II genes, it remains unclear how efficiently SAGA mediates transcription from TATA-like element-containing promoters independently of TFIID. We found that transcription from the TATA box-containing AGP1 promoter was greatly stimulated in a Spt3p-dependent manner after inactivation of Taf1p/TFIID. Thus, this promoter provides a novel experimental system in which to evaluate SAGA-mediated transcription from TATA-like element(s). We quantitatively measured transcription from various TATA-like elements in the Taf1p-dependent CYC1 promoter and Taf1p-independent AGP1 promoter. The results revealed that SAGA could mediate transcription from at least some TATA-like elements independently of Taf1p/TFIID, and that Taf1p-dependence or -independence is highly robust with respect to variation of the TATA sequence. Furthermore, chimeric promoter mapping revealed that Taf1p-dependence or independence was conferred by the upstream activating sequence (UAS), whereas Spt3p-dependent transcriptional stimulation after inactivation of Taf1p/TFIID was specific to the AGP1 promoter and dependent on core promoter regions other than the TATA box. These results suggest that TFIID and/or SAGA are regulated in two steps: the UAS first specifies TFIID or SAGA as the predominant factor on a given promoter, and then the core promoter structure guides the pertinent factor to conduct transcription in an appropriate manner.
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Affiliation(s)
- Kiyoshi Watanabe
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Tetsuro Kokubo
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
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27
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Harwig A, Landick R, Berkhout B. The Battle of RNA Synthesis: Virus versus Host. Viruses 2017; 9:v9100309. [PMID: 29065472 PMCID: PMC5691660 DOI: 10.3390/v9100309] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022] Open
Abstract
Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage.
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Affiliation(s)
- Alex Harwig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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Eychenne T, Werner M, Soutourina J. Toward understanding of the mechanisms of Mediator function in vivo: Focus on the preinitiation complex assembly. Transcription 2017; 8:328-342. [PMID: 28841352 DOI: 10.1080/21541264.2017.1329000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation.
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Affiliation(s)
- Thomas Eychenne
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France.,b Institut Pasteur, (Epi)genomics of Animal Development Unit , Development and Stem Cell Biology Department, CNRS UMR3778 , Paris , France
| | - Michel Werner
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
| | - Julie Soutourina
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
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29
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Xue Y, Pradhan SK, Sun F, Chronis C, Tran N, Su T, Van C, Vashisht A, Wohlschlegel J, Peterson CL, Timmers HTM, Kurdistani SK, Carey MF. Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals. Mol Cell 2017; 67:594-607.e4. [PMID: 28735899 DOI: 10.1016/j.molcel.2017.06.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/12/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023]
Abstract
Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 co-localize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs). In yeast, all three proteins bind subtelomeric heterochromatin through a Sir3-stimulated mechanism and to euchromatin via a TBP-stimulated mechanism. In mESCs, the proteins bind to active and poised TBP-bound promoters along with promoters of polycomb-silenced genes apparently lacking TBP. Depletion of Mot1, Ino80C, or NC2 by anchor away in yeast or RNAi in mESCs leads to near-identical transcriptome phenotypes, with new subtelomeric transcription in yeast, and greatly increased pervasive transcription in both yeast and mESCs.
