1
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Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
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Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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2
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Zhang X, Guo J, Shi X, Zhou X, Chen Q. LUC7L3 is a downstream factor of SRSF1 and prevents genomic instability. CELL INSIGHT 2024; 3:100170. [PMID: 38590928 PMCID: PMC10999515 DOI: 10.1016/j.cellin.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024]
Abstract
The RNA-binding protein LUC7L3 is the human homolog of yeast U1 small nuclear RNA (snRNA)-related splicing factor Luc7p. While the primary function of LUC7L3 as an RNA-binding protein is believed to be involved in RNA metabolism, particularly in the splicing process, its exact role and other functions are still not fully understood. In this study, we aimed to elucidate the role of LUC7L3 and its impact on cell proliferation. Our study revealed that LUC7L3 depletion impairs cell proliferation compared to the other Luc7p paralogs, resulting in cell apoptosis and senescence. We explored the underlying mechanisms and found that LUC7L3 depletion leads to R-loop accumulation, DNA replication stress, and genome instability. Furthermore, we discovered that LUC7L3 depletion caused abnormalities in spindle assembly, leading to the formation of multinuclear cells. This was attributed to the dysregulation of protein translation of spindle-associated proteins. Additionally, we investigated the interplay between LUC7L3 and SRSF1 and identified SRSF1 as an upper stream regulator of LUC7L3, promoting the translation of LUC7L3 protein. These findings highlight the importance of LUC7L3 in maintaining genome stability and its relationship with SRSF1 in this regulatory pathway.
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Affiliation(s)
- Xiaqing Zhang
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Jing Guo
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Xin Shi
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Xin Zhou
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Qiang Chen
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
- Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Wuhan, 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Province Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
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3
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Petropoulos M, Karamichali A, Rossetti GG, Freudenmann A, Iacovino LG, Dionellis VS, Sotiriou SK, Halazonetis TD. Transcription-replication conflicts underlie sensitivity to PARP inhibitors. Nature 2024; 628:433-441. [PMID: 38509368 PMCID: PMC11006605 DOI: 10.1038/s41586-024-07217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
An important advance in cancer therapy has been the development of poly(ADP-ribose) polymerase (PARP) inhibitors for the treatment of homologous recombination (HR)-deficient cancers1-6. PARP inhibitors trap PARPs on DNA. The trapped PARPs are thought to block replisome progression, leading to formation of DNA double-strand breaks that require HR for repair7. Here we show that PARP1 functions together with TIMELESS and TIPIN to protect the replisome in early S phase from transcription-replication conflicts. Furthermore, the synthetic lethality of PARP inhibitors with HR deficiency is due to an inability to repair DNA damage caused by transcription-replication conflicts, rather than by trapped PARPs. Along these lines, inhibiting transcription elongation in early S phase rendered HR-deficient cells resistant to PARP inhibitors and depleting PARP1 by small-interfering RNA was synthetic lethal with HR deficiency. Thus, inhibiting PARP1 enzymatic activity may suffice for treatment efficacy in HR-deficient settings.
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Affiliation(s)
- Michalis Petropoulos
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Angeliki Karamichali
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | | | - Alena Freudenmann
- FoRx Therapeutics AG, Basel, Switzerland
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Vasilis S Dionellis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Sotirios K Sotiriou
- FoRx Therapeutics AG, Basel, Switzerland
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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4
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Chatzinikolaou G, Stratigi K, Siametis A, Goulielmaki E, Akalestou-Clocher A, Tsamardinos I, Topalis P, Austin C, Bouwman BA, Crosetto N, Altmüller J, Garinis GA. XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes. SCIENCE ADVANCES 2023; 9:eadi2095. [PMID: 37939182 PMCID: PMC10631727 DOI: 10.1126/sciadv.adi2095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Co-transcriptional RNA-DNA hybrids can not only cause DNA damage threatening genome integrity but also regulate gene activity in a mechanism that remains unclear. Here, we show that the nucleotide excision repair factor XPF interacts with the insulator binding protein CTCF and the cohesin subunits SMC1A and SMC3, leading to R-loop-dependent DNA looping upon transcription activation. To facilitate R-loop processing, XPF interacts and recruits with TOP2B on active gene promoters, leading to double-strand break accumulation and the activation of a DNA damage response. Abrogation of TOP2B leads to the diminished recruitment of XPF, CTCF, and the cohesin subunits to promoters of actively transcribed genes and R-loops and the concurrent impairment of CTCF-mediated DNA looping. Together, our findings disclose an essential role for XPF with TOP2B and the CTCF/cohesin complex in R-loop processing for transcription activation with important ramifications for DNA repair-deficient syndromes associated with transcription-associated DNA damage.
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Affiliation(s)
- Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Tsamardinos
- Computer Science Department of University of Crete, Heraklion, Crete, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Caroline Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Britta A. M. Bouwman
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
| | - Nicola Crosetto
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157 Milan, Italy
| | - Janine Altmüller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Facility Genomics, Charitéplatz 1, 10117 Berlin, Germany
| | - George A. Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
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5
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Friedl MS, Djakovic L, Kluge M, Hennig T, Whisnant AW, Backes S, Dölken L, Friedel CC. HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform. PLoS One 2022; 17:e0276467. [PMID: 36279270 PMCID: PMC9591066 DOI: 10.1371/journal.pone.0276467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
The herpes simplex virus 1 (HSV-1) virion host shut-off (vhs) protein cleaves both cellular and viral mRNAs by a translation-initiation-dependent mechanism, which should spare circular RNAs (circRNAs). Here, we show that vhs-mediated degradation of linear mRNAs leads to an enrichment of circRNAs relative to linear mRNAs during HSV-1 infection. This was also observed in influenza A virus (IAV) infection, likely due to degradation of linear host mRNAs mediated by the IAV PA-X protein and cap-snatching RNA-dependent RNA polymerase. For most circRNAs, enrichment was not due to increased circRNA synthesis but due to a general loss of linear RNAs. In contrast, biogenesis of a circRNA originating from the long isoform (NEAT1_2) of the nuclear paraspeckle assembly transcript 1 (NEAT1) was induced both in HSV-1 infection-in a vhs-independent manner-and in IAV infection. This was associated with induction of novel linear splicing of NEAT1_2 both within and downstream of the circRNA. NEAT1_2 forms a scaffold for paraspeckles, nuclear bodies located in the interchromatin space, must likely remain unspliced for paraspeckle assembly and is up-regulated in HSV-1 and IAV infection. We show that NEAT1_2 splicing and up-regulation can be induced by ectopic co-expression of the HSV-1 immediate-early proteins ICP22 and ICP27, potentially linking increased expression and splicing of NEAT1_2. To identify other conditions with NEAT1_2 splicing, we performed a large-scale screen of published RNA-seq data. This uncovered both induction of NEAT1_2 splicing and poly(A) read-through similar to HSV-1 and IAV infection in cancer cells upon inhibition or knockdown of CDK7 or the MED1 subunit of the Mediator complex phosphorylated by CDK7. In summary, our study reveals induction of novel circular and linear NEAT1_2 splicing isoforms as a common characteristic of HSV-1 and IAV infection and highlights a potential role of CDK7 in HSV-1 or IAV infection.
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Affiliation(s)
- Marie-Sophie Friedl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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6
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Sun Y, Zhang Y, Schultz C, Pommier Y, Thomas A. CDK7 Inhibition Synergizes with Topoisomerase I Inhibition in Small Cell Lung Cancer Cells by Inducing Ubiquitin-Mediated Proteolysis of RNA Polymerase II. Mol Cancer Ther 2022; 21:1430-1438. [PMID: 35830858 PMCID: PMC10476602 DOI: 10.1158/1535-7163.mct-21-0891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/14/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022]
Abstract
Small cell lung cancers (SCLC) are highly aggressive, and currently there are no available targeted therapies. To identify clinically actionable drug combinations, we analyzed our previously reported chemogenomics screens and identified a synergistically cytotoxic combination of the topoisomerase I (TOP1) inhibitor topotecan and cycle-dependent kinase 7 (CDK7) inhibitor THZ1. Topotecan causes cell death by generating TOP1-induced DNA breaks and DNA-protein cross-links (TOP1-DPC) that require proteolysis by the ubiquitin-proteasome pathway for their repair. We find that inhibition of the transcriptional kinase CDK7 by THZ1 induces ubiquitin-mediated proteasomal degradation of RNA polymerase II and prevents the proteasomal degradation of TOP1-DPCs. We provide a mechanistic basis for combinatorial targeting of transcription using selective inhibitors of CDK7 and TOP1 in clinical trials to advance SCLC therapeutics.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch, Center for Cancer Research National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yang Zhang
- Developmental Therapeutics Branch, Center for Cancer Research National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Christopher Schultz
- Developmental Therapeutics Branch, Center for Cancer Research National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research National Cancer Institute, NIH, Bethesda, MD 20892, USA
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7
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Aromolaran KA, Do J, Bernardi J, Aromolaran AS. mTOR Modulation of IKr through hERG1b-Dependent Mechanisms in Lipotoxic Heart. Int J Mol Sci 2022; 23:8061. [PMID: 35897638 PMCID: PMC9329916 DOI: 10.3390/ijms23158061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
In the atria, the rapid delayed rectifier channel (IKr) is a critical contributor to repolarization. In lipotoxic atria, increased activity of the serine/threonine mammalian target of rapamycin (mTOR) may remodel IKr and predispose patients to arrhythmias. To investigate whether mTOR produced defects in IKr channel function (protein expression and gating mechanisms), electrophysiology and biochemical assays in HEK293 cells stably expressing hERG1a/1b, and adult guinea pig atrial myocytes were used. Feeding with the saturated fatty acid palmitic acid high-fat diet (HFD) was used to induce lipotoxicity. Lipotoxicity-challenged HEK293 cells displayed an increased density of hERG1a/1b currents due to a targeted and significant increase in hERG1b protein expression. Furthermore, lipotoxicity significantly slowed the hERG1a/1b inactivation kinetics, while the activation and deactivation remained essentially unchanged. mTOR complex 1 (mTORC1) inhibition with rapamycin (RAP) reversed the increase in hERG1a/1b density and inactivation. Compared to lipotoxic myocytes, RAP-treated cells displayed action potential durations (APDs) and IKr densities similar to those of controls. HFD feeding triggered arrhythmogenic changes (increased the IKr density and shortened the APD) in the atria, but this was not observed in low-fat-fed controls. The data are the first to show the modulation of IKr by mTORC1, possibly through the remodeling of hERG1b, in lipotoxic atrial myocytes. These results offer mechanistic insights with implications for targeted therapeutic options for the therapy of acquired supraventricular arrhythmias in obesity and associated pathologies.
