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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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52
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Prince TL, Lang BJ, Guerrero-Gimenez ME, Fernandez-Muñoz JM, Ackerman A, Calderwood SK. HSF1: Primary Factor in Molecular Chaperone Expression and a Major Contributor to Cancer Morbidity. Cells 2020; 9:E1046. [PMID: 32331382 PMCID: PMC7226471 DOI: 10.3390/cells9041046] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023] Open
Abstract
Heat shock factor 1 (HSF1) is the primary component for initiation of the powerful heat shock response (HSR) in eukaryotes. The HSR is an evolutionarily conserved mechanism for responding to proteotoxic stress and involves the rapid expression of heat shock protein (HSP) molecular chaperones that promote cell viability by facilitating proteostasis. HSF1 activity is amplified in many tumor contexts in a manner that resembles a chronic state of stress, characterized by high levels of HSP gene expression as well as HSF1-mediated non-HSP gene regulation. HSF1 and its gene targets are essential for tumorigenesis across several experimental tumor models, and facilitate metastatic and resistant properties within cancer cells. Recent studies have suggested the significant potential of HSF1 as a therapeutic target and have motivated research efforts to understand the mechanisms of HSF1 regulation and develop methods for pharmacological intervention. We review what is currently known regarding the contribution of HSF1 activity to cancer pathology, its regulation and expression across human cancers, and strategies to target HSF1 for cancer therapy.
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Affiliation(s)
- Thomas L. Prince
- Department of Molecular Functional Genomics, Geisinger Clinic, Danville, PA 17821, USA
| | - Benjamin J. Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Martin E. Guerrero-Gimenez
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Buenos Aires B1657, Argentina
| | - Juan Manuel Fernandez-Muñoz
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Buenos Aires B1657, Argentina
| | - Andrew Ackerman
- Department of Molecular Functional Genomics, Geisinger Clinic, Danville, PA 17821, USA
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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53
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Kindgren P, Ivanov M, Marquardt S. Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis. Nucleic Acids Res 2020; 48:2332-2347. [PMID: 31863587 PMCID: PMC7049701 DOI: 10.1093/nar/gkz1189] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 01/12/2023] Open
Abstract
Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal RNAPII stalling in predisposing genes for transcriptional activation during plant-environment interactions. At gene 3'-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.
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Affiliation(s)
- Peter Kindgren
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Frederiksberg, Denmark
| | - Maxim Ivanov
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Frederiksberg, Denmark
| | - Sebastian Marquardt
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Frederiksberg, Denmark
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54
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Zicari S, Sharma AL, Sahu G, Dubrovsky L, Sun L, Yue H, Jada T, Ochem A, Simon G, Bukrinsky M, Tyagi M. DNA dependent protein kinase (DNA-PK) enhances HIV transcription by promoting RNA polymerase II activity and recruitment of transcription machinery at HIV LTR. Oncotarget 2020; 11:699-726. [PMID: 32133046 PMCID: PMC7041937 DOI: 10.18632/oncotarget.27487] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/29/2020] [Indexed: 01/24/2023] Open
Abstract
Despite reductions in mortality from the use of highly active antiretroviral therapy (HAART), the presence of latent or transcriptionally silent proviruses prevents HIV cure/eradication. We have previously reported that DNA-dependent protein kinase (DNA-PK) facilitates HIV transcription by interacting with the RNA polymerase II (RNAP II) complex recruited at HIV LTR. In this study, using different cell lines and peripheral blood mononuclear cells (PBMCs) of HIV-infected patients, we found that DNA-PK stimulates HIV transcription at several stages, including initiation, pause-release and elongation. We are reporting for the first time that DNA-PK increases phosphorylation of RNAP II C-terminal domain (CTD) at serine 5 (Ser5) and serine 2 (Ser2) by directly catalyzing phosphorylation and by augmenting the recruitment of the positive transcription elongation factor (P-TEFb) at HIV LTR. Our findings suggest that DNA-PK expedites the establishment of euchromatin structure at HIV LTR. DNA-PK inhibition/knockdown leads to the severe impairment of HIV replication and reactivation of latent HIV provirus. DNA-PK promotes the recruitment of Tripartite motif-containing 28 (TRIM28) at LTR and assists the release of paused RNAP II through TRIM28 phosphorylation. These results provide the mechanisms through which DNA-PK controls the HIV gene expression and, likely, can be extended to cellular gene expression, including during cell malignancy, where the role of DNA-PK has been well-established.
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Affiliation(s)
- Sonia Zicari
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.,Section of Intercellular Interactions, Eunice-Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Department of Pediatric Medicine, The Bambino Gesù Children's Hospital, Rome, Italy.,These authors contributed equally to this work
| | - Adhikarimayum Lakhikumar Sharma
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.,These authors contributed equally to this work
| | - Geetaram Sahu
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA.,These authors contributed equally to this work
| | - Larisa Dubrovsky
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC 20037, USA
| | - Lin Sun
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Han Yue
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Tejaswi Jada
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Alex Ochem
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Wernher and Beit Building (South), Observatory 7925, Cape Town, South Africa
| | - Gary Simon
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Michael Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC 20037, USA
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.,Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA.,Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC 20037, USA
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55
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Kauzlaric A, Jang SM, Morchikh M, Cassano M, Planet E, Benkirane M, Trono D. KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190334. [PMID: 32068487 PMCID: PMC7061982 DOI: 10.1098/rstb.2019.0334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation, notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
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Affiliation(s)
- Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mehdi Morchikh
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France.,Institute of Molecular Genetics of Montpellier, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Marco Cassano
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Monsef Benkirane
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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56
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Luo ZZ, Sun HM, Guo JW, Luo P, Hu CQ, Huang W, Shu H. Molecular characterization of a RNA polymerase (RNAP) II (DNA directed) polypeptide H (POLR2H) in Pacific white shrimp (Litopenaeus vannamei) and its role in response to high-pH stress. FISH & SHELLFISH IMMUNOLOGY 2020; 96:245-253. [PMID: 31830564 DOI: 10.1016/j.fsi.2019.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/26/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
RNA polymerase (RNAP) II (DNA-directed) (POLR2) genes are essential for cell viability under environmental stress and for the transfer of biological information from DNA to RNA. However, the function and characteristics of POLR2 genes in crustaceans are still unknown. In the present study, a POLR2H cDNA was isolated from Pacific white shrimp (Litopenaeus vannamei) and designated as Lv-POLR2H. The full-length Lv-POLR2H cDNA is 772 bp in length and contains a 32-bp 5'- untranslated region (UTR), a 284-bp 3'- UTR with a poly (A) sequence, and an open reading frame (ORF) of 456 bp encoding an Lv-POLR2H protein of 151 amino acids with a deduced molecular weight of 17.21 kDa. The Lv-POLR2H protein only contains one functional domain, harbors no transmembrane domains and mainly locates in the nucleus. The expression of the Lv-POLR2H mRNA was ubiquitously detected in all selected tissues, with the highest level in the gills. In situ hybridization (ISH) analysis showed that Lv-POLR2H was mainly located in the secondary gill filaments, the transcript levels of Lv-POLR2H in the gills were found to be significantly affected after challenge by pH, low salinity and high concentrations of NO2- and NH4+, indicating that Lv-POLR2H in gill tissues might play roles under various physical stresses. Specifically, under high-pH stress, knockdown of Lv-POLR2H via siRNA significantly decreased the survival rate of the shrimp, indicating its key roles in the response to high-pH stress. Our study may provide the first evidence of the role of POLR2H in shrimp responding to high-pH stress and provides new insight into molecular regulation in response to high pH in crustaceans.