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Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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30
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PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription. Sci Rep 2017; 7:45394. [PMID: 28345603 PMCID: PMC5366948 DOI: 10.1038/srep45394] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/22/2017] [Indexed: 12/23/2022] Open
Abstract
Transcription complexes that assemble at the HIV-1 promoter efficiently initiate transcription but generate paused RNA polymerase II downstream from the start site. The virally encoded Tat protein hijacks positive transcription elongation factor b (P-TEFb) to phosphorylate and activate this paused polymerase. In addition, Tat undergoes a series of reversible post-translational modifications that regulate distinct steps of the transcription cycle. To identify additional functionally important Tat cofactors, we performed RNAi knockdowns of sixteen previously identified Tat interactors and found that a novel E3 ligase, PJA2, ubiquitinates Tat in a non-degradative manner and specifically regulates the step of HIV transcription elongation. Interestingly, several different lysine residues in Tat can function as ubiquitin acceptor sites, and variable combinations of these lysines support both full transcriptional activity and viral replication. Further, the polyubiquitin chain conjugated to Tat by PJA2 can itself be assembled through variable ubiquitin lysine linkages. Importantly, proper ubiquitin chain assembly by PJA2 requires that Tat first binds its P-TEFb cofactor. These results highlight that both the Tat substrate and ubiquitin modification have plastic site usage, and this plasticity is likely another way in which the virus exploits the host molecular machinery to expand its limited genetic repertoire.
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31
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Asamitsu K, Hirokawa T, Okamoto T. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding. PLoS One 2017; 12:e0171727. [PMID: 28178316 PMCID: PMC5298246 DOI: 10.1371/journal.pone.0171727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/24/2017] [Indexed: 02/02/2023] Open
Abstract
In this study, we applied molecular dynamics (MD) simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs), lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.
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Grants
- Ministry of Education, Culture, Sports, Science, and Technology "The Platform Project for Supporting Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science)"
- Ministry of Education, Culture, Sports, Science, and Technology
- Asahi Grass Foundation
- Japan Agency for Medical Research and Development
- Junwakai Foundation
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (TH); (TO)
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
- * E-mail: (TH); (TO)
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Fuchs A, Torroba M, Kinkley S. PHF13: A new player involved in RNA polymerase II transcriptional regulation and co-transcriptional splicing. Transcription 2017; 8:106-112. [PMID: 28102760 DOI: 10.1080/21541264.2016.1274813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
We recently identified PHF13 as an H3K4me2/3 chromatin reader and transcriptional co-regulator. We found that PHF13 interacts with RNAPIIS5P and PRC2 stabilizing their association with active and bivalent promoters. Furthermore, mass spectrometry analysis identified ∼50 spliceosomal proteins in PHF13s interactome. Here, we will discuss the potential role of PHF13 in RNAPII pausing and co-transcriptional splicing.
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Affiliation(s)
- Alisa Fuchs
- a Max Planck Institute for Molecular Genetics , Berlin , Germany
| | - Marcos Torroba
- a Max Planck Institute for Molecular Genetics , Berlin , Germany
| | - Sarah Kinkley
- a Max Planck Institute for Molecular Genetics , Berlin , Germany
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Dugan A, Majmudar CY, Pricer R, Niessen S, Lancia JK, Fung HYH, Cravatt BF, Mapp AK. Discovery of Enzymatic Targets of Transcriptional Activators via in Vivo Covalent Chemical Capture. J Am Chem Soc 2016; 138:12629-35. [PMID: 27611834 PMCID: PMC5217703 DOI: 10.1021/jacs.6b07680] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The network of activator protein-protein interactions (PPIs) that underpin transcription initiation is poorly defined, particularly in the cellular context. The transient nature of these contacts and the often low abundance of the participants present significant experimental hurdles. Through the coupling of in vivo covalent chemical capture and shotgun LC-MS/MS (MuDPIT) analysis, we can trap the PPIs of transcriptional activators in a cellular setting and identify the binding partners in an unbiased fashion. Using this approach, we discover that the prototypical activators Gal4 and VP16 target the Snf1 (AMPK) kinase complex via direct interactions with both the core enzymatic subunit Snf1 and the exchangeable subunit Gal83. Further, we use a tandem reversible formaldehyde and irreversible covalent chemical capture approach (TRIC) to capture the Gal4-Snf1 interaction at the Gal1 promoter in live yeast. Together, these data support a critical role for activator PPIs in both the recruitment and positioning of important enzymatic complexes at a gene promoter and represent a technical advancement in the discovery of new cellular binding targets of transcriptional activators.