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Affiliation(s)
- Kelly A. Aromolaran
- Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah School of Medicine, Salt Lake City, UT 84112, USA;
| | - Jenny Do
- Masonic Medical Research Institute, Utica, NY 13501, USA; (J.D.); (J.B.)
| | - Joyce Bernardi
- Masonic Medical Research Institute, Utica, NY 13501, USA; (J.D.); (J.B.)
| | - Ademuyiwa S. Aromolaran
- Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah School of Medicine, Salt Lake City, UT 84112, USA;
- Masonic Medical Research Institute, Utica, NY 13501, USA; (J.D.); (J.B.)
- Department of Surgery, Division of Cardiothoracic Surgery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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8
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Ghouraba MH, Masad RJ, Mpingirika EZ, Abdelraheem OM, Zeghlache R, Alserw AM, Amleh A. Role of NELF-B in supporting epithelial-mesenchymal transition and cell proliferation during hepatocellular carcinoma progression. Oncol Lett 2021; 22:761. [PMID: 34539865 PMCID: PMC8436359 DOI: 10.3892/ol.2021.13022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Negative elongation factor-B (NELF-B), also known as cofactor of BRCA1 (COBRA1), is one of the four subunits of the NELF complex. It interacts with BRCA1, in addition to other transcription complexes in various tissues. The NELF complex represses the transcription of several genes by stalling RNA polymerase II during the early phase of transcription elongation. The role of NELF-B in liver cancer and hepatocellular carcinoma (HCC), the most prevalent type of liver cancer, remains to be elucidated. It has been previously demonstrated that silencing of NELF-B inhibits the proliferation and migration of HepG2 cells. The present study aimed to investigate the consequences of ectopic expression and silencing of NELF-B in liver cancer HepG2 and SNU449 cell lines. Functional assays were performed to examine the effects on gene and protein expression, viability, migration and invasion of cells. Overexpression of NELF-B did not alter the proliferation and migration of HepG2 cells, or the expression of tested genes, indicating that overexpression alone may not be sufficient for altering these features in HepG2 cells. By contrast, knockdown of NELF-B in SNU449 cells resulted in decreased cell proliferation, together with induction of apoptosis and decreased expression levels of Ki-67 and survivin, which are markers of proliferation and inhibition of apoptosis, respectively. Additionally, silencing of NELF-B resulted in a significant decrease in the hallmarks of epithelial-mesenchymal transition (EMT), including cell migration and invasion, and decreased the expression levels of EMT markers, such as N-cadherin, vimentin and β-catenin. Decreased expression levels of forkhead box F2 transcription factor and increased mRNA levels of trefoil factor 1, a putative tumor suppressor, were also detected following the silencing of NELF-B. The current results demonstrated that NELF-B enhanced the manifestation of most hallmarks of cancer, including cell proliferation, migration, invasion and inhibition of apoptosis, indicating its critical role in the progression of HCC.
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Affiliation(s)
- Mennatallah Hani Ghouraba
- Department of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Razan Jamil Masad
- Department of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Eric Zadok Mpingirika
- Department of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Omnia Mahmoud Abdelraheem
- Department of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Rached Zeghlache
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Aya M Alserw
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Asma Amleh
- Department of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt.,Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt
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9
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Shoaib M, Chen Q, Shi X, Nair N, Prasanna C, Yang R, Walter D, Frederiksen KS, Einarsson H, Svensson JP, Liu CF, Ekwall K, Lerdrup M, Nordenskiöld L, Sørensen CS. Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. Nat Commun 2021; 12:4800. [PMID: 34417450 PMCID: PMC8379281 DOI: 10.1038/s41467-021-25051-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
Histone lysine methylations have primarily been linked to selective recruitment of reader or effector proteins that subsequently modify chromatin regions and mediate genome functions. Here, we describe a divergent role for histone H4 lysine 20 mono-methylation (H4K20me1) and demonstrate that it directly facilitates chromatin openness and accessibility by disrupting chromatin folding. Thus, accumulation of H4K20me1 demarcates highly accessible chromatin at genes, and this is maintained throughout the cell cycle. In vitro, H4K20me1-containing nucleosomal arrays with nucleosome repeat lengths (NRL) of 187 and 197 are less compact than unmethylated (H4K20me0) or trimethylated (H4K20me3) arrays. Concordantly, and in contrast to trimethylated and unmethylated tails, solid-state NMR data shows that H4K20 mono-methylation changes the H4 conformational state and leads to more dynamic histone H4-tails. Notably, the increased chromatin accessibility mediated by H4K20me1 facilitates gene expression, particularly of housekeeping genes. Altogether, we show how the methylation state of a single histone H4 residue operates as a focal point in chromatin structure control. While H4K20me1 directly promotes chromatin openness at highly transcribed genes, it also serves as a stepping-stone for H4K20me3-dependent chromatin compaction. The effect of histone H4 lysine 20 methylation (H4K20me) on chromatin accessibility are not well established. Here the authors show how H4K20 methylation regulates chromatin structure and accessibility to ensure precise transcriptional outputs through the cell cycle using genome-wide approaches, in vitro biophysical assays, and NMR.
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Affiliation(s)
- Muhammad Shoaib
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nidhi Nair
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Wilmar International Limited, Jurong Island, Singapore
| | - David Walter
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Hjorleifur Einarsson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Mads Lerdrup
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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10
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Li Y, Xue B, Zhang M, Zhang L, Hou Y, Qin Y, Long H, Su QP, Wang Y, Guan X, Jin Y, Cao Y, Li G, Sun Y. Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency. Genome Biol 2021; 22:206. [PMID: 34253239 PMCID: PMC8276456 DOI: 10.1186/s13059-021-02424-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/30/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. RESULTS We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. CONCLUSION Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.
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Affiliation(s)
- Yongzheng Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yizhi Qin
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Haizhen Long
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Guan
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yanyan Jin
- Department of Neurobiology, Beijing Centre of Neural Regeneration and Repair, Capital Medical University, Beijing, 100101, China
| | - Yuan Cao
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
- College of Future Technology, Peking University, Beijing, 100871, China.
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11
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Bossaert M, Pipier A, Riou JF, Noirot C, Nguyên LT, Serre RF, Bouchez O, Defrancq E, Calsou P, Britton S, Gomez D. Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands. eLife 2021; 10:65184. [PMID: 34180392 PMCID: PMC8279764 DOI: 10.7554/elife.65184] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/16/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2α (TOP2A) as a major effector of cytotoxicity induced by two clastogenic G4 ligands, pyridostatin and CX-5461, the latter molecule currently undergoing phase I/II clinical trials in oncology. We show that both TOP2 activity and transcription account for DNA break production following G4 ligand treatments. In contrast, clastogenic activity of these G4 ligands is countered by topoisomerase 1 (TOP1), which limits co-transcriptional G4 formation, and by factors promoting transcriptional elongation. Altogether our results support that clastogenic G4 ligands act as DNA structure-driven TOP2 poisons at transcribed regions bearing G4 structures.
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Affiliation(s)
- Madeleine Bossaert
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Angélique Pipier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Jean-Francois Riou
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Céline Noirot
- INRAE, UR 875, Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo, Castanet-Tolosan, France
| | - Linh-Trang Nguyên
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Eric Defrancq
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, Grenoble, France
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
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12
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Sheinboim D, Parikh S, Parikh R, Menuchin A, Shapira G, Kapitansky O, Elkoshi N, Ruppo S, Shaham L, Golan T, Elgavish S, Nevo Y, Bell RE, Malcov H, Shomron N, Taub JW, Izraeli S, Levy C. Slow transcription of the 99a/let-7c/125b-2 cluster results in differential miRNA expression and promotes melanoma phenotypic plasticity. J Invest Dermatol 2021; 141:2944-2956.e6. [PMID: 34186058 DOI: 10.1016/j.jid.2021.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/21/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
Almost half of human miRNAs are encoded in clusters. Although transcribed as a single unit, the levels of individual mature miRNAs often differ. The mechanisms underlying differential biogenesis of clustered miRNAs and the resulting physiological implications are mostly unknown. Here, we report that the melanoma master transcription regulator MITF regulates the differential expression of the 99a/let-7c/125b-2 cluster by altering the distribution of RNA polymerase II (Pol-II) along the cluster. We discovered that MITF interacts with TRIM28, a known inhibitor of Pol-II transcription elongation, at the let-7c region resulting in Pol-II pausing and causing its elevated expression, whereas low levels of Pol-II occupation over miR-99a and miR-125b-2 regions decreases their biogenesis. Furthermore, we showed that this differential expression affects the phenotypic state of melanoma cells. RNA-seq analysis of proliferative melanoma cells that express miR-99a and miR-125b mimics revealed a transcriptomic shift toward an invasive phenotype. Conversely, expression of a let-7c mimic in invasive melanoma cells induced a shift to a more proliferative state. We confirmed direct target genes of these miRNAs: FGFR3, BAP1, Bcl2, TGFBR1, and CDKN1A. Our study demonstrates a MITF-governed biogenesis mechanism that results in differential expression of clustered 99a/let-7c/125b-2 miRNAs that control melanoma progression.