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Affiliation(s)
- Zhi-Zhan Luo
- School of Life Science/School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China; Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hui-Ming Sun
- School of Life Science/School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jing-Wen Guo
- School of Life Science/School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Chao-Qun Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wen Huang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China; CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Hu Shu
- School of Life Science/School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
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57
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Affiliation(s)
- Soyeon Jeon
- Department of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sang-Hyeop Lee
- Department of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jaechul Roh
- Department of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jang-Eok Kim
- Department of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Heeyoun Bunch
- Department of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, Republic of Korea
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58
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Critical role for TRIM28 and HP1β/γ in the epigenetic control of T cell metabolic reprograming and effector differentiation. Proc Natl Acad Sci U S A 2019; 116:25839-25849. [PMID: 31776254 PMCID: PMC6925996 DOI: 10.1073/pnas.1901639116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
CD4 T cells are major regulators of immune responses against both self and pathogens. Understanding pathways that govern CD4 T cell differentiation and regulation are thus key for the discovery of new immunoregulatory drug targets. Here, we have identified an epigenetic pathway that regulates the expression of a set of proteins that determine T cell responsiveness. By silencing enhancers distal to a set of genes known to be involved in regulatory T cell function, the epigenetic modifiers TRIM28 and HP1β/γ regulate T cell receptor signaling. This leads to defective metabolic reprograming and inefficient effector differentiation of naive T cells. This mechanism provides an exciting opportunity to regulate T cell responsivity in both autoimmunity and T cell-based immunodeficiencies. Naive CD4+ T lymphocytes differentiate into different effector types, including helper and regulatory cells (Th and Treg, respectively). Heritable gene expression programs that define these effector types are established during differentiation, but little is known about the epigenetic mechanisms that install and maintain these programs. Here, we use mice defective for different components of heterochromatin-dependent gene silencing to investigate the epigenetic control of CD4+ T cell plasticity. We show that, upon T cell receptor (TCR) engagement, naive and regulatory T cells defective for TRIM28 (an epigenetic adaptor for histone binding modules) or for heterochromatin protein 1 β and γ isoforms (HP1β/γ, 2 histone-binding factors involved in gene silencing) fail to effectively signal through the PI3K–AKT–mTOR axis and switch to glycolysis. While differentiation of naive TRIM28−/− T cells into cytokine-producing effector T cells is impaired, resulting in reduced induction of autoimmune colitis, TRIM28−/− regulatory T cells also fail to expand in vivo and to suppress autoimmunity effectively. Using a combination of transcriptome and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses for H3K9me3, H3K9Ac, and RNA polymerase II, we show that reduced effector differentiation correlates with impaired transcriptional silencing at distal regulatory regions of a defined set of Treg-associated genes, including, for example, NRP1 or Snai3. We conclude that TRIM28 and HP1β/γ control metabolic reprograming through epigenetic silencing of a defined set of Treg-characteristic genes, thus allowing effective T cell expansion and differentiation into helper and regulatory phenotypes.
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59
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Takii R, Fujimoto M, Matsumoto M, Srivastava P, Katiyar A, Nakayama KI, Nakai A. The pericentromeric protein shugoshin 2 cooperates with HSF1 in heat shock response and RNA Pol II recruitment. EMBO J 2019; 38:e102566. [PMID: 31657478 DOI: 10.15252/embj.2019102566] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/17/2022] Open
Abstract
The recruitment of RNA polymerase II (Pol II) to core promoters is highly regulated during rapid induction of genes. In response to heat shock, heat shock transcription factor 1 (HSF1) is activated and occupies heat shock gene promoters. Promoter-bound HSF1 recruits general transcription factors and Mediator, which interact with Pol II, but stress-specific mechanisms of Pol II recruitment are unclear. Here, we show in comparative analyses of HSF1 paralogs and their mutants that HSF1 interacts with the pericentromeric adaptor protein shugoshin 2 (SGO2) during heat shock in mouse cells, in a manner dependent on inducible phosphorylation of HSF1 at serine 326, and recruits SGO2 to the HSP70 promoter. SGO2-mediated binding and recruitment of Pol II with a hypophosphorylated C-terminal domain promote expression of HSP70, implicating SGO2 as one of the coactivators that facilitate Pol II recruitment by HSF1. Furthermore, the HSF1-SGO2 complex supports cell survival and maintenance of proteostasis in heat shock conditions. These results exemplify a proteotoxic stress-specific mechanism of Pol II recruitment, which is triggered by phosphorylation of HSF1 during the heat shock response.
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Affiliation(s)
- Ryosuke Takii
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Mitsuaki Fujimoto
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Masaki Matsumoto
- Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Pratibha Srivastava
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Arpit Katiyar
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Keiich I Nakayama
- Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akira Nakai
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
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60
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Ding S, Zhang Y, Hu Z, Huang X, Zhang B, Lu Q, Wen X, Wang Y, Lu C. mTERF5 Acts as a Transcriptional Pausing Factor to Positively Regulate Transcription of Chloroplast psbEFLJ. MOLECULAR PLANT 2019; 12:1259-1277. [PMID: 31128276 DOI: 10.1016/j.molp.2019.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/22/2019] [Accepted: 05/16/2019] [Indexed: 05/21/2023]
Abstract
RNA polymerase transcriptional pausing represents a major checkpoint in transcription in bacteria and metazoans, but it is unknown whether this phenomenon occurs in plant organelles. Here, we report that transcriptional pausing occurs in chloroplasts. We found that mTERF5 specifically and positively regulates the transcription of chloroplast psbEFLJ in Arabidopsis thaliana that encodes four key subunits of photosystem II. We found that mTERF5 causes the plastid-encoded RNA polymerase (PEP) complex to pause at psbEFLJ by binding to the +30 to +51 region of double-stranded DNA. Moreover, we revealed that mTERF5 interacts with pTAC6, an essential subunit of the PEP complex, although pTAC6 is not involved in the transcriptional pausing at psbEFLJ. We showed that mTERF5 recruits additional pTAC6 to the transcriptionally paused region of psbEFLJ, and the recruited pTAC6 proteins could be assembled into the PEP complex to regulate psbEFLJ transcription. Taken together, our findings shed light on the role of transcriptional pausing in chloroplast transcription in plants.
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Affiliation(s)
- Shunhua Ding
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yi Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Hu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bohan Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingtao Lu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaogang Wen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yingchun Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
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61
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Fonti G, Marcaida MJ, Bryan LC, Träger S, Kalantzi AS, Helleboid PYJ, Demurtas D, Tully MD, Grudinin S, Trono D, Fierz B, Dal Peraro M. KAP1 is an antiparallel dimer with a functional asymmetry. Life Sci Alliance 2019; 2:2/4/e201900349. [PMID: 31427381 PMCID: PMC6701479 DOI: 10.26508/lsa.201900349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 01/10/2023] Open
Abstract
This study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1. KAP1 (KRAB domain–associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 small ubiquitin modifier ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering data, integrative modeling, and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with an asymmetry at the C-terminal domains. This conformation is consistent with the finding that the Really Interesting New Gene (RING) domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
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Affiliation(s)
- Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Louise C Bryan
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra S Kalantzi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pierre-Yves Jl Helleboid
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Davide Demurtas
- Interdisciplinary Centre for Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mark D Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Sergei Grudinin
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Inria, Grenoble Institut Polytechnique de Grenoble, Laboratoire Jean Kuntzmann, Grenoble, France
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Gressel S, Schwalb B, Cramer P. The pause-initiation limit restricts transcription activation in human cells. Nat Commun 2019; 10:3603. [PMID: 31399571 PMCID: PMC6689055 DOI: 10.1038/s41467-019-11536-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/18/2019] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic gene transcription is often controlled at the level of RNA polymerase II (Pol II) pausing in the promoter-proximal region. Pausing Pol II limits the frequency of transcription initiation ('pause-initiation limit'), predicting that the pause duration must be decreased for transcriptional activation. To test this prediction, we conduct a genome-wide kinetic analysis of the heat shock response in human cells. We show that the pause-initiation limit restricts transcriptional activation at most genes. Gene activation generally requires the activity of the P-TEFb kinase CDK9, which decreases the duration of Pol II pausing and thereby enables an increase in the productive initiation frequency. The transcription of enhancer elements is generally not pause limited and can be activated without CDK9 activity. Our results define the kinetics of Pol II transcriptional regulation in human cells at all gene classes during a natural transcription response.