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Affiliation(s)
- Amanda Dugan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chinmay Y. Majmudar
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel Pricer
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sherry Niessen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jody K. Lancia
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hugo Yik-Hong Fung
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Anna K. Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Mück F, Bracharz S, Marschalek R. DDX6 transfers P-TEFb kinase to the AF4/AF4N (AFF1) super elongation complex. AMERICAN JOURNAL OF BLOOD RESEARCH 2016; 6:28-45. [PMID: 27679741 PMCID: PMC5030405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/19/2016] [Indexed: 06/06/2023]
Abstract
AF4/AFF1 and AF5/AFF4 are both backbones for the assembly of "super elongation complexes" (SECs) that exert 2 distinct functions after the recruitment of P-TEFb from the 7SK snRNP: (1) initiation and elongation of RNA polymerase II gene transcription, and (2) modification of transcribed gene regions by distinct histone methylation patterns. In this study we aimed to investigate one of the initial steps, namely how P-TEFb is transferred from 7SK snRNPs to the SECs. In particular, we were interested in the role of DDX6 that we have recently identified as part of the AF4 complex. DDX6 is an evolutionarily conserved member of the DEAD-box RNA helicase family that is known to control miRNA and mRNA biology (translation, storage and degradation). Overexpressed DDX6 is associated with different cancer types and with c-Myc protein overexpression. We could demonstrate that DDX6 binds to 7SK snRNA and causes the release and transfer of P-TEFb to the AF4/AF4N SEC. DDX6 also binds stably to AF4 and AF4N as demonstrated by GST pull-down and co-immunoprecipitation experiments. As a consequence, overexpression of either AF4/AF4N or DDX6 resulted in a strong increase of mRNA production (5-6 fold), while their simultaneous expression increased the cellular mRNA production by 11-fold. Conversely, the corresponding knockdown of DDX6 decreased mRNA production by 70%. In conclusion, AF4/AF4N and DDX6 represent key molecules for the elongation process of gene transcription and a model will be proposed for the hand-over process of P-TEFb to SECs.
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Affiliation(s)
- Fabian Mück
- Institute of Pharmaceutical Biology/DCAL, Goethe-University of Frankfurt, Biocenter Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Silvia Bracharz
- Institute of Pharmaceutical Biology/DCAL, Goethe-University of Frankfurt, Biocenter Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University of Frankfurt, Biocenter Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
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Ahn JH, Rechsteiner A, Strome S, Kelly WG. A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans. PLoS Genet 2016; 12:e1006227. [PMID: 27541139 PMCID: PMC4991786 DOI: 10.1371/journal.pgen.1006227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023] Open
Abstract
The elongation phase of transcription by RNA Polymerase II (Pol II) involves numerous events that are tightly coordinated, including RNA processing, histone modification, and chromatin remodeling. RNA splicing factors are associated with elongating Pol II, and the interdependent coupling of splicing and elongation has been documented in several systems. Here we identify a conserved, multi-domain cyclophilin family member, SIG-7, as an essential factor for both normal transcription elongation and co-transcriptional splicing. In embryos depleted for SIG-7, RNA levels for over a thousand zygotically expressed genes are substantially reduced, Pol II becomes significantly reduced at the 3' end of genes, marks of transcription elongation are reduced, and unspliced mRNAs accumulate. Our findings suggest that SIG-7 plays a central role in both Pol II elongation and co-transcriptional splicing and may provide an important link for their coordination and regulation.
