1
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Lai C, Xu L, Dai S. The nuclear export protein exportin-1 in solid malignant tumours: From biology to clinical trials. Clin Transl Med 2024; 14:e1684. [PMID: 38783482 PMCID: PMC11116501 DOI: 10.1002/ctm2.1684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Exportin-1 (XPO1), a crucial protein regulating nuclear-cytoplasmic transport, is frequently overexpressed in various cancers, driving tumor progression and drug resistance. This makes XPO1 an attractive therapeutic target. Over the past few decades, the number of available nuclear export-selective inhibitors has been increasing. Only KPT-330 (selinexor) has been successfully used for treating haematological malignancies, and KPT-8602 (eltanexor) has been used for treating haematologic tumours in clinical trials. However, the use of nuclear export-selective inhibitors for the inhibition of XPO1 expression has yet to be thoroughly investigated in clinical studies and therapeutic outcomes for solid tumours. METHODS We collected numerous literatures to explain the efficacy of XPO1 Inhibitors in preclinical and clinical studies of a wide range of solid tumours. RESULTS In this review, we focus on the nuclear export function of XPO1 and results from clinical trials of its inhibitors in solid malignant tumours. We summarized the mechanism of action and therapeutic potential of XPO1 inhibitors, as well as adverse effects and response biomarkers. CONCLUSION XPO1 inhibition has emerged as a promising therapeutic strategy in the fight against cancer, offering a novel approach to targeting tumorigenic processes and overcoming drug resistance. SINE compounds have demonstrated efficacy in a wide range of solid tumours, and ongoing research is focused on optimizing their use, identifying response biomarkers, and developing effective combination therapies. KEY POINTS Exportin-1 (XPO1) plays a critical role in mediating nucleocytoplasmic transport and cell cycle. XPO1 dysfunction promotes tumourigenesis and drug resistance within solid tumours. The therapeutic potential and ongoing researches on XPO1 inhibitors in the treatment of solid tumours. Additional researches are essential to address safety concerns and identify biomarkers for predicting patient response to XPO1 inhibitors.
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Affiliation(s)
- Chuanxi Lai
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| | - Lingna Xu
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| | - Sheng Dai
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
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2
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Ngo LH, Bert AG, Dredge BK, Williams T, Murphy V, Li W, Hamilton WB, Carey KT, Toubia J, Pillman KA, Liu D, Desogus J, Chao JA, Deans AJ, Goodall GJ, Wickramasinghe VO. Nuclear export of circular RNA. Nature 2024; 627:212-220. [PMID: 38355801 DOI: 10.1038/s41586-024-07060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
Circular RNAs (circRNAs), which are increasingly being implicated in a variety of functions in normal and cancerous cells1-5, are formed by back-splicing of precursor mRNAs in the nucleus6-10. circRNAs are predominantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here we identify a pathway that is specific for the nuclear export of circular RNA. This pathway requires Ran-GTP, exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter CRM1 selectively increases the nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Depletion or knockout of exportin-2 specifically inhibits nuclear export of circRNA. Analysis of nuclear circRNA-binding proteins reveals that interaction between IGF2BP1 and circRNA is enhanced by Ran-GTP. The formation of circRNA export complexes in the nucleus is promoted by Ran-GTP through its interactions with exportin-2, circRNA and IGF2BP1. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Ran-GTP and exportin-2 to export circRNAs in a mechanism that is analogous to protein export, rather than mRNA export.
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Affiliation(s)
- Linh H Ngo
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Tobias Williams
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Vincent Murphy
- Genome Stability Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Wanqiu Li
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - William B Hamilton
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kirstyn T Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Dawei Liu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Jessica Desogus
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia.
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia.
- Department of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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3
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Ariyapala IS, Buddika K, Hundley HA, Calvi BR, Sokol NS. The RNA binding protein Swm is critical for Drosophila melanogaster intestinal progenitor cell maintenance. Genetics 2022; 222:6619166. [PMID: 35762963 DOI: 10.1093/genetics/iyac099] [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: 01/03/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The regulation of stem cell survival, self-renewal, and differentiation is critical for the maintenance of tissue homeostasis. Although the involvement of signaling pathways and transcriptional control mechanisms in stem cell regulation have been extensively investigated, the role of post-transcriptional control is still poorly understood. Here we show that the nuclear activity of the RNA-binding protein Second Mitotic Wave Missing (Swm) is critical for Drosophila melanogaster intestinal stem cells (ISCs) and their daughter cells, enteroblasts (EBs), to maintain their progenitor cell properties and functions. Loss of swm causes ISCs and EBs to stop dividing and instead detach from the basement membrane, resulting in severe progenitor cell loss. swm loss is further characterized by nuclear accumulation of poly(A)+ RNA in progenitor cells. Swm associates with transcripts involved in epithelial cell maintenance and adhesion, and the loss of swm, while not generally affecting the levels of these Swm-bound mRNAs, leads to elevated expression of proteins encoded by some of them, including the fly ortholog of Filamin. Taken together, this study indicates a nuclear role for Swm in adult stem cell maintenance, raising the possibility that nuclear post-transcriptional regulation of mRNAs encoding cell adhesion proteins ensures proper attachment of progenitor cells.
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Affiliation(s)
| | - Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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4
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Kamp JA, Lemmens BBLG, Romeijn RJ, González-Prieto R, Olsen J, Vertegaal ACO, van Schendel R, Tijsterman M. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic Acids Res 2022; 50:6235-6250. [PMID: 35670662 PMCID: PMC9226523 DOI: 10.1093/nar/gkac472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, induce a shift in DNA repair in dividing and non-dividing tissues. Loss of SMG-1, an ATM/ATR-like kinase central to RNA surveillance by nonsense-mediated decay (NMD), restores DNA repair and radio-resistance in THO-deficient animals. Mechanistically, we find SMG-1 and its downstream target SMG-2/UPF1, but not NMD per se, to suppress DNA repair by non-homologous end-joining in favour of single strand annealing. We postulate that moonlighting proteins create short-circuits in vivo, allowing aberrant RNA to redirect DNA repair.