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Affiliation(s)
- Saskia Gressel
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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63
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Jung YH, Kremsky I, Gold HB, Rowley MJ, Punyawai K, Buonanotte A, Lyu X, Bixler BJ, Chan AWS, Corces VG. Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo. Mol Cell 2019; 75:154-171.e5. [PMID: 31056445 PMCID: PMC6625867 DOI: 10.1016/j.molcel.2019.04.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/02/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022]
Abstract
The epigenetic information present in mammalian gametes and whether it is transmitted to the progeny are relatively unknown. We find that many promoters in mouse sperm are occupied by RNA polymerase II (Pol II) and Mediator. The same promoters are accessible in GV and MII oocytes and preimplantation embryos. Sperm distal ATAC-seq sites containing motifs for various transcription factors are conserved in monkeys and humans. ChIP-seq analyses confirm that Foxa1, ERα, and AR occupy distal enhancers in sperm. Accessible sperm enhancers containing H3.3 and H2A.Z are also accessible in oocytes and preimplantation embryos. Furthermore, their interactions with promoters in the gametes persist during early development. Sperm- or oocyte-specific interactions mediated by CTCF and cohesin are only present in the paternal or maternal chromosomes, respectively, in the zygote and 2-cell stages. These interactions converge in both chromosomes by the 8-cell stage. Thus, mammalian gametes contain complex patterns of 3D interactions that can be transmitted to the zygote after fertilization.
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Affiliation(s)
- Yoon Hee Jung
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Isaac Kremsky
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Hannah B Gold
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - M Jordan Rowley
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Kanchana Punyawai
- Yerkes National Primate Research Center, 954 Gatewood Rd. NE, Atlanta, GA 39329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, USA
| | - Alyx Buonanotte
- Yerkes National Primate Research Center, 954 Gatewood Rd. NE, Atlanta, GA 39329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA
| | - Xiaowen Lyu
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Brianna J Bixler
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA
| | - Anthony W S Chan
- Yerkes National Primate Research Center, 954 Gatewood Rd. NE, Atlanta, GA 39329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA.
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64
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Bi X, Xu Y, Li T, Li X, Li W, Shao W, Wang K, Zhan G, Wu Z, Liu W, Lu JY, Wang L, Zhao J, Wu J, Na J, Li G, Li P, Shen X. RNA Targets Ribogenesis Factor WDR43 to Chromatin for Transcription and Pluripotency Control. Mol Cell 2019; 75:102-116.e9. [DOI: 10.1016/j.molcel.2019.05.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 01/09/2019] [Accepted: 04/16/2019] [Indexed: 11/30/2022]
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Abstract
In this review, Core et al. discuss the recent advances in our understanding of the early steps in Pol II transcription, highlighting the events and factors involved in the establishment and release of paused Pol II. They also discuss a number of unanswered questions about the regulation and function of Pol II pausing. Precise spatio–temporal control of gene activity is essential for organismal development, growth, and survival in a changing environment. Decisive steps in gene regulation involve the pausing of RNA polymerase II (Pol II) in early elongation, and the controlled release of paused polymerase into productive RNA synthesis. Here we describe the factors that enable pausing and the events that trigger Pol II release into the gene. We also discuss open questions in the field concerning the stability of paused Pol II, nucleosomes as obstacles to elongation, and potential roles of pausing in defining the precision and dynamics of gene expression.
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Affiliation(s)
- Leighton Core
- Department of Molecular and Cell Biology, Institute of Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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66
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Gooding AJ, Parker KA, Valadkhan S, Schiemann WP. The IncRNA BORG: A novel inducer of TNBC metastasis, chemoresistance, and disease recurrence. ACTA ACUST UNITED AC 2019; 5. [PMID: 31435529 DOI: 10.20517/2394-4722.2019.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although greater than 90% of breast cancer-related mortality can be attributed to metastases, the molecular mechanisms underpinning the dissemination of primary breast tumor cells and their ability to establish malignant lesions in distant tissues remain incompletely understood. Genomic and transcriptomic analyses identified a class of transcripts called long noncoding RNA (lncRNA), which interact both directly and indirectly with key components of gene regulatory networks to alter cell proliferation, invasion, and metastasis. We identified a pro-metastatic lncRNA BORG whose aberrant expression promotes metastatic relapse by reactivating proliferative programs in dormant disseminated tumor cells (DTCs). BORG expression is broadly and strongly induced by environmental and chemotherapeutic stresses, a transcriptional response that facilitates the survival of DTCs. Transcriptomic reprogramming in response to BORG resulted in robust signaling via survival and viability pathways, as well as decreased activation of cell death pathways. As such, BORG expression acts as a (i) marker capable of predicting which breast cancer patients are predisposed to develop secondary metastatic lesions, and (ii) unique therapeutic target to maximize chemosensitivity of DTCs. Here we review the molecular and cellular factors that contribute to the pathophysiological activities of BORG during its regulation of breast cancer metastasis, chemoresistance, and disease recurrence.
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Affiliation(s)
- Alex J Gooding
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kimberly A Parker
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
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67
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Bunch H, Choe H, Kim J, Jo DS, Jeon S, Lee S, Cho DH, Kang K. P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes. Front Genet 2019; 10:342. [PMID: 31068966 PMCID: PMC6491683 DOI: 10.3389/fgene.2019.00342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/29/2019] [Indexed: 01/16/2023] Open
Abstract
Many non-coding RNAs (ncRNAs) serve as regulatory molecules in various physiological pathways, including gene expression in mammalian cells. Distinct from protein-coding RNA expression, ncRNA expression is regulated solely by transcription and RNA processing/stability. It is thus important to understand transcriptional regulation in ncRNA genes but is yet to be known completely. Previously, we identified that a subset of mammalian ncRNA genes is transcriptionally regulated by RNA polymerase II (Pol II) promoter-proximal pausing and in a tissue-specific manner. In this study, human ncRNA genes that are expressed in the early G1 phase, termed immediate early ncRNA genes, were monitored to assess the function of positive transcription elongation factor b (P-TEFb), a master Pol II pausing regulator for protein-coding genes, in ncRNA transcription. Our findings indicate that the expression of many ncRNA genes is induced in the G0–G1 transition and regulated by P-TEFb. Interestingly, a biphasic characteristic of P-TEFb-dependent transcription of serum responsive ncRNA genes was observed: Pol II carboxyl-terminal domain phosphorylated at serine 2 (S2) was largely increased in the transcription start site (TSS, -300 to +300) whereas overall, it was decreased in the gene body (GB, > +350) upon chemical inhibition of P-TEFb. In addition, the three representative, immediate early ncRNAs, whose expression is dependent on P-TEFb, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), nuclear enriched abundant transcript 1 (NEAT1), and X-inactive specific transcript (XIST), were further analyzed for determining P-TEFb association. Taken together, our data suggest that transcriptional activation of many human ncRNAs utilizes the pausing and releasing of Pol II, and that the regulatory mechanism of transcriptional elongation in these genes requires the function of P-TEFb. Furthermore, we propose that ncRNA and mRNA transcription are regulated by similar mechanisms while P-TEFb inhibition unexpectedly increases S2 Pol II phosphorylation in the TSSs in many ncRNA genes. One Sentence Summary: P-TEFb regulates Pol II phosphorylation for transcriptional activation in many stimulus-inducible ncRNA genes.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Hyeseung Choe
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Jongbum Kim
- Department of Transcriptome & Epigenome, Macrogen Incorporated, Seoul, South Korea
| | - Doo Sin Jo
- Institute of Life Science and Biotechnology, College of Natural Science, Kyungpook National University, Daegu, South Korea
| | - Soyeon Jeon
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Sanghwa Lee
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Dong-Hyung Cho
- Department of Life Science, College of Natural Science, Kyungpook National University, Daegu, South Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, South Korea
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68
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Lee J, Crickard JB, Reese JC, Lee TH. Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II. Methods 2019; 159-160:51-58. [PMID: 30660864 PMCID: PMC6589119 DOI: 10.1016/j.ymeth.2019.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/07/2019] [Accepted: 01/14/2019] [Indexed: 12/27/2022] Open
Abstract
Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.