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Affiliation(s)
- Jeong H. Ahn
- Biology Department, Emory University, Atlanta, Georgia, United States of America
- Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, United States of America
| | - Andreas Rechsteiner
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - William G. Kelly
- Biology Department, Emory University, Atlanta, Georgia, United States of America
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A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting. Nat Commun 2016; 7:12248. [PMID: 27461529 PMCID: PMC4974459 DOI: 10.1038/ncomms12248] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Live-cell imaging has revealed unexpected features of gene expression. Here using improved single-molecule RNA microscopy, we show that synthesis of HIV-1 RNA is achieved by groups of closely spaced polymerases, termed convoys, as opposed to single isolated enzymes. Convoys arise by a Mediator-dependent reinitiation mechanism, which generates a transient but rapid succession of polymerases initiating and escaping the promoter. During elongation, polymerases are spaced by few hundred nucleotides, and physical modelling suggests that DNA torsional stress may maintain polymerase spacing. We additionally observe that the HIV-1 promoter displays stochastic fluctuations on two time scales, which we refer to as multi-scale bursting. Each time scale is regulated independently: Mediator controls minute-scale fluctuation (convoys), while TBP-TATA-box interaction controls sub-hour fluctuations (long permissive/non-permissive periods). A cellular promoter also produces polymerase convoys and displays multi-scale bursting. We propose that slow, TBP-dependent fluctuations are important for phenotypic variability of single cells. HIV-1 viral gene expression stochastically switches between active and inactive states. Here, using improved single molecule RNA microscopy, the authors show that HIV-1 RNA stochastic transcription is achieved by groups of closely spaced polymerases, and is regulated by Mediator and TBP at different time scales.
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37
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Steinhäuser SS, Andrésson ÓS, Pálsson A, Werth S. Fungal and cyanobacterial gene expression in a lichen symbiosis: Effect of temperature and location. Fungal Biol 2016; 120:1194-208. [PMID: 27647237 DOI: 10.1016/j.funbio.2016.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/27/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Organisms have evolved different cellular mechanisms to deal with environmental stress, primarily through complex molecular mechanisms including protein refolding and DNA repair. As mutualistic symbioses, lichens offer the possibility of analyzing molecular stress responses in a particularly tight interspecific relationship. We study the widespread cyanolichen Peltigera membranacea, a key player in carbon and nitrogen cycling in terrestrial ecosystems at northern latitudes. We ask whether increased temperature is reflected in mRNA levels of selected damage control genes, and do the response patterns show geographical associations? Using real-time PCR quantification of 38 transcripts, differential expression was demonstrated for nine cyanobacterial and nine fungal stress response genes (plus the fungal symbiosis-related lec2 gene) when the temperature was increased from 5 °C to 15 °C and 25 °C. Principle component analysis (PCA) revealed two gene groups with different response patterns. Whereas a set of cyanobacterial DNA repair genes and the fungal lec2 (PC1 group) showed an expression drop at 15 °C vs. 5 °C, most fungal candidates (PC2 group) showed increased expression at 25 °C vs. 5 °C. PC1 responses also correlated with elevation. The correlated downregulation of lec2 and cyanobacterial DNA repair genes suggests a possible interplay between the symbionts warranting further studies.
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Affiliation(s)
- Sophie S Steinhäuser
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Ólafur S Andrésson
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Arnar Pálsson
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Silke Werth
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland; Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria.
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38
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Asamitsu K, Omagari K, Okuda T, Hibi Y, Okamoto T. Quantification of the HIV transcriptional activator complex in live cells by image-based protein-protein interaction analysis. Genes Cells 2016; 21:706-16. [PMID: 27193293 DOI: 10.1111/gtc.12375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/17/2016] [Indexed: 01/16/2023]
Abstract
The virus-encoded Tat protein is essential for HIV transcription in infected cells. The interaction of Tat with the cellular transcription elongation factor P-TEFb (positive transcriptional elongation factor b) containing cyclin T1 (CycT1) and cyclin-dependent kinase 9 (CDK9) is critical for its activity. In this study, we use the Fluoppi (fluorescent-based technology detecting protein-protein interaction) system, which enables the quantification of interactions between biomolecules, such as proteins, in live cells. Quantitative measurement of the molecular interactions among Tat, CycT1 and CDK9 has showed that any third molecule enhances the binding between the other two molecules. These findings suggest that each component of the Tat:P-TEFb complex stabilizes the overall complex, thereby supporting the efficient transcriptional elongation during viral RNA synthesis. These interactions may serve as appropriate targets for novel anti-HIV therapy.