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Affiliation(s)
- Danna Sheinboim
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shivang Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roma Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amitai Menuchin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oxana Kapitansky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nadav Elkoshi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shmuel Ruppo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Lital Shaham
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Division of Pediatric Hematology-Oncology Department, Schneider Children's Medical Center, Petah Tikva 49202, Israel
| | - Tamar Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Rachel E Bell
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hagar Malcov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Edmond J. Safra Center of Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jeffrey W Taub
- Wayne State University School of Medicine, Detroit, MI 48201, USA; Division of Pediatric Hematology and Oncology, Children's Hospital of Michigan, Detroit, MI 48201, USA
| | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Carmit Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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13
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Lee JH, Ryu SW, Ender NA, Paull TT. Poly-ADP-ribosylation drives loss of protein homeostasis in ATM and Mre11 deficiency. Mol Cell 2021; 81:1515-1533.e5. [PMID: 33571423 DOI: 10.1016/j.molcel.2021.01.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/14/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
Loss of the ataxia-telangiectasia mutated (ATM) kinase causes cerebellum-specific neurodegeneration in humans. We previously demonstrated that deficiency in ATM activation via oxidative stress generates insoluble protein aggregates in human cells, reminiscent of protein dysfunction in common neurodegenerative disorders. Here, we show that this process is driven by poly-ADP-ribose polymerases (PARPs) and that the insoluble protein species arise from intrinsically disordered proteins associating with PAR-associated genomic sites in ATM-deficient cells. The lesions implicated in this process are single-strand DNA breaks dependent on reactive oxygen species, transcription, and R-loops. Human cells expressing Mre11 A-T-like disorder mutants also show PARP-dependent aggregation identical to ATM deficiency. Lastly, analysis of A-T patient cerebellum samples shows widespread protein aggregation as well as loss of proteins known to be critical in human spinocerebellar ataxias that is not observed in neocortex tissues. These results provide a hypothesis accounting for loss of protein integrity and cerebellum function in A-T.
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Affiliation(s)
- Ji-Hoon Lee
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Seung W Ryu
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Nicolette A Ender
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Tanya T Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA.
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14
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Crossley MP, Bocek MJ, Hamperl S, Swigut T, Cimprich KA. qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide. Nucleic Acids Res 2020; 48:e84. [PMID: 32544226 PMCID: PMC7641308 DOI: 10.1093/nar/gkaa500] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes but can also cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA–DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here, we describe quantitative differential DNA–RNA immunoprecipitation (qDRIP), a method combining synthetic RNA–DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions. We also use these quantitative comparisons to make the first estimates of the absolute count of RNA–DNA hybrids per cell and their half-lives genome-wide. Finally, we identify a subset of RNA–DNA hybrids with high GC skew which are partially resistant to RNase H. Overall, qDRIP allows for accurate normalization in conditions where R-loops are perturbed and for quantitative measurements that provide previously unattainable biological insights.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephan Hamperl
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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15
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TRIM28 functions as the SUMO E3 ligase for PCNA in prevention of transcription induced DNA breaks. Proc Natl Acad Sci U S A 2020; 117:23588-23596. [PMID: 32900933 DOI: 10.1073/pnas.2004122117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In human cells, the DNA replication factor proliferating cell nuclear antigen (PCNA) can be conjugated to either the small ubiquitinlike modifier SUMO1 or SUMO2, but only SUMO2-conjugated PCNA is induced by transcription to facilitate resolution of transcription-replication conflict (TRC). To date, the SUMO E3 ligase that provides substrate specificity for SUMO2-PCNA conjugation in response to TRC remains unknown. Using a proteomic approach, we identified TRIM28 as the E3 ligase that catalyzes SUMO2-PCNA conjugation. In vitro, TRIM28, together with the RNA polymerase II (RNAPII)-interacting protein RECQ5, promotes SUMO2-PCNA conjugation but inhibits SUMO1-PCNA formation. This activity requires a PCNA-interacting protein (PIP) motif located within the bromodomain of TRIM28. In cells, TRIM28 interaction with PCNA on human chromatin is dependent on both transcription and RECQ5, and SUMO2-PCNA level correlates with TRIM28 expression. As a consequence, TRIM28 depletion led to RNAPII accumulation at TRC sites, and expression of a TRIM28 PIP mutant failed to suppress TRC-induced DNA breaks.
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16
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Ladds MJGW, Laín S. Small molecule activators of the p53 response. J Mol Cell Biol 2020; 11:245-254. [PMID: 30689917 PMCID: PMC6478124 DOI: 10.1093/jmcb/mjz006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/21/2018] [Accepted: 01/18/2019] [Indexed: 01/10/2023] Open
Abstract
Drugging the p53 pathway has been a goal for both academics and pharmaceutical companies since the designation of p53 as the 'guardian of the genome'. Through growing understanding of p53 biology, we can see multiple routes for activation of both wild-type p53 function and restoration of mutant p53. In this review, we focus on small molecules that activate wild-type p53 and that do so in a non-genotoxic manner. In particular, we will describe potential approaches to targeting proteins that alter p53 stability and function through posttranslational modification, affect p53's subcellular localization, or target RNA synthesis or the synthesis of ribonucleotides. The plethora of pathways for exploitation of p53, as well as the wide-ranging response to p53 activation, makes it an attractive target for anti-cancer therapy.
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Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Solnavägen 9, Karolinska Institutet, Stockholm, Sweden.,SciLifeLab, Tomtebodavägen 23A, Solna, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Solnavägen 9, Karolinska Institutet, Stockholm, Sweden.,SciLifeLab, Tomtebodavägen 23A, Solna, Stockholm, Sweden
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17
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Ziegler V, Deußen M, Schumacher L, Roos WP, Fritz G. Anticancer drug and ionizing radiation-induced DNA damage differently influences transcription activity and DDR-related stress responses of an endothelial monolayer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118678. [PMID: 32061892 DOI: 10.1016/j.bbamcr.2020.118678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 01/05/2023]
Abstract
The endothelium contributes to the pathophysiology of adverse effects caused by conventional (genotoxic) anticancer therapeutics (cAT). The relevance of structurally different types of cAT-induced DNA lesions for eliciting selected endothelial stress responses is largely unknown. Here, we analyzed the cAT-induced formation of DNA double-strand breaks (DSB), transcription blockage and DNA damage response (DDR) in time kinetic analyses employing a monolayer of primary human endothelial cells (HUVEC). We observed that the degree of cAT-induced transcription blockage, the number of DSB and activation of DDR-related factors diverge. For instance, ionizing radiation caused the formation of numerous DSB and triggerd a substantial activation of ATM/Chk2 signaling, which however were not accompanied by a significant transcription inhibition. By contrast, the DNA cross-linking cAT cisplatin triggered a rapid and substantial blockage of transcription, which yet was not reflected by an appreciable number of DSB or increased levels of pATM/pChk2. In general, cAT-stimulated ATM-dependent phosphorylation of Kap1 (Ser824) and p53 (Ser15) reflected best cAT-induced transcription blockage. In conclusion, cAT-induced formation of DSB and profound activation of prototypical DDR factors is independent of the inhibition of RNA polymerase II-regulated transcription in an endothelial monolayer. We suggest that DSB formed directly or indirectly following cAT-treatment do not act as comprehensive triggers of superior signaling pathways shutting-down transcription while, at the same time, causing an appreciable stimulation of the DDR. Rather, it appears that distinct cAT-induced DNA lesions elicit diverging signaling pathways, which separately control transcription vs. DDR activity in the endothelium.
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Affiliation(s)
- Verena Ziegler
- Institute of Toxicology, Medical Faculty, Heinrich Heine University, Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany.
| | - Marco Deußen
- Institute of Toxicology, Medical Faculty, Heinrich Heine University, Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany.
| | - Lena Schumacher
- Institute of Toxicology, Medical Faculty, Heinrich Heine University, Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany.
| | - Wynand P Roos
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, 55131 Mainz, Germany.
| | - Gerhard Fritz
- Institute of Toxicology, Medical Faculty, Heinrich Heine University, Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany.