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Affiliation(s)
- Jaehyoun Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - J Brooks Crickard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Joseph C Reese
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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69
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Morton EL, Forst CV, Zheng Y, DePaula-Silva AB, Ramirez NGP, Planelles V, D'Orso I. Transcriptional Circuit Fragility Influences HIV Proviral Fate. Cell Rep 2019; 27:154-171.e9. [PMID: 30943398 PMCID: PMC6461408 DOI: 10.1016/j.celrep.2019.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/14/2018] [Accepted: 02/28/2019] [Indexed: 01/12/2023] Open
Abstract
Transcriptional circuit architectures in several organisms have been evolutionarily selected to dictate precise given responses. Unlike these cellular systems, HIV is regulated through a complex circuit composed of two successive phases (host and viral), which create a positive feedback loop facilitating viral replication. However, it has long remained unclear whether both phases operate identically and to what extent the host phase influences the entire circuit. Here, we report that, although the host phase is regulated by a checkpoint whereby KAP1 mediates transcription activation, the virus evolved a minimalist system bypassing KAP1. Given the complex circuit's architecture, cell-to-cell KAP1 fluctuations impart heterogeneity in the host transcriptional responses, thus affecting the feedback loop. Mathematical modeling of a complete circuit reveals how these oscillations ultimately influence homogeneous reactivation potential of a latent virus. Thus, although HIV drives molecular innovation to fuel robust gene activation, it experiences transcriptional fragility, thereby influencing viral fate and cure efforts.
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Affiliation(s)
- Emily L Morton
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yue Zheng
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ana B DePaula-Silva
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nora-Guadalupe P Ramirez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Iván D'Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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70
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Aprile-Garcia F, Tomar P, Hummel B, Khavaran A, Sawarkar R. Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells. Nat Struct Mol Biol 2019; 26:137-146. [DOI: 10.1038/s41594-018-0182-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
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72
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Abstract
SummaryTRIM28/KAP1/TIF1β was identified as a universal transcriptional co-repressor and is critical for regulating post-fertilization methylation reprogramming in preimplantation embryos. In this study, three siRNAs (si647, si742, and si1153) were designed to target the TRIM28 mRNA sequence. After transfection of the mixture of the three siRNA (siMix) into bovine fibroblast cells, the most effective one for TRIM28 knockdown was selected. By injecting RNAi directed against TRIM28 mRNA, we found that TRIM28 knockdown in oocytes had the most effect on the H19 gene, in which differentially methylated region (DMR) methylation was almost completely absent at the 2-cell stage (1.4%), while control embryos showed 74% methylation. In addition, global H3K9me3 levels at the 2-cell stage were significantly higher in the in vitro fertilization (IVF) group than in the TRIM28 knockdown group (P<0.05). We further show that TRIM28 is highly expressed during oocyte maturation and reaches peak levels at the 2-cell stage. In contrast, at this stage, TRIM28 expression in somatic cell nuclear transfer (SCNT) embryos decreased significantly (P<0.05), suggesting that Trim28 transcripts are lost during SCNT. TRIM28 is required for the maintenance of methylation imprints in bovine preimplantation embryos, and the loss of TRIM28 during SCNT may contribute to the unfaithful maintenance of imprints in cloned embryos.
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73
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Ma X, Yang T, Luo Y, Wu L, Jiang Y, Song Z, Pan T, Liu B, Liu G, Liu J, Yu F, He Z, Zhang W, Yang J, Liang L, Guan Y, Zhang X, Li L, Cai W, Tang X, Gao S, Deng K, Zhang H. TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb. eLife 2019; 8:42426. [PMID: 30652970 PMCID: PMC6361614 DOI: 10.7554/elife.42426] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
Comprehensively elucidating the molecular mechanisms of human immunodeficiency virus type 1 (HIV-1) latency is a priority to achieve a functional cure. As current 'shock' agents failed to efficiently reactivate the latent reservoir, it is important to discover new targets for developing more efficient latency-reversing agents (LRAs). Here, we found that TRIM28 potently suppresses HIV-1 expression by utilizing both SUMO E3 ligase activity and epigenetic adaptor function. Through global site-specific SUMO-MS study and serial SUMOylation assays, we identified that P-TEFb catalytic subunit CDK9 is significantly SUMOylated by TRIM28 with SUMO4. The Lys44, Lys56 and Lys68 residues on CDK9 are SUMOylated by TRIM28, which inhibits CDK9 kinase activity or prevents P-TEFb assembly by directly blocking the interaction between CDK9 and Cyclin T1, subsequently inhibits viral transcription and contributes to HIV-1 latency. The manipulation of TRIM28 and its consequent SUMOylation pathway could be the target for developing LRAs. The human immunodeficiency virus-1, or HIV-1, infects certain human cells, including white blood cells. One reason the infection is incurable is because the virus can integrate its genetic information into its host, and essentially ‘sleep’ within the host cell, a process called latency. This helps to hide HIV-1 from the immune system and stops it getting destroyed. Latency represents a critical challenge in treating and curing HIV-1. One proposed cure for HIV-1 involves ‘shocking’ the viruses out of latency so that they can be eliminated. Applying this so-called shock and kill approach means scientists need to understand more about how latency is maintained. Previous evidence shows that latency requires proteins known as histone deacetylases and histone methyltransferases. Certain gene-silencing proteins called transcription suppressors are also involved. Ma et al. have now examined latent HIV-1 in several kinds of human cells grown in the laboratory. The cells were modified to make certain proteins at much lower levels than normal. The experiments showed that the loss of a protein called TRIM28 ‘wakes up’ latent HIV-1. TRIM28 attaches chemical marks called SUMOylations to gene regulators in the cell. These SUMOylations restrict the activity of HIV-1’s genes, which is important to maintain latency. Specifically, TRIM28 adds SUMOylations to a protein named CDK9 at three key positions. Reducing the levels of TRIM28 made it easier to shock many HIV-1 in infected cells out of latency. With further investigation, targeting TRIM28 may one day be used to treat HIV-1 infection through a shock and kill method.