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Affiliation(s)
| | | | - Ron J Romeijn
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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5
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Iwasaki YW, Sriswasdi S, Kinugasa Y, Adachi J, Horikoshi Y, Shibuya A, Iwasaki W, Tashiro S, Tomonaga T, Siomi H. Piwi-piRNA complexes induce stepwise changes in nuclear architecture at target loci. EMBO J 2021; 40:e108345. [PMID: 34337769 PMCID: PMC8441340 DOI: 10.15252/embj.2021108345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/04/2021] [Accepted: 07/09/2021] [Indexed: 12/25/2022] Open
Abstract
PIWI‐interacting RNAs (piRNAs) are germline‐specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRNA complexes) and play critical roles for preserving genomic integrity by repressing transposable elements (TEs). Drosophila Piwi transcriptionally silences specific targets through heterochromatin formation and increases histone H3K9 methylation (H3K9me3) and histone H1 deposition at these loci, with nuclear RNA export factor variant Nxf2 serving as a co‐factor. Using ChEP and DamID‐seq, we now uncover a Piwi/Nxf2‐dependent target association with nuclear lamins. Hi‐C analysis of Piwi or Nxf2‐depleted cells reveals decreased intra‐TAD and increased inter‐TAD interactions in regions harboring Piwi–piRNA target TEs. Using a forced tethering system, we analyze the functional effects of Piwi–piRNA/Nxf2‐mediated recruitment of piRNA target regions to the nuclear periphery. Removal of active histone marks is followed by transcriptional silencing, chromatin conformational changes, and H3K9me3 and H1 association. Our data show that the Piwi–piRNA pathway can induce stepwise changes in nuclear architecture and chromatin state at target loci for transcriptional silencing.
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Affiliation(s)
- Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan
| | - Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yasuha Kinugasa
- Department of Cellular Biology, Research Institute for Radiation Biology Medicine, Hiroshima University, Hiroshima, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology Medicine, Hiroshima University, Hiroshima, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology Medicine, Hiroshima University, Hiroshima, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
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6
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Mamon L, Yakimova A, Kopytova D, Golubkova E. The RNA-Binding Protein SBR (Dm NXF1) Is Required for the Constitution of Medulla Boundaries in Drosophila melanogaster Optic Lobes. Cells 2021; 10:1144. [PMID: 34068524 PMCID: PMC8151460 DOI: 10.3390/cells10051144] [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: 04/18/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 11/17/2022] Open
Abstract
Drosophila melanogaster sbr (small bristles) is an orthologue of the Nxf1 (nuclear export factor 1) genes in different Opisthokonta. The known function of Nxf1 genes is the export of various mRNAs from the nucleus to the cytoplasm. The cytoplasmic localization of the SBR protein indicates that the nuclear export function is not the only function of this gene in Drosophila. RNA-binding protein SBR enriches the nucleus and cytoplasm of specific neurons and glial cells. In sbr12 mutant males, the disturbance of medulla boundaries correlates with the defects of photoreceptor axons pathfinding, axon bundle individualization, and developmental neurodegeneration. RNA-binding protein SBR participates in processes allowing axons to reach and identify their targets.
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Affiliation(s)
- Ludmila Mamon
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034 St. Petersburg, Russia; or
| | - Anna Yakimova
- A. Tsyb Medical Radiological Research Center—Branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Koroleva Str. 4, 249036 Obninsk, Russia;
| | - Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov St. 34/5, 119334 Moscow, Russia;
| | - Elena Golubkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034 St. Petersburg, Russia; or
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7
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Bensidoun P, Zenklusen D, Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1660. [PMID: 33938148 DOI: 10.1002/wrna.1660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Pierre Bensidoun
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Marlene Oeffinger
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada
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8
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Abstract
Here we review data suggestive of a role for RNA-binding proteins in vertebrate immunity. We focus on the products of genes found in the class III region of the Major Histocompatibility Complex. Six of these genes, DDX39B (aka BAT1), DXO, LSM2, NELFE, PRRC2A (aka BAT2), and SKIV2L, encode RNA-binding proteins with clear roles in post-transcriptional gene regulation and RNA surveillance. These genes are likely to have important functions in immunity and are associated with autoimmune diseases.
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Affiliation(s)
- Geraldine Schott
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Biochemistry and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Programme in Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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9
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Out or decay: fate determination of nuclear RNAs. Essays Biochem 2020; 64:895-905. [DOI: 10.1042/ebc20200005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 02/08/2023]
Abstract
Abstract
In eukaryotes, RNAs newly synthesized by RNA polymerase II (RNAPII) undergo several processing steps prior to transport to the cytoplasm. It has long been known that RNAs with defects in processing or export are removed in the nucleus. Recent studies revealed that RNAs without apparent defects are also subjected to nuclear degradation, indicating that nuclear RNA fate is determined in a more complex and dynamic way than previously thought. Nuclear RNA sorting directly determines the quality and quantity of RNA pools for future translation and thus is of significant importance. In this essay, we will summarize recent studies on this topic, mainly focusing on findings in mammalian system, and discuss about important remaining questions and possible biological relevance for nuclear RNA fate determination.
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10
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Nguyen LTS, Robinson DN. The Unusual Suspects in Cytokinesis: Fitting the Pieces Together. Front Cell Dev Biol 2020; 8:441. [PMID: 32626704 PMCID: PMC7314909 DOI: 10.3389/fcell.2020.00441] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/11/2020] [Indexed: 01/24/2023] Open
Abstract
Cytokinesis is the step of the cell cycle in which the cell must faithfully separate the chromosomes and cytoplasm, yielding two daughter cells. The assembly and contraction of the contractile network is spatially and temporally coupled with the formation of the mitotic spindle to ensure the successful completion of cytokinesis. While decades of studies have elucidated the components of this machinery, the so-called usual suspects, and their functions, many lines of evidence are pointing to other unexpected proteins and sub-cellular systems as also being involved in cytokinesis. These we term the unusual suspects. In this review, we introduce recent discoveries on some of these new unusual suspects and begin to consider how these subcellular systems snap together to help complete the puzzle of cytokinesis.