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18
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Putative promoters within gene bodies control exon expression via TET1‐mediated H3K36 methylation. J Cell Physiol 2020; 235:6711-6724. [DOI: 10.1002/jcp.29566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/13/2020] [Indexed: 12/31/2022]
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19
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Shi L, Song L, Maurer K, Dou Y, Patel VR, Su C, Leonard ME, Lu S, Hodge KM, Torres A, Chesi A, Grant SFA, Wells AD, Zhang Z, Petri MA, Sullivan KE. IL-1 Transcriptional Responses to Lipopolysaccharides Are Regulated by a Complex of RNA Binding Proteins. THE JOURNAL OF IMMUNOLOGY 2020; 204:1334-1344. [PMID: 31953354 DOI: 10.4049/jimmunol.1900650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/05/2019] [Indexed: 01/02/2023]
Abstract
The IL1A and IL1B genes lie in close proximity on chromosome 2 near the gene for their natural inhibitor, IL1RN Despite diverse functions, they are all three inducible through TLR4 signaling but with distinct kinetics. This study analyzed transcriptional induction kinetics, chromosome looping, and enhancer RNA production to understand the distinct regulation of these three genes in human cells. IL1A, IL1B, and IL1RN were rapidly induced after stimulation with LPS; however, IL1B mRNA production was less inhibitable by iBET151, suggesting it does not use pause-release regulation. Surprisingly, chromatin looping contacts between IL1A and IL1B were highly intermingled, although those of IL1RN were distinct, and we focused on comparing IL1A and IL1B transcriptional pathways. Our studies demonstrated that enhancer RNAs were produced from a subset of the regulatory regions, that they were critical for production of the mRNAs, and that they bound a diverse array of RNA binding proteins, including p300 but not CBP. We, furthermore, demonstrated that recruitment of p300 was dependent on MAPKs. Integrator is another RNA binding protein recruited to the promoters and enhancers, and its recruitment was more dependent on NF-κB than MAPKs. We found that integrator and NELF, an RNA polymerase II pausing protein, were associated with RNA in a manner that facilitated interaction. We conclude that IL1A and IL1B share many regulatory contacts, signaling pathways, and interactions with enhancer RNAs. A complex of protein interactions with enhancer RNAs emphasize the role of enhancer RNAs and the overall structural aspects of transcriptional regulation.
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Affiliation(s)
- Lihua Shi
- Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Li Song
- Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Kelly Maurer
- Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Ying Dou
- Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Vishesh R Patel
- Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Annabel Torres
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104.,Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104.,Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104; and
| | - Michelle A Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Children's Hospital of Philadelphia, Philadelphia, PA 19104;
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20
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Carrieri FA, Murray PJ, Ditsova D, Ferris MA, Davies P, Dale JK. CDK1 and CDK2 regulate NICD1 turnover and the periodicity of the segmentation clock. EMBO Rep 2019; 20:e46436. [PMID: 31267714 PMCID: PMC6607002 DOI: 10.15252/embr.201846436] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 03/11/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022] Open
Abstract
All vertebrates share a segmented body axis. Segments form from the rostral end of the presomitic mesoderm (PSM) with a periodicity that is regulated by the segmentation clock. The segmentation clock is a molecular oscillator that exhibits dynamic clock gene expression across the PSM with a periodicity that matches somite formation. Notch signalling is crucial to this process. Altering Notch intracellular domain (NICD) stability affects both the clock period and somite size. However, the mechanism by which NICD stability is regulated in this context is unclear. We identified a highly conserved site crucial for NICD recognition by the SCF E3 ligase, which targets NICD for degradation. We demonstrate both CDK1 and CDK2 can phosphorylate NICD in the domain where this crucial residue lies and that NICD levels vary in a cell cycle-dependent manner. Inhibiting CDK1 or CDK2 activity increases NICD levels both in vitro and in vivo, leading to a delay of clock gene oscillations and an increase in somite size.
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Affiliation(s)
- Francesca Anna Carrieri
- Division of Cell and Developmental BiologySchool of Life SciencesUniversity of DundeeDundeeUK
| | | | - Dimitrinka Ditsova
- Division of Cell and Developmental BiologySchool of Life SciencesUniversity of DundeeDundeeUK
| | | | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Jacqueline Kim Dale
- Division of Cell and Developmental BiologySchool of Life SciencesUniversity of DundeeDundeeUK
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21
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Kim J, Han KY, Khanna N, Ha T, Belmont AS. Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition. J Cell Sci 2019; 132:jcs.226563. [PMID: 30858197 DOI: 10.1242/jcs.226563] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/03/2019] [Indexed: 01/17/2023] Open
Abstract
Although the formation of RNA-protein bodies has been studied intensively, their mobility and how their number and size are regulated are still poorly understood. Here, we show significantly increased mobility of nuclear speckles after transcriptional inhibition, including long-range directed motion of one speckle towards another speckle, terminated by speckle fusion, over distances up to 4 µm and with velocities between 0.2 µm/min and 1.5 µm/min. Frequently, three or even four speckles follow very similar paths, with new speckles appearing along the path followed by a preceding speckle. Speckle movements and fusion events contribute to fewer, but larger, speckles after transcriptional inhibition. These speckle movements are not actin dependent, but occur within chromatin-depleted channels enriched with small granules containing the speckle marker protein SON. Similar long-range speckle movements and fusion events were observed after heat shock or heavy metal stress, and during late G2 and early prophase. Our observations suggest a mechanism for long-range, directional nuclear speckle movements, contributing to overall regulation of nuclear speckle number and size as well as overall nuclear organization. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jiah Kim
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kyu Young Han
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA.,CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL 32816, USA
| | - Nimish Khanna
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taekjip Ha
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Biophysics and Biophysical Chemistry and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Andrew S Belmont
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA .,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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22
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Bargi-Souza P, Goulart-Silva F, Nunes MT. Posttranscriptional actions of triiodothyronine on Tshb expression in TαT1 cells: New insights into molecular mechanisms of negative feedback. Mol Cell Endocrinol 2018; 478:45-52. [PMID: 30031103 DOI: 10.1016/j.mce.2018.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/10/2018] [Accepted: 07/13/2018] [Indexed: 11/28/2022]
Abstract
Rapid actions of triiodothyronine (T3) on thyrotropin (TSH) synthesis and secretion have been described in hypothyroid male rats. However, the molecular mechanisms remain unknown. TαT1 cells, a thyrotroph cell line, was used herein to characterize the possible non-genomic actions of T3 on the expression of alpha (Cga) and Tshb genes, and the posttranscriptional processing and translation of both transcripts. The involvement of αVβ3 integrin was also assessed. T3 quickly reduced Tshb mRNA content, poly(A) tail length and its association with ribosomes. The effect of T3 on Tshb gene expression was detected even in the presence of a transcription inhibitor. The decrease in Tshb mRNA content and polyadenylation depend on T3 interaction with αVβ3 integrin, while T3 reduced Cga mRNA content by transcriptional action. The translational rate of both transcripts was reduced by a mechanism, which does not depend on T3-αVβ3 integrin interaction. Results indicate that, in parallel with the inhibitory transcriptional action in Cga and Tshb gene expression, T3 rapidly triggers additional posttranscriptional mechanisms, reducing the TSH synthesis. These non-genomic actions partially depend on T3-αVβ3 integrin interaction at the plasma membrane of thyrotrophs and add new insights to the molecular mechanisms involved in T3 negative feedback loop.
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Affiliation(s)
- Paula Bargi-Souza
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, CEP 05508-000, Brazil
| | - Francemilson Goulart-Silva
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, CEP 05508-000, Brazil
| | - Maria Tereza Nunes
- Department of Physiology and Biophysics of the Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, CEP 05508-000, Brazil.
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23
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Shi L, Li S, Maurer K, Zhang Z, Petri M, Sullivan KE. Enhancer RNA and NFκB-dependent P300 regulation of ADAMDEC1. Mol Immunol 2018; 103:312-321. [PMID: 30352365 DOI: 10.1016/j.molimm.2018.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 01/27/2023]
Abstract
We observed increased expression of ADAMDEC1 RNA in monocytes from patients with systemic lupus erythematosus. The precise role of ADAMDEC1 is uncertain and uniquely among metalloproteinases it utilizes a zinc-coordinating aspartic acid residue which allows it to escape inhibition by tissue inhibitor of metalloprotease-3 (TIMP-3). A closely related gene encodes the protein ADAM28, which is not up-regulated in lupus. We leveraged the ability to look at both gene's promoters and enhancers simultaneously. ADAMDEC1 was up-regulated by LPS while ADAM28 was not upregulated in the short term. We identified MAP kinases and NFκB as critical cell pathways regulating the expression of ADAMDEC1. These same pathways were implicated in driving the expression of the ADAMDEC1 upstream enhancer RNAs. We demonstrated that binding of the enhancer RNAs produced from the upstream enhancer were critically important and that p300 bound to both the RNA from the enhancer and the DNA at the enhancer. P300 binding to the enhancer was dependent on NFκB. These data define the critical pathways regulating the expression of ADAMDEC1 and extend our knowledge of the roles of enhancer RNAs and mechanistically links p300 and enhancer RNAs.
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Affiliation(s)
- Lihua Shi
- The Division of Allergy Immunology at The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA, 19104, United states.
| | - Song Li
- The Division of Allergy Immunology at The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA, 19104, United states.
| | - Kelly Maurer
- The Division of Allergy Immunology at The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA, 19104, United states.
| | - Zhe Zhang
- The Department of Biomedical and Health informatics at the Children's Hospital of Philadelphia, 3535 Market St, Philadelphia, PA, 19104, United states.
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD, 21205, United states.
| | - Kathleen E Sullivan
- The Division of Allergy Immunology at The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA, 19104, United states.