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Katsumi Omagari
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Tomoya Okuda
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Yurina Hibi
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
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39
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Abstract
RNA polymerase II (Pol II) pausing at promoter-proximal regions is a highly regulated step in the transcription cycle. Pause release is facilitated by the P-TEFb kinase, which phosphorylates Pol II and negative elongation factors. Recent studies suggest that P-TEFb (as part of the inhibitory 7SK snRNP) is recruited to promoter-proximal regions through interaction with KAP1/TRIM28/TIF1β to facilitate 'on-site' kinase activation and transcription elongation. Here, I discuss features of this model and future challenges to further hone our understanding of transcriptional regulation including Pol II pausing and pause release.
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Affiliation(s)
- Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
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40
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Gómez-Navarro N, Jordán-Pla A, Estruch F, E Pérez-Ortín J. Defects in the NC2 repressor affect both canonical and non-coding RNA polymerase II transcription initiation in yeast. BMC Genomics 2016; 17:183. [PMID: 26939779 PMCID: PMC4778323 DOI: 10.1186/s12864-016-2536-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/25/2016] [Indexed: 11/24/2022] Open
Abstract
Background The formation of the pre-initiation complex in eukaryotic genes is a key step in transcription initiation. The TATA-binding protein (TBP) is a universal component of all pre-initiation complexes for all kinds of RNA polymerase II (RNA pol II) genes, including those with a TATA or a TATA-like element, both those that encode proteins and those that transcribe non-coding RNAs. Mot1 and the negative cofactor 2 (NC2) complex are regulators of TBP, and it has been shown that depletion of these factors in yeast leads to defects in the control of transcription initiation that alter cryptic transcription levels in selected yeast loci. Results In order to cast light on the molecular functions of NC2, we performed genome-wide studies in conditional mutants in yeast NC2 essential subunits Ydr1 and Bur6. Our analyses show a generally increased level of cryptic transcription in all kinds of genes upon depletion of NC2 subunits, and that each kind of gene (canonical or ncRNAs, TATA or TATA-like) shows some differences in the cryptic transcription pattern for each NC2 mutant. Conclusions We conclude that NC2 plays a general role in transcription initiation in RNA polymerase II genes that is related with its known TBP interchange function from free to promoter bound states. Therefore, loss of the NC2 function provokes increases in cryptic transcription throughout the yeast genome. Our results also suggest functional differences between NC2 subunits Ydr1 and Bur6.
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Affiliation(s)
- Natalia Gómez-Navarro
- Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain. .,Present address: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Antonio Jordán-Pla
- Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain. .,Present address: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Francisco Estruch
- Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain.
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain.
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41
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Ravarani CNJ, Chalancon G, Breker M, de Groot NS, Babu MM. Affinity and competition for TBP are molecular determinants of gene expression noise. Nat Commun 2016; 7:10417. [PMID: 26832815 PMCID: PMC4740812 DOI: 10.1038/ncomms10417] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
Cell-to-cell variation in gene expression levels (noise) generates phenotypic diversity and is an important phenomenon in evolution, development and disease. TATA-box binding protein (TBP) is an essential factor that is required at virtually every eukaryotic promoter to initiate transcription. While the presence of a TATA-box motif in the promoter has been strongly linked with noise, the molecular mechanism driving this relationship is less well understood. Through an integrated analysis of multiple large-scale data sets, computer simulation and experimental validation in yeast, we provide molecular insights into how noise arises as an emergent property of variable binding affinity of TBP for different promoter sequences, competition between interaction partners to bind the same surface on TBP (to either promote or disrupt transcription initiation) and variable residence times of TBP complexes at a promoter. These determinants may be fine-tuned under different conditions and during evolution to modulate eukaryotic gene expression noise.