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Affiliation(s)
- Ly T. S. Nguyen
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Douglas N. Robinson
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, United States
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11
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Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex. Mol Cell 2020; 79:251-267.e6. [PMID: 32504555 DOI: 10.1016/j.molcel.2020.05.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/23/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022]
Abstract
The core components of the nuclear RNA export pathway are thought to be required for export of virtually all polyadenylated RNAs. Here, we depleted different proteins that act in nuclear export in human cells and quantified the transcriptome-wide consequences on RNA localization. Different genes exhibited substantially variable sensitivities, with depletion of NXF1 and TREX components causing some transcripts to become strongly retained in the nucleus while others were not affected. Specifically, NXF1 is preferentially required for export of single- or few-exon transcripts with long exons or high A/U content, whereas depletion of TREX complex components preferentially affects spliced and G/C-rich transcripts. Using massively parallel reporter assays, we identified short sequence elements that render transcripts dependent on NXF1 for their export and identified synergistic effects of splicing and NXF1. These results revise the current model of how nuclear export shapes the distribution of RNA within human cells.
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12
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Woldegebriel R, Kvist J, Andersson N, Õunap K, Reinson K, Wojcik MH, Bijlsma EK, Hoffer MJV, Ryan MM, Stark Z, Walsh M, Cuppen I, van den Boogaard MJH, Bharucha-Goebel D, Donkervoort S, Winchester S, Zori R, Bönnemann CG, Maroofian R, O’Connor E, Houlden H, Zhao F, Carpén O, White M, Sreedharan J, Stewart M, Ylikallio E, Tyynismaa H. Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content. Hum Mol Genet 2020; 29:1426-1439. [PMID: 32202298 PMCID: PMC7297229 DOI: 10.1093/hmg/ddaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/15/2022] Open
Abstract
Defects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.
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Affiliation(s)
- Rosa Woldegebriel
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
| | - Noora Andersson
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Genomics and Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique M Ryan
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Royal Children’s Hospital, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Zornitza Stark
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Maie Walsh
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
| | - Inge Cuppen
- Department of Pediatric Neurology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Division of Neurology, Children's National Health System, Washington, DC, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sara Winchester
- Child Neurology Center of Northwest Florida, Pensacola, FL, USA
| | - Roberto Zori
- Division of Genetics and Metabolism, University of Florida, Gainesville, FL, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Emer O’Connor
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Fang Zhao
- Department of Pathology and Genetics, HUSLAB Laboratories, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Matthew White
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jemeen Sreedharan
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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13
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Luna R, Rondón AG, Pérez-Calero C, Salas-Armenteros I, Aguilera A. The THO Complex as a Paradigm for the Prevention of Cotranscriptional R-Loops. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:105-114. [PMID: 32493765 DOI: 10.1101/sqb.2019.84.039594] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Different proteins associate with the nascent RNA and the RNA polymerase (RNAP) to catalyze the transcription cycle and RNA export. If these processes are not properly controlled, the nascent RNA can thread back and hybridize to the DNA template forming R-loops capable of stalling replication, leading to DNA breaks. Given the transcriptional promiscuity of the genome, which leads to large amounts of RNAs from mRNAs to different types of ncRNAs, these can become a major threat to genome integrity if they form R-loops. Consequently, cells have evolved nuclear factors to prevent this phenomenon that includes THO, a conserved eukaryotic complex acting in transcription elongation and RNA processing and export that upon inactivation causes genome instability linked to R-loop accumulation. We revise and discuss here the biological relevance of THO and a number of RNA helicases, including the THO partner UAP56/DDX39B, as a paradigm of the cellular mechanisms of cotranscriptional R-loop prevention.
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Affiliation(s)
- Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Carmen Pérez-Calero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Irene Salas-Armenteros
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
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14
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Shi P, Guo Y, Su Y, Zhu M, Fu Y, Chi H, Wu J, Huang J. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. THE JOURNAL OF IMMUNOLOGY 2020; 205:168-180. [DOI: 10.4049/jimmunol.2000053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022]
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15
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Fujita KI, Yamazaki T, Harada K, Seno S, Matsuda H, Masuda S. URH49 exports mRNA by remodeling complex formation and mediating the NXF1-dependent pathway. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194480. [PMID: 31917363 DOI: 10.1016/j.bbagrm.2020.194480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 12/27/2022]
Abstract
The TREX complex integrates information from nuclear mRNA processing events to ensure the timely export of mRNA to the cytoplasm. In humans, UAP56 and its paralog URH49 form distinct complexes, the TREX complex and the AREX complex, respectively, which cooperatively regulate the expression of a specific set of mRNA species on a genome wide scale. The difference in the complex formation between UAP56 and URH49 are thought to play a critical role in the regulation of target mRNAs. To date, the underlying mechanism remains poorly understood. Here we characterize the formation of the TREX complex and the AREX complex. In the ATP depleted condition, UAP56 formed an Apo-TREX complex containing the THO subcomplex but not ALYREF and CIP29. URH49 formed an Apo-AREX complex containing CIP29 but not ALYREF and the THO subcomplex. However, with the addition of ATP, both the Apo-TREX complex and the Apo-AREX complex were remodeled to highly similar ATP-TREX complex containing the THO subcomplex, ALYREF and CIP29. The knockdown of URH49 caused a reduction in its target mRNAs and a cytokinesis failure. Similarly, cytokinesis abnormality was observed in CIP29 knockdown cells, suggesting that CIP29 belongs to the URH49 regulated mRNA export pathway. Lastly, we confirmed that the export of mRNA in URH49-dependent pathway is achieved by NXF1, which is also observed in UAP56-dependent pathway. Our studies propose an mRNA export model that the mRNA selectivity depends on the Apo-form TREX/AREX complex, which is remodeled to the highly similar ATP-form complex upon ATP loading, and integrated to NXF1.
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Affiliation(s)
- Ken-Ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Tomohiro Yamazaki
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kotaro Harada
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Hideo Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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16
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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17
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Bera M, Kalyana Sundaram RV. Chromosome Territorial Organization Drives Efficient Protein Complex Formation: A Hypothesis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2019; 92:541-548. [PMID: 31543715 PMCID: PMC6747946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In eukaryotes, chromosomes often form a transcriptional kissing loop during interphase. We propose that these kissing loops facilitate the formation of protein complexes. mRNA transcripts from these loops could cluster together into phase-separated nuclear granules. Their export into the ER could be ensured by guided diffusion through the inter-chromatin space followed by association with nuclear baskets and export factors. Inside the ER, these mRNAs would form a translation hub. Juxtaposed translation of these mRNAs would increase the cis/trans protein complex assembly among the nascent protein chains. Eukaryotes might employ this pathway to increase complex formation efficiency.