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24
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Policarpi C, Crepaldi L, Brookes E, Nitarska J, French SM, Coatti A, Riccio A. Enhancer SINEs Link Pol III to Pol II Transcription in Neurons. Cell Rep 2018; 21:2879-2894. [PMID: 29212033 PMCID: PMC5732322 DOI: 10.1016/j.celrep.2017.11.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 06/30/2017] [Accepted: 11/02/2017] [Indexed: 12/25/2022] Open
Abstract
Spatiotemporal regulation of gene expression depends on the cooperation of multiple mechanisms, including the functional interaction of promoters with distally located enhancers. Here, we show that, in cortical neurons, a subset of short interspersed nuclear elements (SINEs) located in the proximity of activity-regulated genes bears features of enhancers. Enhancer SINEs (eSINEs) recruit the Pol III cofactor complex TFIIIC in a stimulus-dependent manner and are transcribed by Pol III in response to neuronal depolarization. Characterization of an eSINE located in proximity to the Fos gene (FosRSINE1) indicated that the FosRSINE1-encoded transcript interacts with Pol II at the Fos promoter and mediates Fos relocation to Pol II factories, providing an unprecedented molecular link between Pol III and Pol II transcription. Strikingly, knockdown of the FosRSINE1 transcript induces defects of both cortical radial migration in vivo and activity-dependent dendritogenesis in vitro, demonstrating that FosRSINE1 acts as a strong enhancer of Fos expression in diverse physiological contexts.
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Affiliation(s)
- Cristina Policarpi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Luca Crepaldi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Emily Brookes
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Justyna Nitarska
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Sarah M French
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Alessandro Coatti
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Antonella Riccio
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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25
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Li M, Xu X, Chang CW, Zheng L, Shen B, Liu Y. SUMO2 conjugation of PCNA facilitates chromatin remodeling to resolve transcription-replication conflicts. Nat Commun 2018; 9:2706. [PMID: 30006506 PMCID: PMC6045570 DOI: 10.1038/s41467-018-05236-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
During DNA synthesis, DNA replication and transcription machinery can collide, and the replication fork may temporarily dislodge RNA polymerase II (RNAPII) to resolve the transcription-replication conflict (TRC), a major source of endogenous DNA double-strand breaks (DSBs) and common fragile site (CFS) instability. However, the mechanism of TRC resolution remains unclear. Here, we show that conjugation of SUMO2, but not SUMO1 or SUMO3, to the essential replication factor PCNA is induced on transcribed chromatin by the RNAPII-bound helicase RECQ5. Proteomic analysis reveals that SUMO2-PCNA enriches histone chaperones CAF1 and FACT in the replication complex via interactions with their SUMO-interacting motifs. SUMO2-PCNA enhances CAF1-dependent histone deposition, which correlates with increased histone H3.1 at CFSs and repressive histone marks in the chromatin to reduce chromatin accessibility. Hence, SUMO2-PCNA dislodges RNAPII at CFSs, and overexpressing either SUMO2-PCNA or CAF1 reduces the incidence of DSBs in TRC-prone RECQ5-deficient cells.
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Affiliation(s)
- Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Xiaohua Xu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Chou-Wei Chang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA.
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26
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Giberson AN, Saha B, Campbell K, Christou C, Poulin KL, Parks RJ. Human adenoviral DNA association with nucleosomes containing histone variant H3.3 during the early phase of infection is not dependent on viral transcription or replication. Biochem Cell Biol 2018; 96:797-807. [PMID: 29874470 DOI: 10.1139/bcb-2018-0117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Adenovirus (Ad) DNA undergoes dynamic changes in protein association as the virus progresses through its replicative cycle. Within the virion, the Ad DNA associates primarily with the virus-encoded, protamine-like protein VII. During the early phase of infection (∼6 h), the viral DNA showed declining association with VII, suggesting that VII was removed from at least some regions of the viral DNA. Within 6 h, the viral DNA was wrapped into a repeating nucleosome-like array containing the histone variant H3.3. Transcription elongation was not required to strip VII from the viral DNA or for deposition of H3.3. H3.1 did not associate with the viral DNA at any point during infection. During the late phase of infection (i.e., active DNA replication ∼12-24 h), association with H3 was dramatically reduced and the repeating nucleosome-like pattern was no longer evident. Thus, we have uncovered some of the changes in nucleoprotein structure that occur during lytic Ad infection.
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Affiliation(s)
- Andrea N Giberson
- a Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,b Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,c Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Bratati Saha
- a Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,b Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,c Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kalisa Campbell
- a Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Carin Christou
- a Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Kathy L Poulin
- a Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Robin J Parks
- a Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,b Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,c Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,d Department of Medicine, The Ottawa Hospital and University of Ottawa, Ottawa, ON K1H 8L6, Canada
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27
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Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J. Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 2018; 359:1050-1055. [PMID: 29371426 PMCID: PMC6590518 DOI: 10.1126/science.aao3136] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
To achieve guide RNA (gRNA) multiplexing and an efficient delivery of tens of distinct gRNAs into single cells, we developed a molecular assembly strategy termed chimeric array of gRNA oligonucleotides (CARGO). We coupled CARGO with dCas9 (catalytically dead Cas9) imaging to quantitatively measure the movement of enhancers and promoters that undergo differentiation-associated activity changes in live embryonic stem cells. Whereas all examined functional elements exhibited subdiffusive behavior, their relative mobility increased concurrently with transcriptional activation. Furthermore, acute perturbation of RNA polymerase II activity can reverse these activity-linked increases in loci mobility. Through quantitative CARGO-dCas9 imaging, we provide direct measurements of cis-regulatory element dynamics in living cells and distinct cellular and activity states and uncover an intrinsic connection between cis-regulatory element mobility and transcription.
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Affiliation(s)
- Bo Gu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Spencley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew R Bauer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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28
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Brustel J, Kozik Z, Gromak N, Savic V, Sweet SMM. Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase Senataxin. Sci Rep 2018; 8:3850. [PMID: 29497062 PMCID: PMC5832799 DOI: 10.1038/s41598-018-21806-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/09/2018] [Indexed: 01/04/2023] Open
Abstract
Deletions and chromosome re-arrangements are common features of cancer cells. We have established a new two-component system reporting on epigenetic silencing or deletion of an actively transcribed gene adjacent to a double-strand break (DSB). Unexpectedly, we find that a targeted DSB results in a minority (<10%) misrepair event of kilobase deletions encompassing the DSB site and transcribed gene. Deletions are reduced upon RNaseH1 over-expression and increased after knockdown of the DNA:RNA helicase Senataxin, implicating a role for DNA:RNA hybrids. We further demonstrate that the majority of these large deletions are dependent on the 3′ flap endonuclease XPF. DNA:RNA hybrids were detected by DNA:RNA immunoprecipitation in our system after DSB generation. These hybrids were reduced by RNaseH1 over-expression and increased by Senataxin knock-down, consistent with a role in deletions. Overall, these data are consistent with DNA:RNA hybrid generation at the site of a DSB, mis-processing of which results in genome instability in the form of large deletions.
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Affiliation(s)
- Julien Brustel
- Genome Damage and Stability Centre (GDSC), University of Sussex, Brighton, BN1 9RQ, UK
| | - Zuzanna Kozik
- Genome Damage and Stability Centre (GDSC), University of Sussex, Brighton, BN1 9RQ, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, South Parks Road, OX1 3RE, UK
| | - Velibor Savic
- Brighton and Sussex Medical School (BSMS), University of Sussex, Brighton, BN1 9RQ, UK.,Horizon Discovery Ltd, 8100 Cambridge Research Park, Cambridge, CB25 9TL, UK
| | - Steve M M Sweet
- Genome Damage and Stability Centre (GDSC), University of Sussex, Brighton, BN1 9RQ, UK. .,NantOmics, 9600 Medical Center Drive, Rockville, MD, 20850, USA.
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29
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Maurer K, Ramen S, Shi L, Song L, Sullivan KE. Rapid induction of expression by LPS is accompanied by favorable chromatin and rapid binding of c-Jun. Mol Immunol 2018; 95:99-106. [PMID: 29433067 DOI: 10.1016/j.molimm.2018.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/20/2023]
Abstract
The response to infection is managed in mammals by a coordinated immune response. Innate responses are rapid and hard wired and have been demonstrated to be regulated at the level of chromatin accessibility. This study examined primary human monocyte responses to LPS as a model of innate responses to bacteria. We utilized inhibitors of chromatin modifying enzymes to understand the inter-relationships of the chromatin complexes regulating transcription. Multiplex digital gene detection was utilized to quantitate changes in mRNA levels for genes induced by LPS. In the first 30 min, genes that were highly induced by LPS as a group exhibited minimal effect of the chemical inhibitors of chromatin modifications. At 60 min, the more highly expressed genes were markedly more inhibitable. The effects of the inhibitors were almost entirely concordant in spite of different mechanisms of action. Two focus groups of genes with either high LPS inducibility at 30 min or high LPS inducibility at 60 min (but not at 30 min) were further examined by ChIP assay. NFκB p65 binding was increased at the promoters of 30- and 60-min highly inducible genes equivalently. Binding of c-Jun was increased after LPS in the 30-min inducible gene set but not the 60-min inducible gene set. H3K4me3 and H4ac were not detectably altered by LPS stimulation. Baseline H3K4me3 and H4ac were higher in the 30-min highly inducible gene set compared to the 60-min highly inducible gene set. NFκB and JNK inhibitors led to diminished H4ac after LPS. The effects of DRB and C646 were greater for LPS-induced IL6 transcription at 30 min and LPS-stimulated H4ac compared to TNF where transcription was largely unaffected by the inhibitors. In conclusion, genes with very rapidly induced expression after LPS exhibited more favorable chromatin characteristics at baseline and were less inhibitable than genes induced at the later time points.