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Affiliation(s)
- Xiancai Ma
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tao Yang
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuewen Luo
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liyang Wu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yawen Jiang
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zheng Song
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ting Pan
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bingfeng Liu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guangyan Liu
- College of Basic Medical Sciences, Shenyang Medical College, Shenyang, China
| | - Jun Liu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fei Yu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhangping He
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wanying Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinyu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liting Liang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuanjun Guan
- Core Laboratory Platform for Medical Science, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xu Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Xiaoping Tang
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kai Deng
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Fernandez-Marrero Y, Bachmann D, Lauber E, Kaufmann T. Negative Regulation of BOK Expression by Recruitment of TRIM28 to Regulatory Elements in Its 3' Untranslated Region. iScience 2018; 9:461-474. [PMID: 30471638 PMCID: PMC6260365 DOI: 10.1016/j.isci.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023] Open
Abstract
BCL-2-related ovarian killer (BOK) is a pro-apoptotic BAX-like member of the BCL-2 family with suggested tumor suppressor activity. The molecular mechanisms regulating BOK expression are poorly understood and fail to explain a frequent lack of concordance between protein and transcript levels. Here, we describe a potent post-transcriptional mechanism that negatively regulates BOK expression mediated by conserved (AU/U)-rich elements within its 3’ UTR. Using proteomics approaches we identified TRIM28 as a key component associating with U-rich elements in the human BOK 3’ UTR, resulting in a dramatic reduction of BOK expression. TRIM28 is overexpressed in several cancers, correlating with poor patient outcome, whereas the BOK locus is frequently deleted or its expression downregulated in human cancers. Data mining indicated that, for certain cancers, high TRIM28 and low BOK expression are significantly correlated in the stratum of patients with the worst survival, suggesting that this mechanism might be of potential therapeutic value. BOK mRNA is destabilized by AU-(mouse) or U-rich (human) elements within its 3’ UTR Mutation of these ARE/URE sequences results in increased BOK RNA and protein levels TRIM28 represses BOK expression by associating with the UREs of human BOK mRNA Inverse correlation of TRIM28 and BOK levels predicts survival in selected cancers
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Affiliation(s)
- Yuniel Fernandez-Marrero
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Daniel Bachmann
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Emanuel Lauber
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Thomas Kaufmann
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland.
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75
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Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell 2018; 174:391-405.e19. [PMID: 29937225 PMCID: PMC6046266 DOI: 10.1016/j.cell.2018.05.043] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 01/07/2023]
Abstract
Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or "junk DNA." The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ESC self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA, and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1, and peri-nucleolar chromatin in the regulation of transcription, developmental potency, and ESC self-renewal.
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Affiliation(s)
- Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- The University of Edinburgh, MRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Yafei Yin
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel A Peixoto
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steffen Biechele
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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76
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Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH. Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. Genome Biol 2018; 19:89. [PMID: 30001206 PMCID: PMC6042338 DOI: 10.1186/s13059-018-1463-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/13/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of high propensity to form stable DNA secondary structure across the human genome using Mfold and ViennaRNA programs with parameters for analyzing DNA. RESULTS The promoter-proximal regions of genes with paused transcription are significantly and energetically more favorable to form DNA secondary structure than non-paused genes or genes without RNA polymerase II (Pol II) binding. Using Pol II ChIP-seq, GRO-seq, NET-seq, and mNET-seq data, we arrive at a robust set of criteria for Pol II pausing, independent of annotation, and find that a highly stable secondary structure is likely to form about 10-50 nucleotides upstream of a Pol II pausing site. Structure probing data confirm the existence of DNA secondary structures enriched at the promoter-proximal regions of paused genes in human cells. Using an in vitro transcription assay, we demonstrate that Pol II pausing at HSPA1B, a human heat shock gene, is affected by manipulating DNA secondary structure upstream of the pausing site. CONCLUSIONS Our results indicate alternative DNA secondary structure formation as a mechanism for how GC-rich sequences regulate RNA Pol II promoter-proximal pausing genome-wide.
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Affiliation(s)
- Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | - Ryan G Thys
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | | | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA.
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA.
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77
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Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA, Beli P. p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Nat Commun 2018. [PMID: 29523821 PMCID: PMC5845016 DOI: 10.1038/s41467-018-03417-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ultraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV-light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here we employ quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA-binding proteins as primary substrates and 14-3-3 as direct readers of p38-MK2-dependent phosphorylation induced by UV light. Mechanistically, we show that MK2 phosphorylates the RNA-binding subunit of the NELF complex NELFE on Serine 115. NELFE phosphorylation promotes the recruitment of 14-3-3 and rapid dissociation of the NELF complex from chromatin, which is accompanied by RNA polymerase II elongation. UV-light-induced DNA damage affects RNA metabolism but the underlying signalling pathways are largely unexplored. Here, the authors show that UV light triggers p38-MK2-mediated phosphorylation of the NELF complex, promoting its release from chromatin and concurrent transcriptional elongation.
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Affiliation(s)
- Marina E Borisova
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Maxim A X Tollenaere
- Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark
| | - Sanjeeb Kumar Sahu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Nastasja Kreim
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Niels Mailand
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics and Cell Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark
| | - Masato Akutsu
- Institute of Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von Laue-Strasse 15, 60438, Frankfurt, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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78
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Murshid A, Prince TL, Lang B, Calderwood SK. Role of Heat Shock Factors in Stress-Induced Transcription. Methods Mol Biol 2018; 1709:23-34. [PMID: 29177648 DOI: 10.1007/978-1-4939-7477-1_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Heat shock proteins (HSP) are rapidly induced after stresses such as heat shock and accumulate at high concentrations in cells. HSP induction involves primarily a family of heat shock transcription factors (HSF) that bind the heat shock elements of the HSP genes and mediate transcription in trans. We discuss methods for the study of HSP binding to HSP promoters and the consequent increases in HSP gene expression in vitro and in vivo.
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Affiliation(s)
- Ayesha Murshid
- Molecular and Cellular Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA
| | - Thomas L Prince
- Department of Urology, Weis Center for Research, Geisinger Clinic, Danville, PA, 17822, USA
| | - Ben Lang
- Molecular and Cellular Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA.
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79
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Abstract
The heat shock response (HSR) is a cellular mechanism for counteracting acute proteotoxic stress. In eukaryotes, transcriptional activation of the HSR is regulated by heat shock factor 1 (HSF1). Activation of HSF1 induces the expression of heat shock proteins (HSPs) that function as molecular chaperones to fold and maintain the three-dimensional structure of misfolded proteins. The regulation of the degree and duration of the HSR is controlled by multiple biochemical mechanisms that include posttranslational modification of HSF1 and numerous protein-protein interactions. In this chapter, we describe a method to evaluate the activation and deactivation of the HSR at the transcriptional level using a short half-life luciferase reporter assay. This assay can be used to further characterize the HSR or as a screen for small-molecule inducers, amplifiers, or repressors.
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80
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RNA polymerase II pausing and transcriptional regulation of the HSP70 expression. Eur J Cell Biol 2017; 96:739-745. [DOI: 10.1016/j.ejcb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 08/16/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022] Open
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81
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Boulianne B, Feldhahn N. Transcribing malignancy: transcription-associated genomic instability in cancer. Oncogene 2017; 37:971-981. [DOI: 10.1038/onc.2017.402] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022]
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82
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Galganski L, Urbanek MO, Krzyzosiak WJ. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res 2017; 45:10350-10368. [PMID: 28977640 PMCID: PMC5737799 DOI: 10.1093/nar/gkx759] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022] Open
Abstract
The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.