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Affiliation(s)
- Manindra Bera
- To whom all correspondence should be addressed: Manindra Bera, Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT USA, 06520; Tel: 203-737-3269,
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18
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Murano K, Iwasaki YW, Ishizu H, Mashiko A, Shibuya A, Kondo S, Adachi S, Suzuki S, Saito K, Natsume T, Siomi MC, Siomi H. Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing. EMBO J 2019; 38:e102870. [PMID: 31368590 PMCID: PMC6717896 DOI: 10.15252/embj.2019102870] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway preserves genomic integrity by repressing transposable elements (TEs) in animal germ cells. Among PIWI-clade proteins in Drosophila, Piwi transcriptionally silences its targets through interactions with cofactors, including Panoramix (Panx) and forms heterochromatin characterized by H3K9me3 and H1. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms complexes with Piwi, Panx, and p15. Panx-Nxf2-P15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. In addition, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Panx-Nxf2-P15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway. Our results provide an unexpected connection between an NXF variant and small RNA-mediated co-transcriptional silencing.
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Affiliation(s)
- Kensaku Murano
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
| | - Yuka W Iwasaki
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
| | - Hirotsugu Ishizu
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
| | - Akane Mashiko
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
- Graduate School of EngineeringYokohama National UniversityYokohamaJapan
| | - Aoi Shibuya
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
| | - Shu Kondo
- Invertebrate Genetics LaboratoryNational Institute of GeneticsMishimaShizuokaJapan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug DiscoveryNational Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Saori Suzuki
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Kuniaki Saito
- Invertebrate Genetics LaboratoryNational Institute of GeneticsMishimaShizuokaJapan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug DiscoveryNational Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Mikiko C Siomi
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Haruhiko Siomi
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
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19
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Homolka D, Pillai RS. An RNA exporter that enforces a no-export policy. Nat Struct Mol Biol 2019; 26:758-759. [DOI: 10.1038/s41594-019-0294-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Zheleva A, Gómez-Orte E, Sáenz-Narciso B, Ezcurra B, Kassahun H, de Toro M, Miranda-Vizuete A, Schnabel R, Nilsen H, Cabello J. Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.
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Affiliation(s)
- Angelina Zheleva
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Eva Gómez-Orte
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | | | - Begoña Ezcurra
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Henok Kassahun
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María de Toro
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Juan Cabello
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
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21
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ElMaghraby MF, Andersen PR, Pühringer F, Hohmann U, Meixner K, Lendl T, Tirian L, Brennecke J. A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production. Cell 2019; 178:964-979.e20. [PMID: 31398345 DOI: 10.1016/j.cell.2019.07.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/18/2019] [Accepted: 06/29/2019] [Indexed: 01/22/2023]
Abstract
PIWI-interacting RNAs (piRNAs) guide transposon silencing in animals. The 22-30 nt piRNAs are processed in the cytoplasm from long non-coding RNAs that often lack RNA processing hallmarks of export-competent transcripts. By studying how these transcripts achieve nuclear export, we uncover an RNA export pathway specific for piRNA precursors in the Drosophila germline. This pathway requires Nxf3-Nxt1, a variant of the hetero-dimeric mRNA export receptor Nxf1-Nxt1. Nxf3 interacts with UAP56, a nuclear RNA helicase essential for mRNA export, and CG13741/Bootlegger, which recruits Nxf3-Nxt1 and UAP56 to heterochromatic piRNA source loci. Upon RNA cargo binding, Nxf3 achieves nuclear export via the exportin Crm1 and accumulates together with Bootlegger in peri-nuclear nuage, suggesting that after export, Nxf3-Bootlegger delivers precursor transcripts to the piRNA processing sites. These findings indicate that the piRNA pathway bypasses nuclear RNA surveillance systems to export unprocessed transcripts to the cytoplasm, a strategy also exploited by retroviruses.
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Affiliation(s)
- Mostafa F ElMaghraby
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Peter Refsing Andersen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria.
| | - Florian Pühringer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ulrich Hohmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria; Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Katharina Meixner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Thomas Lendl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria; Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Laszlo Tirian
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria.
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22
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Batki J, Schnabl J, Wang J, Handler D, Andreev VI, Stieger CE, Novatchkova M, Lampersberger L, Kauneckaite K, Xie W, Mechtler K, Patel DJ, Brennecke J. The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Nat Struct Mol Biol 2019; 26:720-731. [PMID: 31384064 PMCID: PMC6828549 DOI: 10.1038/s41594-019-0270-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway protects genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA-guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (silencing factor interacting nuclear export variant), an interdependent protein complex required for Piwi-mediated cotranscriptional silencing in Drosophila. SFiNX consists of Nxf2-Nxt1, a gonad-specific variant of the heterodimeric messenger RNA export receptor Nxf1-Nxt1 and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon derepression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits heterochromatin effectors, while the RNA binding protein Nxf2 licenses cotranscriptional silencing. Our data reveal how Nxf2 might have evolved from an RNA transport receptor into a cotranscriptional silencing factor. Thus, NXF variants, which are abundant in metazoans, can have diverse molecular functions and might have been coopted for host genome defense more broadly.
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Affiliation(s)
- Julia Batki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Veselin I Andreev
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Christian E Stieger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Lisa Lampersberger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Kotryna Kauneckaite
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Wei Xie
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria.
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23
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Fabry MH, Ciabrelli F, Munafò M, Eastwood EL, Kneuss E, Falciatori I, Falconio FA, Hannon GJ, Czech B. piRNA-guided co-transcriptional silencing coopts nuclear export factors. eLife 2019; 8:e47999. [PMID: 31219034 PMCID: PMC6677536 DOI: 10.7554/elife.47999] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal gonads. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx); however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its co-factor, Nxt1, form a complex with Panx and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 or Nxt1 to RNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing.