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Affiliation(s)
- Charles N J Ravarani
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guilhem Chalancon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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42
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The mRNA cap-binding protein Cbc1 is required for high and timely expression of genes by promoting the accumulation of gene-specific activators at promoters. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:405-19. [PMID: 26775127 DOI: 10.1016/j.bbagrm.2016.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/15/2022]
Abstract
The highly conserved Saccharomyces cerevisiae cap-binding protein Cbc1/Sto1 binds mRNA co-transcriptionally and acts as a key coordinator of mRNA fate. Recently, Cbc1 has also been implicated in transcription elongation and pre-initiation complex (PIC) formation. Previously, we described Cbc1 to be required for cell growth under osmotic stress and to mediate osmostress-induced translation reprogramming. Here, we observe delayed global transcription kinetics in cbc1Δ during osmotic stress that correlates with delayed recruitment of TBP and RNA polymerase II to osmo-induced promoters. Interestingly, we detect an interaction between Cbc1 and the MAPK Hog1, which controls most gene expression changes during osmostress, and observe that deletion of CBC1 delays the accumulation of the activator complex Hot1-Hog1 at osmostress promoters. Additionally, CBC1 deletion specifically reduces transcription rates of highly transcribed genes under non-stress conditions, such as ribosomal protein (RP) genes, while having low impact on transcription of weakly expressed genes. For RP genes, we show that recruitment of the specific activator Rap1, and subsequently TBP, to promoters is Cbc1-dependent. Altogether, our results indicate that binding of Cbc1 to the capped mRNAs is necessary for the accumulation of specific activators as well as PIC components at the promoters of genes whose expression requires high and rapid transcription.
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43
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Gudipaty SA, D’Orso I. Functional interplay between PPM1G and the transcription elongation machinery. RNA & DISEASE 2016; 3:e1215. [PMID: 27088130 PMCID: PMC4830430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transcription elongation is a critical regulatory step in the gene expression cycle. One key regulator of the switch between transcription initiation and elongation is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) and several negative elongation factors to relieve the elongation block at paused promoters to facilitate productive elongation. Here, we highlight recent findings signifying the role of the PPM1G/PP2Cγ phosphatase in activating and maintaining the active transcription elongation state by regulating the availability of P-TEFb and blocking its assembly into the catalytic inactive 7SK small nuclear ribonucleoprotein (snRNP) complex.
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Affiliation(s)
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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44
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Rodríguez-Lima O, García-Gutierrez P, Jiménez L, Zarain-Herzberg Á, Lazzarini R, Landa A. Molecular Cloning of a cDNA Encoding for Taenia solium TATA-Box Binding Protein 1 (TsTBP1) and Study of Its Interactions with the TATA-Box of Actin 5 and Typical 2-Cys Peroxiredoxin Genes. PLoS One 2015; 10:e0141818. [PMID: 26529408 PMCID: PMC4631506 DOI: 10.1371/journal.pone.0141818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
TATA-box binding protein (TBP) is an essential regulatory transcription factor for the TATA-box and TATA-box-less gene promoters. We report the cloning and characterization of a full-length cDNA that encodes a Taenia solium TATA-box binding protein 1 (TsTBP1). Deduced amino acid composition from its nucleotide sequence revealed that encodes a protein of 238 residues with a predicted molecular weight of 26.7 kDa, and a theoretical pI of 10.6. The NH2-terminal domain shows no conservation when compared with to pig and human TBP1s. However, it shows high conservation in size and amino acid identity with taeniids TBP1s. In contrast, the TsTBP1 COOH-terminal domain is highly conserved among organisms, and contains the amino acids involved in interactions with the TATA-box, as well as with TFIIA and TFIIB. In silico TsTBP1 modeling reveals that the COOH-terminal domain forms the classical saddle structure of the TBP family, with one α-helix at the end, not present in pig and human. Native TsTBP1 was detected in T. solium cysticerci´s nuclear extract by western blot using rabbit antibodies generated against two synthetic peptides located in the NH2 and COOH-terminal domains of TsTBP1. These antibodies, through immunofluorescence technique, identified the TBP1 in the nucleus of cells that form the bladder wall of cysticerci of Taenia crassiceps, an organism close related to T. solium. Electrophoretic mobility shift assays using nuclear extracts from T. solium cysticerci and antibodies against the NH2-terminal domain of TsTBP1 showed the interaction of native TsTBP1 with the TATA-box present in T. solium actin 5 (pAT5) and 2-Cys peroxiredoxin (Ts2-CysPrx) gene promoters; in contrast, when antibodies against the anti-COOH-terminal domain of TsTBP1 were used, they inhibited the binding of TsTBP1 to the TATA-box of the pAT5 promoter gene.