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Affiliation(s)
- Kelly Maurer
- The Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Swathi Ramen
- The Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Lihua Shi
- The Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Li Song
- The Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Kathleen E Sullivan
- The Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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30
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AMPK blocks starvation-inducible transgenerational defects in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2017; 114:E2689-E2698. [PMID: 28289190 DOI: 10.1073/pnas.1616171114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Life history events, such as traumatic stress, illness, or starvation, can influence us through molecular changes that are recorded in a pattern of characteristic chromatin modifications. These modifications are often associated with adaptive adjustments in gene expression that can persist throughout the lifetime of the organism, or even span multiple generations. Although these adaptations may confer some selective advantage, if they are not appropriately regulated they can also be maladaptive in a context-dependent manner. We show here that during periods of acute starvation in Caenorhabditis elegans larvae, the master metabolic regulator AMP-activated protein kinase (AMPK) plays a critical role in blocking modifications to the chromatin landscape. This ensures that gene expression remains inactive in the germ-line precursors during adverse conditions. In its absence, critical chromatin modifications occur in the primordial germ cells (PGCs) of emergent starved L1 larvae that correlate with compromised reproductive fitness of the generation that experienced the stress, but also in the subsequent generations that never experienced the initial event. Our findings suggest that AMPK regulates the activity of the chromatin modifying COMPASS complex (complex proteins associated with Set1) to ensure that chromatin marks are not established until nutrient/energy contingencies are satisfied. Our study provides molecular insight that links metabolic adaptation to transgenerational epigenetic modification in response to acute periods of starvation.
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31
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Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, Maldotti M, Anselmi F, Oliviero S. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017; 543:72-77. [PMID: 28225755 DOI: 10.1038/nature21373] [Citation(s) in RCA: 445] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3. Furthermore, the spurious transcripts can either be degraded by the RNA exosome complex or capped, polyadenylated, and delivered to the ribosome to produce aberrant proteins. Elongating RNA polymerase II therefore triggers an epigenetic crosstalk mechanism that involves SetD2, H3K36me3, Dnmt3b and DNA methylation to ensure the fidelity of gene transcription initiation, with implications for intragenic hypomethylation in cancer.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Giulia Basile
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Mara Maldotti
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Anselmi
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
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Abstract
Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the "torpedo" exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle.
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Affiliation(s)
- Robert P Fisher
- a Department of Oncological Sciences , Icahn School of Medicine at Mount Sinai , New York , NY , USA
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Pinhero R, Yankulov K. Expression and Purification of Recombinant CDKs: CDK7, CDK8, and CDK9. Methods Mol Biol 2016; 1336:13-28. [PMID: 26231705 DOI: 10.1007/978-1-4939-2926-9_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclin-dependent kinases have established roles in the regulation of cell cycle, in gene expression and in cell differentiation. Many of these kinases have been considered as drug targets and numerous efforts have been made to develop specific and potent inhibitors against them. The first step in all of these attempts and in many other biochemical analyses is the production of highly purified and reliable kinase, most frequently in a recombinant form. In this chapter we describe our experience in the cloning, expression, and purification of CDKs using CDK7/CycH, CDK8/CycC, and CDK9/CycT1 as an example.
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Affiliation(s)
- Reena Pinhero
- Department of Molecular Biology and Genetics, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
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Carmel JB, Young W, Hart RP. Flipping the transcriptional switch from myelin inhibition to axon growth in the CNS. Front Mol Neurosci 2015; 8:34. [PMID: 26236189 PMCID: PMC4505142 DOI: 10.3389/fnmol.2015.00034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/06/2015] [Indexed: 01/01/2023] Open
Abstract
Poor regeneration of severed axons in the central nervous system (CNS) limits functional recovery. Regeneration failure involves interplay of inhibitory environmental elements and the growth state of the neuron. To find internal changes in gene expression that might overcome inhibitory environmental cues, we compared several paradigms that allow growth in the inhibitory environment. Conditions that allow axon growth by axotomized and cultured dorsal root ganglion (DRG) neurons on CNS myelin include immaturity (the first few postnatal days), high levels of cyclic adenosine mono phosphate (cAMP), and conditioning with a peripheral nerve lesion before explant. This shift from inhibition to growth depends on transcription. Seeking to understand the transcriptome changes that allow axon growth in the CNS, we collaborated with the Marie Filbin laboratory to identify several mRNAs that are functionally relevant, as determined by gain- and loss-of-function studies. In this Perspective, we review evidence from these experiments and discuss the merits of comparing multiple regenerative paradigms to identify a core transcriptional program for CNS axon regeneration.
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Affiliation(s)
- Jason B Carmel
- Brain Mind Research Institute and Departments of Pediatrics and Neurology, Weill Cornell Medical College New York, NY, USA ; Burke-Cornell Medical Research Institute White Plains, NY, USA
| | - Wise Young
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University Piscataway, NJ, USA
| | - Ronald P Hart
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University Piscataway, NJ, USA
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35
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Madabhushi R, Gao F, Pfenning A, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott R, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell 2015; 161:1592-605. [DOI: 10.1016/j.cell.2015.05.032] [Citation(s) in RCA: 364] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/19/2015] [Accepted: 04/07/2015] [Indexed: 12/16/2022]
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36
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Rybakova KN, Tomaszewska A, van Mourik S, Blom J, Westerhoff HV, Carlberg C, Bruggeman FJ. Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. Nucleic Acids Res 2014; 43:153-61. [PMID: 25477385 PMCID: PMC4288170 DOI: 10.1093/nar/gku1272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a diseased state. The method employs a mathematical model, for which the kinetics of gene regulation, splicing, elongation and mRNA degradation were estimated from experimental data of transcriptional dynamics. The time-dependent dynamics of several species of adipose differentiation-related protein (ADRP) mRNA were measured in response to ligand activation of the transcription factor peroxisome proliferator-activated receptor δ (PPARδ). We validated the method by monitoring the mRNA dynamics upon gene activation in the presence of a splicing inhibitor. Our mathematical model correctly identifies splicing as the inhibitor target, despite the noise in the data.
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Affiliation(s)
- Katja N Rybakova
- Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1087, NL-1081 HV Amsterdam, The Netherlands
| | - Aleksandra Tomaszewska
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Simon van Mourik
- Biometris, Plant Sciences Group, Wageningen University and Research Center, NL-6708 PB Wageningen, The Netherlands
| | - Joke Blom
- Life Sciences, Centre for Mathematics and Computer Science (CWI), NL-1098 XG Amsterdam, The Netherlands
| | - Hans V Westerhoff
- Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1087, NL-1081 HV Amsterdam, The Netherlands Manchester Centre for Integrative Systems Biology, CEAS, University of Manchester, Manchester M60 1QD, UK Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, NL-1098 XH Amsterdam, The Netherlands
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Frank J Bruggeman
- Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1087, NL-1081 HV Amsterdam, The Netherlands
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37
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Villicaña C, Cruz G, Zurita M. The basal transcription machinery as a target for cancer therapy. Cancer Cell Int 2014; 14:18. [PMID: 24576043 PMCID: PMC3942515 DOI: 10.1186/1475-2867-14-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/21/2014] [Indexed: 01/11/2023] Open
Abstract
General transcription is required for the growth and survival of all living cells. However, tumor cells require extraordinary levels of transcription, including the transcription of ribosomal RNA genes by RNA polymerase I (RNPI) and mRNA by RNA polymerase II (RNPII). In fact, cancer cells have mutations that directly enhance transcription and are frequently required for cancer transformation. For example, the recent discovery that MYC enhances the transcription of the majority genes in the genome correlates with the fact that several transcription interfering drugs preferentially kill cancer cells. In recent years, advances in the mechanistic studies of the basal transcription machinery and the discovery of drugs that interfere with multiple components of transcription are being used to combat cancer. For example, drugs such as triptolide that targets the general transcription factors TFIIH and JQ1 to inhibit BRD4 are administered to target the high proliferative rate of cancer cells. Given the importance of finding new strategies to preferentially sensitize tumor cells, this review primarily focuses on several transcription inhibitory drugs to demonstrate that the basal transcription machinery constitutes a potential target for the design of novel cancer drugs. We highlight the drugs’ mechanisms for interfering with tumor cell survival, their importance in cancer treatment and the challenges of clinical application.
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Affiliation(s)
| | | | - Mario Zurita
- Departament of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico.
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38
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Shelkovnikova TA, Robinson HK, Troakes C, Ninkina N, Buchman VL. Compromised paraspeckle formation as a pathogenic factor in FUSopathies. Hum Mol Genet 2013; 23:2298-312. [PMID: 24334610 PMCID: PMC3976330 DOI: 10.1093/hmg/ddt622] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Paraspeckles are nuclear bodies formed by a set of specialized proteins assembled on the long non-coding RNA NEAT1; they have a role in nuclear retention of hyperedited transcripts and are associated with response to cellular stress. Fused in sarcoma (FUS) protein, linked to a number of neurodegenerative disorders, is an essential paraspeckle component. We have shown that its recruitment to these nuclear structures is mediated by the N-terminal region and requires prion-like activity. FUS interacts with p54nrb/NONO, a major constituent of paraspeckles, in an RNA-dependent manner and responds in the same way as other paraspeckle proteins to alterations in cellular homeostasis such as changes in transcription rates or levels of protein methylation. FUS also regulates NEAT1 levels and paraspeckle formation in cultured cells, and FUS deficiency leads to loss of paraspeckles. Pathological gain-of-function FUS mutations might be expected to affect paraspeckle function in human diseases because mislocalized amyotrophic lateral sclerosis (ALS)-linked FUS variants sequester other paraspeckle proteins into aggregates formed in cultured cells and into neuronal inclusions in a transgenic mouse model of FUSopathy. Furthermore, we detected abundant p54nrb/NONO-positive inclusions in motor neurons of patients with familial forms of ALS caused by FUS mutations, but not in other ALS cases. Our results suggest that both loss and gain of FUS function can trigger disruption of paraspeckle assembly, which may impair protective responses in neurons and thereby contribute to the pathogenesis of FUSopathies.