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Affiliation(s)
- Martin H Fabry
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Filippo Ciabrelli
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Ilaria Falciatori
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Federica A Falconio
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
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24
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Abstract
To ensure efficient and accurate gene expression, pre-mRNA processing and mRNA export need to be balanced. However, how this balance is ensured remains largely unclear. Here, we found that SF3b, a component of U2 snRNP that participates in splicing and 3' processing of pre-mRNAs, interacts with the key mRNA export adaptor THO in vivo and in vitro. Depletion of SF3b reduces THO binding with the mRNA and causes nuclear mRNA retention. Consistently, introducing SF3b binding sites into the mRNA enhances THO recruitment and nuclear export in a dose-dependent manner. These data demonstrate a role of SF3b in promoting mRNA export. In support of this role, SF3b binds with mature mRNAs in the cells. Intriguingly, disruption of U2 snRNP by using a U2 antisense morpholino oligonucleotide does not inhibit, but promotes, the role of SF3b in mRNA export as a result of enhanced SF3b-THO interaction and THO recruitment to the mRNA. Together, our study uncovers a U2-snRNP-independent role of SF3b in mRNA export and suggests that SF3b contributes to balancing pre-mRNA processing and mRNA export.
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25
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Singh AK, Choudhury SR, De S, Zhang J, Kissane S, Dwivedi V, Ramanathan P, Petric M, Orsini L, Hebenstreit D, Brogna S. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. eLife 2019; 8:e41444. [PMID: 30907728 PMCID: PMC6447362 DOI: 10.7554/elife.41444] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
UPF1 is an RNA helicase that is required for nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3'UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm by a mechanism that requires its RNA helicase activity. UPF1 is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary glands and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNAs, and cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and their export from the nucleus.
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Affiliation(s)
- Anand K Singh
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Sandip De
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Jie Zhang
- Life SciencesUniversity of WarwickCoventryUnited Kingdom
| | - Stephen Kissane
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Vibha Dwivedi
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Marija Petric
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Luisa Orsini
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Saverio Brogna
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
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26
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Abstract
Although it was long assumed that eukaryotic pre-mRNAs are almost always spliced to generate linear mRNAs, it is now clear that thousands of protein-coding genes can be non-canonically spliced using backsplicing to produce circular RNAs (circRNAs). Most mature circRNAs accumulate in the cytoplasm; however, little is known about how circRNAs are exported from the nucleus to the cytoplasm as they lack many of the common signals used for mRNA export. In this point-of-view article, we will discuss our recently identified circRNA nuclear export pathway and address important open questions in the field.
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Affiliation(s)
- Zhengguo Li
- a School of Life Sciences , Chongqing University , Chongqing , China.,b Institute of Advanced Interdisciplinary Studies , Chongqing University , Chongqing , China
| | - Michael G Kearse
- c Department of Biochemistry and Biophysics , University of Pennsylvania, Perelman School of Medicine , Philadelphia , PA , USA
| | - Chuan Huang
- a School of Life Sciences , Chongqing University , Chongqing , China.,b Institute of Advanced Interdisciplinary Studies , Chongqing University , Chongqing , China
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Chiba S, Hill-Batorski L, Neumann G, Kawaoka Y. The Cellular DExD/H-Box RNA Helicase UAP56 Co-localizes With the Influenza A Virus NS1 Protein. Front Microbiol 2018; 9:2192. [PMID: 30258431 PMCID: PMC6144874 DOI: 10.3389/fmicb.2018.02192] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
UAP56, a member of the DExD/H-box RNA helicase family, is essential for pre-mRNA splicing and mRNA export in eukaryotic cells. In influenza A virus-infected cells, UAP56 mediates viral mRNA nuclear export, facilitates viral ribonucleoprotein complex formation through direct interaction with the viral nucleoprotein, and may indirectly affect antiviral host responses by binding to and/or facilitating the activation of the antiviral host factors MxA and PKR. Here, we demonstrate that UAP56 also co-localizes with the influenza A viral NS1 protein, which counteracts host cell innate immune responses stimulated by virus infection. The UAP56-NS1 association relies on the RNA-binding residues R38 and K41 in NS1 and may be mediated by single-stranded RNA. UAP56 association with NS1 does not affect the NS1-mediated downregulation of cellular innate immune pathways in reporter gene assays, leaving in question the exact biological role and relevance of the UAP56-NS1 association.
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Affiliation(s)
- Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Lindsay Hill-Batorski
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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28
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Yakimova AO, Golubkova EV, Sarantseva SV, Mamon LA. Ellipsoid Body and Medulla Defects and Locomotion Disturbances in sbr (small bristles) Mutants of Drosophila melanogaster. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Huang C, Liang D, Tatomer DC, Wilusz JE. A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev 2018; 32:639-644. [PMID: 29773557 PMCID: PMC6004072 DOI: 10.1101/gad.314856.118] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/24/2018] [Indexed: 11/26/2022]
Abstract
Here, Huang et al. investigated how circRNA localization or nuclear export is controlled and, using RNAi screening, found that depletion of the Drosophila DExH/D-box helicase Hel25E results in nuclear accumulation of long (>800-nt), but not short, circRNAs. Their findings suggest that the lengths of mature circRNAs are measured to dictate the mode of nuclear export. Circular RNAs (circRNAs) are generated from many protein-coding genes. Most accumulate in the cytoplasm, but how circRNA localization or nuclear export is controlled remains unclear. Using RNAi screening, we found that depletion of the Drosophila DExH/D-box helicase Hel25E results in nuclear accumulation of long (>800-nucleotide), but not short, circRNAs. The human homologs of Hel25E similarly regulate circRNA localization, as depletion of UAP56 (DDX39B) or URH49 (DDX39A) causes long and short circRNAs, respectively, to become enriched in the nucleus. These data suggest that the lengths of mature circRNAs are measured to dictate the mode of nuclear export.
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Affiliation(s)
- Chuan Huang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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30
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Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. eLife 2017; 6:32537. [PMID: 29280736 PMCID: PMC5762160 DOI: 10.7554/elife.32537] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning (‘intron definition’) or exon-spanning (‘exon definition’) pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila, using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60–70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. We observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.