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Affiliation(s)
- Lukasz Galganski
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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83
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Gooding AJ, Zhang B, Jahanbani FK, Gilmore HL, Chang JC, Valadkhan S, Schiemann WP. The lncRNA BORG Drives Breast Cancer Metastasis and Disease Recurrence. Sci Rep 2017; 7:12698. [PMID: 28983112 PMCID: PMC5629202 DOI: 10.1038/s41598-017-12716-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as potent regulators of breast cancer development and progression, including the metastatic spread of disease. Through in silico and biological analyses, we identified a novel lncRNA, BMP/OP-Responsive Gene (BORG), whose expression directly correlates with aggressive breast cancer phenotypes, as well as with metastatic competence and disease recurrence in multiple clinical cohorts. Mechanistically, BORG elicits the metastatic outgrowth of latent breast cancer cells by promoting the localization and transcriptional repressive activity of TRIM28, which binds BORG and induces substantial alterations in carcinoma proliferation and survival. Moreover, inhibiting BORG expression in metastatic breast cancer cells impedes their metastatic colonization of the lungs of mice, implying that BORG acts as a novel driver of the genetic and epigenetic alterations that underlie the acquisition of metastatic and recurrent phenotypes by breast cancer cells.
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Affiliation(s)
- Alex J Gooding
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Bing Zhang
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Fereshteh Kenari Jahanbani
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Hannah L Gilmore
- Department of Pathology, University Hospitals, Case Medical Center and Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jenny C Chang
- Houston Methodist Research Center, Houston, TX, 77030, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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84
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Bunch H. Gene regulation of mammalian long non-coding RNA. Mol Genet Genomics 2017; 293:1-15. [PMID: 28894972 DOI: 10.1007/s00438-017-1370-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported. Transcription of lncRNAs utilizes some transcription factors and mechanisms shared in that of protein-coding genes. In addition, tissue specificity in lncRNA gene expression has been shown. LncRNAs play essential roles in regulating the expression of neighboring or distal genes through different mechanisms. This leads to the implication of lncRNAs in a wide variety of biological pathways and pathological development. In this review, the newly discovered transcription mechanisms, characteristics, and functions of lncRNA are discussed.
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Affiliation(s)
- Heeyoun Bunch
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Agriculture & Life Sciences Building 1, Room 207, 80 Dae-Hak Ro, Daegu, Republic of Korea.
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85
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Czerwińska P, Mazurek S, Wiznerowicz M. The complexity of TRIM28 contribution to cancer. J Biomed Sci 2017; 24:63. [PMID: 28851455 PMCID: PMC5574234 DOI: 10.1186/s12929-017-0374-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/24/2017] [Indexed: 01/07/2023] Open
Abstract
Since the first discovery in 1996, the engagement of TRIM28 in distinct aspects of cellular biology has been extensively studied resulting in identification of a complex nature of TRIM28 protein. In this review, we summarize core biological functions of TRIM28 that emerge from TRIM28 multi-domain structure and possessed enzymatic activities. Moreover, we will discuss whether the complexity of TRIM28 engagement in cancer biology makes TRIM28 a possible candidate for targeted anti-cancer therapy. Briefly, we will demonstrate the role of TRIM28 in regulation of target gene transcription, response to DNA damage, downregulation of p53 activity, stimulation of epithelial-to-mesenchymal transition, stemness sustainability, induction of autophagy and regulation of retrotransposition, to provide the answer whether TRIM28 functions as a stimulator or inhibitor of tumorigenesis. To date, number of studies demonstrate significant upregulation of TRIM28 expression in cancer tissues which correlates with worse overall patient survival, suggesting that TRIM28 supports cancer progression. Here, we present distinct aspects of TRIM28 involvement in regulation of cancer cell homeostasis which collectively imply pro-tumorigenic character of TRIM28. Thorough analyses are further needed to verify whether TRIM28 possess the potential to become a new anti-cancer target.
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Affiliation(s)
- Patrycja Czerwińska
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866, Poznan, Poland. .,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.
| | - Sylwia Mazurek
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Wiznerowicz
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
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86
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Wang Y, Li J, Huang Y, Dai X, Liu Y, Liu Z, Wang Y, Wang N, Zhang P. Tripartite motif-containing 28 bridges endothelial inflammation and angiogenic activity by retaining expression of TNFR-1 and -2 and VEGFR2 in endothelial cells. FASEB J 2017; 31:2026-2036. [PMID: 28159803 DOI: 10.1096/fj.201600988rr] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/17/2017] [Indexed: 11/11/2022]
Abstract
Angiogenesis and inflammation are regarded as important factors in the pathogenesis of chronic inflammation, cancer, and wound healing. Recent studies have supported prior evidence that common signaling pathways are involved in angiogenesis and inflammatory responses; however, key factors controlling both processes remain unclear. Although tripartite motif-containing (TRIM)-28 is known to have an immunosuppressive role in immune cells, its expression level and role in endothelial cells (ECs) are still unclear. In this study, we investigated the role of TRIM28 in inflammatory responses and angiogenic activity of ECs for the first time. We showed that TRIM28 is the most abundant TRIM family member and is localized in nuclei of ECs. Small interfering RNA-mediated knockdown of TRIM28 strikingly suppressed expression of TNF receptor (TNFR)-1 and -2, decreased TNF-α-induced phosphorylation of IKKα/β and IκBα and degradation of IκBα and nuclear translocation of p65, and suppressed basal level and TNF-α-induced expression of chemokines and adhesion molecules, including VCAM-1, IL-6, ICAM-1, E-selectin, and monocyte chemoattractant protein (MCP)-1. Unexpectedly, IL-8 was potentiated by TRIM28 knockdown in ECs in an NF-κB-inducing kinase-dependent manner. Meanwhile, knockdown of TRIM28 inhibited expression of VEGF receptor 2 and suppressed VEGF-induced proliferation and tube formation by ECs. Finally, knockdown of TRIM28 suppressed recruitment of ECs in vivo in a murine synthetic basement membrane model. In summary, we found that TRIM28 acts as a central factor in controlling endothelial inflammatory responses and angiogenic activities by retaining expression of TNFR-1 and -2 and VEGF receptor 2 in ECs.-Wang, Y., Li, J., Huang Y., Dai, X., Liu, Y., Liu, Z., Wang, Y., Wang, N., Zhang, P. Tripartite motif-containing 28 bridges endothelial inflammation and angiogenic activity by retaining expression of TNFR1 and -2 and VEGFR2 in endothelial cells.
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Affiliation(s)
- Yinfang Wang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jinping Li
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yitong Huang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiuqin Dai
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Youbin Liu
- Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zongjun Liu
- Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, Florida, USA; and
| | - Nanping Wang
- The Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Peng Zhang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China;
- Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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87
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Niskanen EA, Palvimo JJ. Chromatin SUMOylation in heat stress: To protect, pause and organise?: SUMO stress response on chromatin. Bioessays 2017; 39. [PMID: 28440894 DOI: 10.1002/bies.201600263] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Post-translational modifications, e.g. SUMO modifications (SUMOylation), provide a mechanism for swiftly changing a protein's activity. Various stress conditions trigger a SUMO stress response (SSR) - a stress-induced rapid change in the conjugation of SUMO to multiple proteins, which predominantly targets nuclear proteins. The SSR has been postulated to protect stressed cells by preserving the functionality of crucial proteins. However, it is unclear how it exerts its protective functions. Interestingly, heat stress (HS) increases SUMOylation of proteins at active promoters and enhancers. In promoters, HS-induced SUMOylation correlates with gene transcription and stress-induced RNA polymerase II (Pol2) pausing. Conversely, a disappearance of SUMOylation in HS occurs at chromatin anchor points that maintain chromatin-looping structures and the spatial organisation of chromatin. In reviewing the literature, we hypothesise that the SSR regulates Pol2 pausing by modulating the interactions of pausing-regulating proteins, whereas deSUMOylation alters the function of chromatin anchors.