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39
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Samuelson DR, Konkel ME. Serine phosphorylation of cortactin is required for maximal host cell invasion by Campylobacter jejuni. Cell Commun Signal 2013; 11:82. [PMID: 24188565 PMCID: PMC3832248 DOI: 10.1186/1478-811x-11-82] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campylobacter jejuni causes acute disease characterized by severe diarrhea containing blood and leukocytes, fever, and abdominal cramping. Disease caused by C. jejuni is dependent on numerous bacterial and host factors. C. jejuni invasion of the intestinal epithelial cells is seen in both clinical samples and animal models indicating that host cell invasion is, in part, necessary for disease. C. jejuni utilizes a flagellar Type III Secretion System (T3SS) to deliver the Campylobacter invasion antigens (Cia) to host cells. The Cia proteins modulate host cell signaling leading to actin cytoskeleton rearrangement necessary for C. jejuni host cell invasion, and are required for the development of disease. RESULTS This study was based on the hypothesis that the C. jejuni CiaD effector protein mediates Erk 1/2 dependent cytoskeleton rearrangement. We showed that CiaD was required for the maximal phosphorylation of Erk 1/2 by performing an immunoblot with a p-Erk 1/2 specific antibody and that Erk 1/2 participates in C. jejuni invasion of host cells by performing the gentamicin protection assay in the presence and absence of the PD98059 (a potent inhibitor of Erk 1/2 activation). CiaD was also found to be required for the maximal phosphorylation of cortactin S405 and S418, as judged by immunoblot analysis. The response of human INT 407 epithelial cells to infection with C. jejuni was evaluated by confocal microscopy and scanning electron microscopy to determine the extent of membrane ruffling. This analysis revealed that CiaD, Erk 1/2, and cortactin participate in C. jejuni-induced membrane ruffling. Finally, cortactin and N-WASP were found to be involved in C. jejuni invasion of host cells using siRNA to N-WASP, and siRNA to cortactin, coupled with the gentamicin protection assay. CONCLUSION We conclude that CiaD is involved in the activation of Erk 1/2 and that activated Erk 1/2 facilitates C. jejuni invasion by phosphorylation of cortactin on serine 405 and 418. This is the first time that cortactin and N-WASP have been shown to be involved in C. jejuni invasion of host cells. These data also provide a mechanistic basis for the requirement of Erk 1/2 in C. jejuni-mediated cytoskeletal rearrangement.
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Affiliation(s)
| | - Michael E Konkel
- School of Molecular Biosciences, Washington State University, College of Veterinary Medicine, Life Sciences Bldg, Room 302c, Pullman, Washington 99164-7520, USA.
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40
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Lutay N, Ambite I, Grönberg Hernandez J, Rydström G, Ragnarsdóttir B, Puthia M, Nadeem A, Zhang J, Storm P, Dobrindt U, Wullt B, Svanborg C. Bacterial control of host gene expression through RNA polymerase II. J Clin Invest 2013; 123:2366-79. [PMID: 23728172 DOI: 10.1172/jci66451] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 02/27/2013] [Indexed: 01/25/2023] Open
Abstract
The normal flora furnishes the host with ecological barriers that prevent pathogen attack while maintaining tissue homeostasis. Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation in which some patients infected with Escherichia coli develop acute pyelonephritis, while other patients with bacteriuria exhibit an asymptomatic carrier state similar to bacterial commensalism. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease-associated responses in the host. Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II–dependent (Pol II–dependent) host gene expression. Over 60% of all genes were suppressed 24 hours after human inoculation with the prototype asymptomatic bacteriuria (ABU) strain E. coli 83972, and inhibition was verified by infection of human cells. Specific repressors and activators of Pol II–dependent transcription were modified, Pol II phosphorylation was inhibited, and pathogen-specific signaling was suppressed in cell lines and inoculated patients. An increased frequency of strains inhibiting Pol II was epidemiologically verified in ABU and fecal strains compared with acute pyelonephritis, and a Pol II antagonist suppressed the disease-associated host response. These results suggest that by manipulating host gene expression, ABU strains promote tissue integrity while inhibiting pathology. Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that potentially destructive immune activation will not occur.
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Affiliation(s)
- Nataliya Lutay
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden
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41
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Visvanathan A, Ahmed K, Even-Faitelson L, Lleres D, Bazett-Jones DP, Lamond AI. Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations. PLoS One 2013; 8:e67689. [PMID: 23840764 PMCID: PMC3694102 DOI: 10.1371/journal.pone.0067689] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/20/2013] [Indexed: 11/23/2022] Open
Abstract
The organisation of the large volume of mammalian genomic DNA within cell nuclei requires mechanisms to regulate chromatin compaction involving the reversible formation of higher order structures. The compaction state of chromatin varies between interphase and mitosis and is also subject to rapid and reversible change upon ATP depletion/repletion. In this study we have investigated mechanisms that may be involved in promoting the hyper-condensation of chromatin when ATP levels are depleted by treating cells with sodium azide and 2-deoxyglucose. Chromatin conformation was analysed in both live and permeabilised HeLa cells using FLIM-FRET, high resolution fluorescence microscopy and by electron spectroscopic imaging microscopy. We show that chromatin compaction following ATP depletion is not caused by loss of transcription activity and that it can occur at a similar level in both interphase and mitotic cells. Analysis of both live and permeabilised HeLa cells shows that chromatin conformation within nuclei is strongly influenced by the levels of divalent cations, including calcium and magnesium. While ATP depletion results in an increase in the level of unbound calcium, chromatin condensation still occurs even in the presence of a calcium chelator. Chromatin compaction is shown to be strongly affected by small changes in the levels of polyamines, including spermine and spermidine. The data are consistent with a model in which the increased intracellular pool of polyamines and divalent cations, resulting from depletion of ATP, bind to DNA and contribute to the large scale hyper-compaction of chromatin by a charge neutralisation mechanism.
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Affiliation(s)
- Ashwat Visvanathan
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kashif Ahmed
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Liron Even-Faitelson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - David Lleres
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - David P. Bazett-Jones
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Angus I. Lamond
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
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42
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Brazão TF, Demmers J, van IJcken W, Strouboulis J, Fornerod M, Romão L, Grosveld FG. A new function of ROD1 in nonsense-mediated mRNA decay. FEBS Lett 2012; 586:1101-10. [PMID: 22575643 DOI: 10.1016/j.febslet.2012.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
Abstract
RNA-binding proteins play a crucial role in the post-transcriptional regulation of gene expression. Polypyrimidine tract binding protein (PTB in humans) has been extensively characterized as an important splicing factor, and has additional functions in 3' end processing and translation. ROD1 is a PTB paralog containing four RRM (RNA recognition motif) domains. Here, we discover a function of ROD1 in nonsense-mediated mRNA decay (NMD). We show that ROD1 and the core NMD factor UPF1 interact and co-regulate an extensive number of target genes. Using a reporter system, we demonstrate that ROD1, similarly to UPF1 and UPF2, is required for the destabilization of a known NMD substrate. Finally, we show through RIP-seq that ROD1 and UPF1 associate with a significant number of common transcripts.
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Affiliation(s)
- T F Brazão
- Department of Cell Biology & Genetics, Erasmus MC, Rotterdam, The Netherlands.
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43
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Protein kinase A regulates molecular chaperone transcription and protein aggregation. PLoS One 2011; 6:e28950. [PMID: 22216146 PMCID: PMC3245242 DOI: 10.1371/journal.pone.0028950] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 12/25/2022] Open
Abstract
Heat shock factor 1 (HSF1) regulates one of the major pathways of protein quality control and is essential for deterrence of protein-folding disorders, particularly in neuronal cells. However, HSF1 activity declines with age, a change that may open the door to progression of neurodegenerative disorders such as Huntington's disease. We have investigated mechanisms of HSF1 regulation that may become compromised with age. HSF1 binds stably to the catalytic domain of protein kinase A (PKAcα) and becomes phosphorylated on at least one regulatory serine residue (S320). We show here that PKA is essential for effective transcription of HSP genes by HSF1. PKA triggers a cascade involving HSF1 binding to the histone acetylase p300 and positive translation elongation factor 1 (p-TEFb) and phosphorylation of the c-terminal domain of RNA polymerase II, a key mechanism in the downstream steps of HSF1-mediated transcription. This cascade appears to play a key role in protein quality control in neuronal cells expressing aggregation-prone proteins with long poly-glutamine (poly-Q) tracts. Such proteins formed inclusion bodies that could be resolved by HSF1 activation during heat shock. Resolution of the inclusions was inhibited by knockdown of HSF1, PKAcα, or the pTEFb component CDK9, indicating a key role for the HSF1-PKA cascade in protein quality control.