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Affiliation(s)
- Athma A Pai
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Kayla McCue
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle, United States
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
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31
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Fan J, Kuai B, Wu G, Wu X, Chi B, Wang L, Wang K, Shi Z, Zhang H, Chen S, He Z, Wang S, Zhou Z, Li G, Cheng H. Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export. EMBO J 2017; 36:2870-2886. [PMID: 28801509 DOI: 10.15252/embj.201696139] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 07/21/2017] [Accepted: 07/23/2017] [Indexed: 12/20/2022] Open
Abstract
The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex (CBC), and this competition is critical for determining whether an RNA is degraded or exported to the cytoplasm. Together, our results indicate that the competition between hMTR4 and ALYREF determines exosome recruitment and functions in creating balanced nuclear RNA pools for degradation and export.
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Affiliation(s)
- Jing Fan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bin Kuai
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guifen Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xudong Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Binkai Chi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lantian Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ke Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhubing Shi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Heng Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Zhisong He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siyuan Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaocai Zhou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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32
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Kopytova D, Popova V, Kurshakova M, Shidlovskii Y, Nabirochkina E, Brechalov A, Georgiev G, Georgieva S. ORC interacts with THSC/TREX-2 and its subunits promote Nxf1 association with mRNP and mRNA export in Drosophila. Nucleic Acids Res 2016; 44:4920-33. [PMID: 27016737 PMCID: PMC4889942 DOI: 10.1093/nar/gkw192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/11/2016] [Indexed: 12/20/2022] Open
Abstract
The origin recognition complex (ORC) of eukaryotes associates with the replication origins and initiates the pre-replication complex assembly. In the literature, there are several reports of interaction of ORC with different RNAs. Here, we demonstrate for the first time a direct interaction of ORC with the THSC/TREX-2 mRNA nuclear export complex. The THSC/TREX-2 was purified from the Drosophila embryonic extract and found to bind with a fraction of the ORC. This interaction occurred via several subunits and was essential for Drosophila viability. Also, ORC was associated with mRNP, which was facilitated by TREX-2. ORC subunits interacted with the Nxf1 receptor mediating the bulk mRNA export. The knockdown of Orc5 led to a drop in the Nxf1 association with mRNP, while Orc3 knockdown increased the level of mRNP-bound Nxf1. The knockdown of Orc5, Orc3 and several other ORC subunits led to an accumulation of mRNA in the nucleus, suggesting that ORC participates in the regulation of the mRNP export.
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Affiliation(s)
- Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Yulii Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Elena Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander Brechalov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Georgii Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Sofia Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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33
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Li P, Noegel AA. Inner nuclear envelope protein SUN1 plays a prominent role in mammalian mRNA export. Nucleic Acids Res 2015; 43:9874-88. [PMID: 26476453 PMCID: PMC4787764 DOI: 10.1093/nar/gkv1058] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 10/01/2015] [Indexed: 11/12/2022] Open
Abstract
Nuclear export of messenger ribonucleoproteins (mRNPs) through the nuclear pore complex (NPC) can be roughly classified into two forms: bulk and specific export, involving an nuclear RNA export factor 1 (NXF1)-dependent pathway and chromosome region maintenance 1 (CRM1)-dependent pathway, respectively. SUN proteins constitute the inner nuclear envelope component of the linker of nucleoskeleton and cytoskeleton (LINC) complex. Here, we show that mammalian cells require SUN1 for efficient nuclear mRNP export. The results indicate that both SUN1 and SUN2 interact with heterogeneous nuclear ribonucleoprotein (hnRNP) F/H and hnRNP K/J. SUN1 depletion inhibits the mRNP export, with accumulations of both hnRNPs and poly(A)+RNA in the nucleus. Leptomycin B treatment indicates that SUN1 functions in mammalian mRNA export involving the NXF1-dependent pathway. SUN1 mediates mRNA export through its association with mRNP complexes via a direct interaction with NXF1. Additionally, SUN1 associates with the NPC through a direct interaction with Nup153, a nuclear pore component involved in mRNA export. Taken together, our results reveal that the inner nuclear envelope protein SUN1 has additional functions aside from being a central component of the LINC complex and that it is an integral component of the mammalian mRNA export pathway suggesting a model whereby SUN1 recruits NXF1-containing mRNP onto the nuclear envelope and hands it over to Nup153.
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Affiliation(s)
- Ping Li
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany
| | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany
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34
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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35
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Viphakone N, Cumberbatch MG, Livingstone MJ, Heath PR, Dickman MJ, Catto JW, Wilson SA. Luzp4 defines a new mRNA export pathway in cancer cells. Nucleic Acids Res 2015; 43:2353-66. [PMID: 25662211 PMCID: PMC4344508 DOI: 10.1093/nar/gkv070] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cancer testis antigens (CTAs) represented a poorly characterized group of proteins whose expression is normally restricted to testis but are frequently up-regulated in cancer cells. Here we show that one CTA, Luzp4, is an mRNA export adaptor. It associates with the TREX mRNA export complex subunit Uap56 and harbours a Uap56 binding motif, conserved in other mRNA export adaptors. Luzp4 binds the principal mRNA export receptor Nxf1, enhances its RNA binding activity and complements Alyref knockdown in vivo. Whilst Luzp4 is up-regulated in a range of tumours, it appears preferentially expressed in melanoma cells where it is required for growth.