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Affiliation(s)
- Oscar Rodríguez-Lima
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | | | - Lucía Jiménez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Roberto Lazzarini
- Departamento de Biología Experimental, Universidad Autónoma Metropolitana–Iztapalapa, México D.F., México
| | - Abraham Landa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
- * E-mail:
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45
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Dieci G, Fermi B, Bosio MC. Investigating transcription reinitiation through in vitro approaches. Transcription 2015; 5:e27704. [PMID: 25764113 DOI: 10.4161/trns.27704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By influencing the number of RNA molecules repeatedly synthesized from the same gene, the control of transcription reinitiation has the potential to shape the transcriptome. Transcription reinitiation mechanisms have been mainly addressed in vitro, through approaches based on both crude and reconstituted systems. These studies support the notion that transcription reinitiation and its regulation rely on dedicated networks of molecular interactions within transcription machineries. At the same time, comparison with in vivo transcription rates suggests that additional mechanisms, factors and conditions must exist in the nucleus, whose biochemical elucidation is a fascinating challenge for future in vitro transcription studies.
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Affiliation(s)
- Giorgio Dieci
- a Dipartimento di Bioscienze; Università degli Studi di Parma; Parma, Italy
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46
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Shir-Shapira H, Sharabany J, Filderman M, Ideses D, Ovadia-Shochat A, Mannervik M, Juven-Gershon T. Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation. J Biol Chem 2015; 290:17293-305. [PMID: 26018075 DOI: 10.1074/jbc.m114.632109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Indexed: 11/06/2022] Open
Abstract
Regulation of RNA polymerase II transcription is critical for the proper development, differentiation, and growth of an organism. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters encompass the RNA start site and consist of functional elements such as the TATA box, initiator, and downstream core promoter element (DPE), which confer specific properties to the core promoter. We have previously discovered that Drosophila Caudal, which is a master regulator of genes involved in development and differentiation, is a DPE-specific transcriptional activator. Here, we show that the mouse Caudal-related homeobox (Cdx) proteins (mCdx1, mCdx2, and mCdx4) are also preferential core promoter transcriptional activators. To elucidate the mechanism that enables Caudal to preferentially activate DPE transcription, we performed structure-function analysis. Using a systematic series of deletion mutants (all containing the intact DNA-binding homeodomain) we discovered that the C-terminal region of Caudal contributes to the preferential activation of the fushi tarazu (ftz) Caudal target gene. Furthermore, the region containing both the homeodomain and the C terminus of Caudal was sufficient to confer core promoter-preferential activation to the heterologous GAL4 DNA-binding domain. Importantly, we discovered that Drosophila CREB-binding protein (dCBP) is a co-activator for Caudal-regulated activation of ftz. Strikingly, dCBP conferred the ability to preferentially activate the DPE-dependent ftz reporter to mini-Caudal proteins that were unable to preferentially activate ftz transcription themselves. Taken together, it is the unique combination of dCBP and Caudal that enables the co-activation of ftz in a core promoter-preferential manner.