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44
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Mikula M, Bomsztyk K. Direct recruitment of ERK cascade components to inducible genes is regulated by heterogeneous nuclear ribonucleoprotein (hnRNP) K. J Biol Chem 2011; 286:9763-75. [PMID: 21233203 DOI: 10.1074/jbc.m110.213330] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Components of the ERK cascade are recruited to genes, but it remains unknown how they are regulated at these sites. The RNA-binding protein heterogeneous nuclear ribonucleoprotein (hnRNP) K interacts with kinases and is found along genes including the mitogen-inducible early response gene EGR-1. Here, we used chromatin immunoprecipitations to study co-recruitment of hnRNP K and ERK cascade activity along the EGR-1 gene. These measurements revealed that the spatiotemporal binding patterns of ERK cascade transducers (GRB2, SOS, B-Raf, MEK, and ERK) at the EGR-1 locus resemble both hnRNP K and RNA polymerase II (Pol II). Inhibition of EGR-1 transcription with either serum-responsive factor knockdown or 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole altered recruitment of all of the above ERK cascade components along this locus that mirrored the changes in Pol II and hnRNP K profiles. siRNA knockdown of hnRNP K decreased the levels of active MEK and ERK at the EGR-1, changes associated with decreased levels of elongating pre-mRNA and less efficient splicing. The hnRNP K dependence and pattern of ERK cascade activation at the c-MYC locus were different from at EGR-1. Ribonucleoprotein immunoprecipitations revealed that hnRNP K was associated with the EGR-1 but not c-MYC mRNAs. These data suggest a model where Pol II transcription-driven recruitment of hnRNP K along the EGR-1 locus compartmentalizes activation of the ERK cascade at these genes, events that regulate synthesis of mature mRNA.
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Affiliation(s)
- Michal Mikula
- Department of Medicine, University of Washington, Seattle, Washington 98109, USA
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45
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Yoder KE, Roddick W, Hoellerbauer P, Fishel R. XPB mediated retroviral cDNA degradation coincides with entry to the nucleus. Virology 2010; 410:291-8. [PMID: 21167544 DOI: 10.1016/j.virol.2010.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 09/22/2010] [Accepted: 11/17/2010] [Indexed: 01/01/2023]
Abstract
Retroviruses must integrate their cDNA to a host chromosome, but a significant fraction of retroviral cDNA is degraded before integration. XPB and XPD are part of the TFIIH complex which mediates basal transcription and DNA nucleotide excision repair. Retroviral infection increases when XPB or XPD are mutant. Here we show that inhibition of mRNA or protein synthesis does not affect HIV cDNA accumulation suggesting that TFIIH transcription activity is not required for degradation. Other host factors implicated in the stability of cDNA are not components of the XPB and XPD degradation pathway. Although an increase of retroviral cDNA in XPB or XPD mutant cells correlates with an increase of integrated provirus, the integration efficiency of pre-integration complexes is unaffected. Finally, HIV and MMLV cDNA degradation appears to coincide with nuclear import. These results suggest that TFIIH mediated cDNA degradation is a nuclear host defense against retroviral infection.
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Affiliation(s)
- Kristine E Yoder
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA.
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46
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Sakashita E, Endo H. SR and SR-related proteins redistribute to segregated fibrillar components of nucleoli in a response to DNA damage. Nucleus 2010; 1:367-80. [PMID: 21327085 DOI: 10.4161/nucl.1.4.12683] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 11/19/2022] Open
Abstract
Pre-mRNA splicing factors are often redistributed to nucleoli in response to physiological conditions and cell stimuli. In telophase nuclei, serine-arginine rich (SR) proteins, which usually reside in nuclear speckles, localize transiently to active ribosomal DNA (rDNA) transcription sites called nucleolar organizing region-associated patches (NAPs). Here, we show that ultraviolet light and DNA damaging chemicals induce the redistribution of SR and SR-related proteins to areas around nucleolar fibrillar components in interphase nuclei that are similar to, but distinct from, NAPs, and these areas have been termed DNA damage-induced NAPs (d-NAPs). In vivo labeling of nascent RNA distinguished d-NAPs from NAPs in that d-NAPs were observed even after full rDNA transcriptional arrest as a result of DNA damage. Studies under a variety of conditions revealed that d-NAP formation requires both RNA polymerase II-dependent transcriptional arrest and nucleolar segregation, in particular, the disorganization of the granular nucleolar components. Despite the redistribution of SR proteins, splicing factor-enriched nuclear speckles were not disrupted because other nuclear speckle components, such as nuclear poly(A) RNA and the U5-116K protein, remained in DNA-damaged cells. These data suggest that the selective redistribution of splicing factors contributes to the regulation of specific genes via RNA metabolism. Finally, we demonstrate that a change in alternative splicing of apoptosis-related genes is coordinated with the occurrence of d-NAPs. Our results reveal a novel response to DNA damage that involves the dynamic redistribution of splicing factors to nucleoli.
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Affiliation(s)
- Eiji Sakashita
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi, Japan.
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47
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The cyclin-dependent kinase inhibitor 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole induces nongenotoxic, DNA replication-independent apoptosis of normal and leukemic cells, regardless of their p53 status. BMC Cancer 2009; 9:281. [PMID: 19674456 PMCID: PMC2743708 DOI: 10.1186/1471-2407-9-281] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 08/12/2009] [Indexed: 11/15/2022] Open
Abstract
Background Current chemotherapy of human cancers focuses on the DNA damage pathway to induce a p53-mediated cellular response leading to either G1 arrest or apoptosis. However, genotoxic treatments may induce mutations and translocations that result in secondary malignancies or recurrent disease. In addition, about 50% of human cancers are associated with mutations in the p53 gene. Nongenotoxic activation of apoptosis by targeting specific molecular pathways thus provides an attractive therapeutic approach. Methods Normal and leukemic cells were evaluated for their sensitivity to 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) through cell viability and caspase activation tests. The apoptotic pathway induced by DRB was analysed by immunfluorescence and immunoblot analysis. H2AX phosphorylation and cell cycle analysis were performed to study the dependance of apoptosis on DNA damage and DNA replication, respectively. To investigate the role of p53 in DRB-induced apoptosis, specific p53 inhibitors were used. Statistical analysis on cell survival was performed with the test of independence. Results Here we report that DRB, an inhibitor of the transcriptional cyclin-dependent kinases (CDKs) 7 and 9, triggers DNA replication-independent apoptosis in normal and leukemic human cells regardless of their p53 status and without inducing DNA damage. Our data indicate that (i) in p53-competent cells, apoptosis induced by DRB relies on a cytosolic accumulation of p53 and subsequent Bax activation, (ii) in the absence of p53, it may rely on p73, and (iii) it is independent of ATM and NBS1 proteins. Notably, even apoptosis-resistant leukemic cells such as Raji were sensitive to DRB. Conclusion Our results indicate that DRB represents a potentially useful cancer chemotherapeutic strategy that employs both the p53-dependent and -independent apoptotic pathways without inducing genotoxic stress, thereby decreasing the risk of secondary malignancies.
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Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A 2009; 106:14276-80. [PMID: 19666497 DOI: 10.1073/pnas.0903642106] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ser-5 phosphorylation of the RNA polymerase II (Pol II) C-terminal domain by TFIIH kinase has been implicated in critical steps in mRNA synthesis, such as Pol II promoter escape and mRNA 5'-capping. However, the general requirement and precise role of TFIIH kinase in Pol II transcription still remain elusive. Here we use a chemical genetics approach to show that, for a majority of budding-yeast genes, specific inhibition of the yeast TFIIH kinase results in a dramatic reduction in both mRNA level and Ser-5 C-terminal domain phosphorylation. Surprisingly, inhibition of TFIIH kinase activity only partially affected both Pol II density and Ser-2 phosphorylation level. The discrepancy between mRNA level and Pol II density is attributed to the defective 5'-capping, which results in the destabilization of mRNAs. Therefore, contrary to the current belief, our study points strongly toward a minor role of TFIIH kinase in Pol II transcription, and a more significant role in mRNA capping in budding yeast.
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Cheok CF, Dey A, Lane DP. Cyclin-Dependent Kinase Inhibitors Sensitize Tumor Cells to Nutlin-Induced Apoptosis: a Potent Drug Combination. Mol Cancer Res 2007; 5:1133-45. [DOI: 10.1158/1541-7786.mcr-07-0161] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Transcription-associated recombination is dependent on replication in Mammalian cells. Mol Cell Biol 2007; 28:154-64. [PMID: 17967877 DOI: 10.1128/mcb.00816-07] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transcription can enhance recombination; this is a ubiquitous phenomenon from prokaryotes to higher eukaryotes. However, the mechanism of transcription-associated recombination in mammalian cells is poorly understood. Here we have developed a construct with a recombination substrate in which levels of recombination can be studied in the presence or absence of transcription. We observed a direct enhancement in recombination when transcription levels through the substrate were increased. This increase in homologous recombination following transcription is locus specific, since homologous recombination at the unrelated hprt gene is unaffected. In addition, we have shown that transcription-associated recombination involves both short-tract and long-tract gene conversions in mammalian cells, which are different from double-strand-break-induced recombination events caused by endonucleases. Transcription fails to enhance recombination in cells that are not in the S phase of the cell cycle. Furthermore, inhibition of transcription suppresses induction of recombination at stalled replication forks, suggesting that recombination may be involved in bypassing transcription during replication.
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