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Affiliation(s)
- Nicolas Viphakone
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, UK
| | - Marcus G Cumberbatch
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, UK Academic Urology Unit, The University of Sheffield, Beech Hill Road, Sheffield, UK
| | - Michaela J Livingstone
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, 385a Glossop Road, Sheffield, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, UK
| | - James W Catto
- Academic Urology Unit, The University of Sheffield, Beech Hill Road, Sheffield, UK
| | - Stuart A Wilson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, UK
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Drayton RM, Rehman I, Clarke R, Zhao Z, Pang K, Miah S, Stoehr R, Hartmann A, Blizard S, Lavin M, Bryant HE, Martens-Uzunova ES, Jenster G, Hamdy FC, Gardiner RA, Catto JWF. Identification and diagnostic performance of a small RNA within the PCA3 and BMCC1 gene locus that potentially targets mRNA. Cancer Epidemiol Biomarkers Prev 2014; 24:268-75. [PMID: 25392181 DOI: 10.1158/1055-9965.epi-14-0377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND PCA3 is a long noncoding RNA (lncRNA) with unknown function, upregulated in prostate cancer. LncRNAs may be processed into smaller active species. We hypothesized this for PCA3. METHODS We computed feasible RNA hairpins within the BMCC1 gene (encompassing PCA3) and searched a prostate transcriptome for these. We measured expression using qRT-PCR in three cohorts of prostate cancer tissues (n = 60), exfoliated urinary cells (n = 484 with cancer and n = 166 controls), and in cell lines (n = 22). We used in silico predictions and RNA knockup to identify potential mRNA targets of short transcribed RNAs. RESULTS We predicted 13 hairpins, of which PCA3-shRNA2 was most abundant within the prostate transcriptome. PCA3-shRNA2 is located within intron 1 of PCA3 and appears regulated by androgens. Expression of PCA3-shRNA2 was upregulated in malignant prostatic tissues, exfoliated urinary cells from men with prostate cancer (13-273 fold change; t test P < 0.003), and closely correlated to PCA3 expression (r = 0.84-0.93; P < 0.001). Urinary PCA3-shRNA2 (C-index, 0.75-0.81) and PCA3 (C-index, 0.78) could predict the presence of cancer in most men. PCA3-shRNA2 knockup altered the expression of predicted target mRNAs, including COPS2, SOX11, WDR48, TEAD1, and Noggin. PCA3-shRNA2 expression was negatively correlated with COPS2 in patient samples (r = -0.32; P < 0.001). CONCLUSION We identified a short RNA within PCA3, whose expression is correlated to PCA3, which may target mRNAs implicated in prostate biology. IMPACT This short RNA is stable ex vivo, suggesting a role as a robust biomarker. We identify cytoplasmic enrichment of this RNA and potential targeting of mRNAs implicated in prostate carcinogenesis.
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Affiliation(s)
- Ross M Drayton
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Ishtiaq Rehman
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Raymond Clarke
- Department of Urology, University of Queensland, Brisbane, Australia
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Karl Pang
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Saiful Miah
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Robert Stoehr
- Department of Pathology, University of Erlangen, Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, University of Erlangen, Erlangen, Germany
| | - Sheila Blizard
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Martin Lavin
- Department of Urology, University of Queensland, Brisbane, Australia
| | - Helen E Bryant
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom
| | | | - Guido Jenster
- Department of Urology, Josephine Nefkens Institute, Erasmus MC, Rotterdam, the Netherlands
| | - Freddie C Hamdy
- Nuffield Department of Surgery, University of Oxford, Oxford, United Kingdom
| | - Robert A Gardiner
- Department of Urology, University of Queensland, Brisbane, Australia
| | - James W F Catto
- Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, United Kingdom.
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Sumoylation is Required for the Cytoplasmic Accumulation of a Subset of mRNAs. Genes (Basel) 2014; 5:982-1000. [PMID: 25333844 PMCID: PMC4276922 DOI: 10.3390/genes5040982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/26/2014] [Accepted: 10/04/2014] [Indexed: 12/17/2022] Open
Abstract
In order to discover novel proteins that promote the nuclear export of newly synthesized mRNAs in mammalian cells, we carried out a limited RNAi screen for proteins required for the proper cytoplasmic distribution of a model intronless mRNA. From this screen we obtained two hits, Ubc9 (SUMO-conjugating E2 enzyme) and GANP (germinal center-associated nuclear protein). Depletion of Ubc9 inhibited the proper cytoplasmic distribution of certain overexpressed intronless mRNAs, while depletion of GANP affected all tested mRNAs. Depletion of Sae1, which is also required for sumoylation, partially inhibited the cytoplasmic distribution of our model mRNA. Interestingly, the block in cytoplasmic accumulation in Ubc9-depleted cells could be overcome if an intron was incorporated into the mRNA. Surprisingly, Ubc9-depleted cells had normal nuclear export of newly synthesized intronless mRNAs, indicating that the observed accumulation of the model mRNA in the nuclei of transfected cells was likely due to some more general perturbation. Indeed, depletion of Ubc9, coupled with the overexpression of the intronless mRNAs, caused the redistribution of the nuclear speckle protein SC35 to cytoplasmic foci. Our results suggest that sumoylation may play a role in the proper assembly of mRNPs and/or the distribution of key RNA binding proteins, and may thus contribute to general protein expression patterns.
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38
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Inoue AH, Serpeloni M, Hiraiwa PM, Yamada-Ogatta SF, Muniz JRC, Motta MCM, Vidal NM, Goldenberg S, Ávila AR. Identification of a novel nucleocytoplasmic shuttling RNA helicase of trypanosomes. PLoS One 2014; 9:e109521. [PMID: 25313564 PMCID: PMC4196910 DOI: 10.1371/journal.pone.0109521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression in trypanosomes is controlled mostly by post-transcriptional pathways. Little is known about the components of mRNA nucleocytoplasmic export routes in these parasites. Comparative genomics has shown that the mRNA transport pathway is the least conserved pathway among eukaryotes. Nonetheless, we identified a RNA helicase (Hel45) that is conserved across eukaryotes and similar to shuttling proteins involved in mRNA export. We used in silico analysis to predict the structure of Trypanosoma cruzi Hel45, including the N-terminal domain and the C-terminal domain, and our findings suggest that this RNA helicase can form complexes with mRNA. Hel45 was present in both nucleus and cytoplasm. Electron microscopy showed that Hel45 is clustered close to the cytoplasmic side of nuclear pore complexes, and is also present in the nucleus where it is associated with peripheral compact chromatin. Deletion of a predicted Nuclear Export Signal motif led to the accumulation of Hel45ΔNES in the nucleus, indicating that Hel45 shuttles between the nucleus and the cytoplasm. This transport was dependent on active transcription but did not depend on the exportin Crm1. Knockdown of Mex67 in T. brucei caused the nuclear accumulation of the T. brucei ortholog of Hel45. Indeed, Hel45 is present in mRNA ribonucleoprotein complexes that are not associated with polysomes. It is still necessary to confirm the precise function of Hel45. However, this RNA helicase is associated with mRNA metabolism and its nucleocytoplasmic shuttling is dependent on an mRNA export route involving Mex67 receptor.