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Affiliation(s)
- Hila Shir-Shapira
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Julia Sharabany
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Matan Filderman
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Diana Ideses
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Avital Ovadia-Shochat
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
| | - Mattias Mannervik
- The Wenner-Gren Institute, Developmental Biology, Stockholm University, Arrhenius Laboratories E3, SE-106 91 Stockholm, Sweden
| | - Tamar Juven-Gershon
- From The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel and
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47
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Koster M, Snel B, Timmers H. Genesis of Chromatin and Transcription Dynamics in the Origin of Species. Cell 2015; 161:724-36. [DOI: 10.1016/j.cell.2015.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 11/15/2022]
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48
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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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49
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Bick MJ, Malik S, Mustaev A, Darst SA. TFIIB is only ∼9 Å away from the 5'-end of a trimeric RNA primer in a functional RNA polymerase II preinitiation complex. PLoS One 2015; 10:e0119007. [PMID: 25774659 PMCID: PMC4361453 DOI: 10.1371/journal.pone.0119007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022] Open
Abstract
Recent X-ray crystallographic studies of Pol II in complex with the general transcription factor (GTF) IIB have begun to provide insights into the mechanism of transcription initiation. These structures have also shed light on the architecture of the transcription preinitiation complex (PIC). However, structural characterization of a functional PIC is still lacking, and even the topological arrangement of the GTFs in the Pol II complex is a matter of contention. We have extended our activity-based affinity crosslinking studies, initially developed to investigate the interaction of bacterial RNA polymerase with σ, to the eukaryotic transcription machinery. Towards that end, we sought to identify GTFs that are within the Pol II active site in a functioning PIC. We provide biochemical evidence that TFIIB is located within ∼9 Å of the -2 site of promoter DNA, where it is positioned to play a role in de novo transcription initiation.
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Affiliation(s)
- Matthew J. Bick
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States of America
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, United States of America
| | - Arkady Mustaev
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, United States of America
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States of America
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50
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Murry JP, Godoy J, Mukim A, Swann J, Bruce JW, Ahlquist P, Bosque A, Planelles V, Spina CA, Young JAT. Sulfonation pathway inhibitors block reactivation of latent HIV-1. Virology 2014; 471-473:1-12. [PMID: 25310595 DOI: 10.1016/j.virol.2014.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/16/2014] [Accepted: 08/18/2014] [Indexed: 12/12/2022]
Abstract
Long-lived pools of latently infected cells are a significant barrier to the development of a cure for HIV-1 infection. A better understanding of the mechanisms of reactivation from latency is needed to facilitate the development of novel therapies that address this problem. Here we show that chemical inhibitors of the sulfonation pathway prevent virus reactivation, both in latently infected J-Lat and U1 cell lines and in a primary human CD4+ T cell model of latency. In each of these models, sulfonation inhibitors decreased transcription initiation from the HIV-1 promoter. These inhibitors block transcription initiation at a step that lies downstream of nucleosome remodeling and affects RNA polymerase II recruitment to the viral promoter. These results suggest that the sulfonation pathway acts by a novel mechanism to regulate efficient virus transcription initiation during reactivation from latency, and further that augmentation of this pathway could be therapeutically useful.
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Affiliation(s)
- Jeffrey P Murry
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Joseph Godoy
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Amey Mukim
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Justine Swann
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - James W Bruce
- Morgridge Institute for Research, Madison, WI, USA; Institute for Molecular Virology, University of Wisconsin, Madison, WI, USA; McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Ahlquist
- Morgridge Institute for Research, Madison, WI, USA; Institute for Molecular Virology, University of Wisconsin, Madison, WI, USA; McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alberto Bosque
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Vicente Planelles
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Celsa A Spina
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA; Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - John A T Young
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
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