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Affiliation(s)
- Einari A Niskanen
- University of Eastern Finland, Institute of Biomedicine, Kuopio, Finland
| | - Jorma J Palvimo
- University of Eastern Finland, Institute of Biomedicine, Kuopio, Finland
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88
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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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89
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Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA. O-GlcNAcase Is an RNA Polymerase II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1β. J Biol Chem 2016; 291:22703-22713. [PMID: 27601472 DOI: 10.1074/jbc.m116.751420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/29/2016] [Indexed: 12/24/2022] Open
Abstract
We describe here the identification and functional characterization of the enzyme O-GlcNAcase (OGA) as an RNA polymerase II elongation factor. Using in vitro transcription elongation assays, we show that OGA activity is required for elongation in a crude nuclear extract system, whereas in a purified system devoid of OGA the addition of rOGA inhibited elongation. Furthermore, OGA is physically associated with the known RNA polymerase II (pol II) pausing/elongation factors SPT5 and TRIM28-KAP1-TIF1β, and a purified OGA-SPT5-TIF1β complex has elongation properties. Lastly, ChIP-seq experiments show that OGA maps to the transcriptional start site/5' ends of genes, showing considerable overlap with RNA pol II, SPT5, TRIM28-KAP1-TIF1β, and O-GlcNAc itself. These data all point to OGA as a component of the RNA pol II elongation machinery regulating elongation genome-wide. Our results add a novel and unexpected dimension to the regulation of elongation by the insertion of O-GlcNAc cycling into the pol II elongation regulatory dynamics.
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Affiliation(s)
- Melissa Resto
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Bong-Hyun Kim
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Alfonso G Fernandez
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Brian J Abraham
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, and.,Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Keji Zhao
- Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Brian A Lewis
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893,
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90
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RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes. Genomics 2016; 108:64-77. [PMID: 27432546 DOI: 10.1016/j.ygeno.2016.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/11/2016] [Accepted: 07/14/2016] [Indexed: 01/13/2023]
Abstract
Mammalian genomes encode a large number of non-coding RNAs (ncRNAs) that greatly exceed mRNA genes. While the physiological and pathological roles of ncRNAs have been increasingly understood, the mechanisms of regulation of ncRNA expression are less clear. Here, our genomic study has shown that a significant number of long non-coding RNAs (lncRNAs, >1000 nucleotides) harbor RNA polymerase II (Pol II) engaged with the transcriptional start site. A pausing and transcriptional elongation factor for protein-coding genes, tripartite motif-containing 28 (TRIM28) regulates the transcription of a subset of lncRNAs in mammalian cells. In addition, the majority of lncRNAs in human and murine cells regulated by Pol II promoter-proximal pausing appear to function in stimulus-inducible biological pathways. Our findings suggest an important role of Pol II pausing for the transcription of mammalian lncRNA genes.
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91
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Tripartite motif containing 28 (TRIM28) promotes breast cancer metastasis by stabilizing TWIST1 protein. Sci Rep 2016; 6:29822. [PMID: 27412325 PMCID: PMC4944148 DOI: 10.1038/srep29822] [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: 09/14/2015] [Accepted: 06/27/2016] [Indexed: 12/16/2022] Open
Abstract
TRIM28 regulates its target genes at both transcriptional and posttranscriptional levels. Here we report that a TRIM28-TWIST1-EMT axis exists in breast cancer cells and TRIM28 promotes breast cancer metastasis by stabilizing TWIST1 and subsequently enhancing EMT. We find that TRIM28 is highly expressed in both cancer cell lines and advanced breast cancer tissues, and the levels of TRIM28 and TWIST1 are positively correlated with the aggressiveness of breast carcinomas. Overexpression and depletion of TRIM28 up- and down-regulates the protein, but not the mRNA levels of TWIST1, respectively, suggesting that TRIM28 upregulates TWIST1 post-transcriptionally. Overexpression of TRIM28 in breast cancer cell line promotes cell migration and invasion. Knockdown of TRIM28 reduces the protein level of TWIST1 with concurrent upregulation of E-cadherin and downregulation of N-cadherin and consequently inhibits cell migration and invasion. Furthermore, Immunoprecipitation and GST pull-down assays demonstrated that TRIM28 interacts with TWIST1 directly and this interaction is presumed to protect TWIST1 from degradation. Our study revealed a novel mechanism in breast cancer cells that TRIM28 enhances metastasis by stabilizing TWIST1, suggesting that targeting TRIM28 could be an efficacious strategy in breast cancer treatment.
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92
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C Quaresma AJ, Bugai A, Barboric M. Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb. Nucleic Acids Res 2016; 44:7527-39. [PMID: 27369380 PMCID: PMC5027500 DOI: 10.1093/nar/gkw585] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023] Open
Abstract
Release of RNA polymerase II (Pol II) from promoter-proximal pausing has emerged as a critical step regulating gene expression in multicellular organisms. The transition of Pol II into productive elongation requires the kinase activity of positive transcription elongation factor b (P-TEFb), which is itself under a stringent control by the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Here, we provide an overview on stimulating Pol II pause release by P-TEFb and on sequestering P-TEFb into 7SK snRNP. Furthermore, we highlight mechanisms that govern anchoring of 7SK snRNP to chromatin as well as means that release P-TEFb from the inhibitory complex, and propose a unifying model of P-TEFb activation on chromatin. Collectively, these studies shine a spotlight on the central role of RNA binding proteins (RBPs) in directing the inhibition and activation of P-TEFb, providing a compelling paradigm for controlling Pol II transcription with a non-coding RNA.
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Affiliation(s)
- Alexandre J C Quaresma
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Andrii Bugai
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Matjaz Barboric
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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93
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Eguchi T, Prince T, Wegiel B, Calderwood SK. Role and Regulation of Myeloid Zinc Finger Protein 1 in Cancer. J Cell Biochem 2016; 116:2146-54. [PMID: 25903835 DOI: 10.1002/jcb.25203] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022]
Abstract
Myeloid zinc finger 1 (MZF1) belongs to the SCAN-Zinc Finger (SCAN-ZF) transcription factor family that has recently been implicated in a number of types of cancer. Although the initial studies concentrated on the role of MZF1 in myeloid differentiation and leukemia, the factor now appears to be involved in the etiology of major solid tumors such as lung, cervical, breast, and colorectal cancer. Here we discuss the regulation of MZF1 that mediated its recruitment and activation in cancer, concentrating on posttranslational modification by phosphorylation, and sumoylation, formation of promyelocytic leukemia nuclear bodies and its association with co-activators and co-repressors.
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Affiliation(s)
- Taka Eguchi
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Thomas Prince
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Barbara Wegiel
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
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94
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Sansó M, Levin RS, Lipp JJ, Wang VYF, Greifenberg AK, Quezada EM, Ali A, Ghosh A, Larochelle S, Rana TM, Geyer M, Tong L, Shokat KM, Fisher RP. P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Genes Dev 2016; 30:117-31. [PMID: 26728557 PMCID: PMC4701974 DOI: 10.1101/gad.269589.115] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sansó et al. identified ∼100 putative substrates of human positive transcription elongation factor b (P-TEFb), which were enriched for proteins implicated in transcription and RNA catabolism. Among the RNA processing factors phosphorylated by Cdk9 was the 5′-to-3′ “torpedo” exoribonuclease Xrn2, required in transcription termination by Pol II. The transcription cycle of RNA polymerase II (Pol II) is regulated at discrete transition points by cyclin-dependent kinases (CDKs). Positive transcription elongation factor b (P-TEFb), a complex of Cdk9 and cyclin T1, promotes release of paused Pol II into elongation, but the precise mechanisms and targets of Cdk9 action remain largely unknown. Here, by a chemical genetic strategy, we identified ∼100 putative substrates of human P-TEFb, which were enriched for proteins implicated in transcription and RNA catabolism. Among the RNA processing factors phosphorylated by Cdk9 was the 5′-to-3′ “torpedo” exoribonuclease Xrn2, required in transcription termination by Pol II, which we validated as a bona fide P-TEFb substrate in vivo and in vitro. Phosphorylation by Cdk9 or phosphomimetic substitution of its target residue, Thr439, enhanced enzymatic activity of Xrn2 on synthetic substrates in vitro. Conversely, inhibition or depletion of Cdk9 or mutation of Xrn2-Thr439 to a nonphosphorylatable Ala residue caused phenotypes consistent with inefficient termination in human cells: impaired Xrn2 chromatin localization and increased readthrough transcription of endogenous genes. Therefore, in addition to its role in elongation, P-TEFb regulates termination by promoting chromatin recruitment and activation of a cotranscriptional RNA processing enzyme, Xrn2.
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Affiliation(s)
- Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rebecca S Levin
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jesse J Lipp
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Vivien Ya-Fan Wang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Ann Katrin Greifenberg
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany
| | - Elizabeth M Quezada
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Animesh Ghosh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Stéphane Larochelle
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Tariq M Rana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA
| | - Matthias Geyer
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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95
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McNamara RP, Bacon CW, D'Orso I. Transcription elongation control by the 7SK snRNP complex: Releasing the pause. Cell Cycle 2016; 15:2115-2123. [PMID: 27152730 DOI: 10.1080/15384101.2016.1181241] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability for the eukaryotic cell to transcriptionally respond to various stimuli is critical for the overall homeostasis of the cell, and in turn, the organism. The human RNA polymerase II complex (Pol II), which is responsible for the transcription of protein-encoding genes and non-coding RNAs, is paused at promoter-proximal regions to ensure their rapid activation. In response to stimulation, Pol II pause release is facilitated by the action of positive transcription elongation factors such as the P-TEFb kinase. However, the majority of P-TEFb is held in a catalytically inactivate state, assembled into the 7SK small nuclear ribonucleoprotein (snRNP) complex, and must be dislodged to become catalytically active. In this review, we discuss mechanisms of 7SK snRNP recruitment to promoter-proximal regions and P-TEFb disassembly from the inhibitory snRNP to regulate 'on site' kinase activation and Pol II pause release.
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Affiliation(s)
- Ryan P McNamara
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Curtis W Bacon
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
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96
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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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97
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Calderwood SK. A critical role for topoisomerase IIb and DNA double strand breaks in transcription. Transcription 2016; 7:75-83. [PMID: 27100743 DOI: 10.1080/21541264.2016.1181142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies have indicated a novel role for topoisomerase IIb in transcription. Transcription of heat shock genes, serum-induced immediate early genes and nuclear receptor-activated genes, each required DNA double strands generated by topoisomerase IIb. Such strand breaks seemed both necessary and sufficient for transcriptional activation. In addition, such transcription was associated with initiation of the DNA damage response pathways, including the activation of the enzymes: ataxia-telangiectasia mutated (ATM), DNA-dependent protein kinase and poly (ADP ribose) polymerase 1. DNA damage response signaling was involved both in transcription and in repair of DNA breaks generated by topoisomerase IIb.
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Affiliation(s)
- Stuart K Calderwood
- a Department of Radiation Oncology , Harvard Medical School at Beth Israel Deaconess Medical Center , Boston , MA , USA
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98
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Pance A. Oct-1, to go or not to go? That is the PolII question. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:820-4. [PMID: 27063953 DOI: 10.1016/j.bbagrm.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 10/22/2022]
Abstract
The Oct transcription factors recognise an octamer DNA element from which they regulate transcription of specific target genes. Oct-1 is the only member of the subfamily that is ubiquitously expressed and has a wide role in transcriptional control. Through interaction with various partner proteins, Oct-1 can modulate accessibility to the chromatin to recruit the transcription machinery and form the pre-initiation complex. The recruited PolII is induced to initiate transcription and stalled until elongation is triggered on interaction with signalling transcription factors. In this way, Oct-1 can fulfil general roles in transcription by opening the chromatin as well as transduce extracellular signals by relaying activation through various interacting partners. The emerging picture of Oct-1 is that of a complex and versatile transcription factor with fundamental functions in cell homeostasis and signal response in general as well as cell specific contexts. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
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Affiliation(s)
- Alena Pance
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK.
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99
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Tasselli L, Xi Y, Zheng W, Tennen RI, Odrowaz Z, Simeoni F, Li W, Chua KF. SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence. Nat Struct Mol Biol 2016; 23:434-40. [PMID: 27043296 PMCID: PMC5826646 DOI: 10.1038/nsmb.3202] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 03/11/2016] [Indexed: 12/12/2022]
Abstract
Pericentric heterochromatin silencing at mammalian centromeres is essential for mitotic fidelity and genomic stability. Defective pericentric silencing has been observed in senescent cells, aging tissues, and mammalian tumors, but the underlying mechanisms and functional consequences of these defects are unclear. Here, we uncover an essential role of the human SIRT6 enzyme in pericentric transcriptional silencing, and we show that this function protects against mitotic defects, genomic instability, and cellular senescence. At pericentric heterochromatin, SIRT6 promotes deacetylation of a new substrate, residue K18 of histone H3 (H3K18), and inactivation of SIRT6 in cells leads to H3K18 hyperacetylation and aberrant accumulation of pericentric transcripts. Strikingly, depletion of these transcripts through RNA interference rescues the mitotic and senescence phenotypes of SIRT6-deficient cells. Together, our findings reveal a new function for SIRT6 and regulation of acetylated H3K18 at heterochromatin, and demonstrate the pathogenic role of deregulated pericentric transcription in aging- and cancer-related cellular dysfunction.
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Affiliation(s)
- Luisa Tasselli
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Yuanxin Xi
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Zheng
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Ruth I Tennen
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Zaneta Odrowaz
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Federica Simeoni
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Katrin F Chua
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
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100
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Bunch H. Role of genome guardian proteins in transcriptional elongation. FEBS Lett 2016; 590:1064-75. [PMID: 27010360 DOI: 10.1002/1873-3468.12152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
Abstract
Maintaining genomic integrity is vital for cell survival and homeostasis. Mutations in critical genes in germ-line and somatic cells are often implicated with the onset or progression of diseases. DNA repair enzymes thus take important roles as guardians of the genome in the cell. Besides the known function to repair DNA damage, recent findings indicate that DNA repair enzymes regulate the transcription of protein-coding and noncoding RNA genes. In particular, a novel role of DNA damage response signaling has been identified in the regulation of transcriptional elongation. Topoisomerases-mediated DNA breaks appear important for the regulation. In this review, recent findings of these DNA break- and repair-associated enzymes in transcription and potential roles of transcriptional activation-coupled DNA breaks are discussed.
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Affiliation(s)
- Heeyoun Bunch
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
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