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Affiliation(s)
| | - Mariana Serpeloni
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- Departamento de Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | | | - Maria Cristina Machado Motta
- Departamento de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Newton Medeiros Vidal
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Wickramasinghe VO, Andrews R, Ellis P, Langford C, Gurdon JB, Stewart M, Venkitaraman AR, Laskey RA. Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP. Nucleic Acids Res 2014; 42:5059-71. [PMID: 24510098 PMCID: PMC4005691 DOI: 10.1093/nar/gku095] [Citation(s) in RCA: 52] [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: 08/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 01/21/2023] Open
Abstract
The nuclear phase of the gene expression pathway culminates in the export of mature messenger RNAs (mRNAs) to the cytoplasm through nuclear pore complexes. GANP (germinal- centre associated nuclear protein) promotes the transfer of mRNAs bound to the transport factor NXF1 to nuclear pore complexes. Here, we demonstrate that GANP, subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex, promotes selective nuclear export of a specific subset of mRNAs whose transport depends on NXF1. Genome-wide gene expression profiling showed that half of the transcripts whose nuclear export was impaired following NXF1 depletion also showed reduced export when GANP was depleted. GANP-dependent transcripts were highly expressed, yet short-lived, and were highly enriched in those encoding central components of the gene expression machinery such as RNA synthesis and processing factors. After injection into Xenopus oocyte nuclei, representative GANP-dependent transcripts showed faster nuclear export kinetics than representative transcripts that were not influenced by GANP depletion. We propose that GANP promotes the nuclear export of specific classes of mRNAs that may facilitate rapid changes in gene expression.
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Affiliation(s)
- Vihandha O. Wickramasinghe
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Robert Andrews
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Peter Ellis
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Cordelia Langford
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - John B. Gurdon
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Murray Stewart
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ashok R. Venkitaraman
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ronald A. Laskey
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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Murine leukemia virus uses TREX components for efficient nuclear export of unspliced viral transcripts. Viruses 2014; 6:1135-48. [PMID: 24618812 PMCID: PMC3970143 DOI: 10.3390/v6031135] [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] [Received: 12/12/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 11/17/2022] Open
Abstract
Previously we reported that nuclear export of both unspliced and spliced murine leukemia virus (MLV) transcripts depends on the nuclear export factor (NXF1) pathway. Although the mRNA export complex TREX, which contains Aly/REF, UAP56, and the THO complex, is involved in the NXF1-mediated nuclear export of cellular mRNAs, its contribution to the export of MLV mRNA transcripts remains poorly understood. Here, we studied the involvement of TREX components in the export of MLV transcripts. Depletion of UAP56, but not Aly/REF, reduced the level of both unspliced and spliced viral transcripts in the cytoplasm. Interestingly, depletion of THO components, including THOC5 and THOC7, affected only unspliced viral transcripts in the cytoplasm. Moreover, the RNA immunoprecipitation assay showed that only the unspliced viral transcript interacted with THOC5. These results imply that MLV requires UAP56, THOC5 and THOC7, in addition to NXF1, for nuclear export of viral transcripts. Given that naturally intronless mRNAs, but not bulk mRNAs, require THOC5 for nuclear export, it is plausible that THOC5 plays a key role in the export of unspliced MLV transcripts.
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Yasunaga A, Hanna SL, Li J, Cho H, Rose PP, Spiridigliozzi A, Gold B, Diamond MS, Cherry S. Genome-wide RNAi screen identifies broadly-acting host factors that inhibit arbovirus infection. PLoS Pathog 2014; 10:e1003914. [PMID: 24550726 PMCID: PMC3923753 DOI: 10.1371/journal.ppat.1003914] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 12/18/2013] [Indexed: 01/12/2023] Open
Abstract
Vector-borne viruses are an important class of emerging and re-emerging pathogens; thus, an improved understanding of the cellular factors that modulate infection in their respective vertebrate and insect hosts may aid control efforts. In particular, cell-intrinsic antiviral pathways restrict vector-borne viruses including the type I interferon response in vertebrates and the RNA interference (RNAi) pathway in insects. However, it is likely that additional cell-intrinsic mechanisms exist to limit these viruses. Since insects rely on innate immune mechanisms to inhibit virus infections, we used Drosophila as a model insect to identify cellular factors that restrict West Nile virus (WNV), a flavivirus with a broad and expanding geographical host range. Our genome-wide RNAi screen identified 50 genes that inhibited WNV infection. Further screening revealed that 17 of these genes were antiviral against additional flaviviruses, and seven of these were antiviral against other vector-borne viruses, expanding our knowledge of invertebrate cell-intrinsic immunity. Investigation of two newly identified factors that restrict diverse viruses, dXPO1 and dRUVBL1, in the Tip60 complex, demonstrated they contributed to antiviral defense at the organismal level in adult flies, in mosquito cells, and in mammalian cells. These data suggest the existence of broadly acting and functionally conserved antiviral genes and pathways that restrict virus infections in evolutionarily divergent hosts.
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Affiliation(s)
- Ari Yasunaga
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sheri L. Hanna
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jianqing Li
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Hyelim Cho
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Patrick P. Rose
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anna Spiridigliozzi
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beth Gold
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael S. Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Wickramasinghe VO, Savill JM, Chavali S, Jonsdottir AB, Rajendra E, Grüner T, Laskey RA, Babu MM, Venkitaraman AR. Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity. Mol Cell 2013; 51:737-50. [PMID: 24074953 DOI: 10.1016/j.molcel.2013.08.031] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/20/2013] [Accepted: 08/14/2013] [Indexed: 01/08/2023]
Abstract
Messenger RNA (mRNA) export from the nucleus is essential for eukaryotic gene expression. Here we identify a transcript-selective nuclear export mechanism affecting certain human transcripts, enriched for functions in genome duplication and repair, controlled by inositol polyphosphate multikinase (IPMK), an enzyme catalyzing inositol polyphosphate and phosphoinositide turnover. We studied transcripts encoding RAD51, a protein essential for DNA repair by homologous recombination (HR), to characterize the mechanism underlying IPMK-regulated mRNA export. IPMK depletion or catalytic inactivation selectively decreases RAD51 protein abundance and the nuclear export of RAD51 mRNA, thereby impairing HR. Recognition of a sequence motif in the untranslated region of RAD51 transcripts by the mRNA export factor ALY requires IPMK. Phosphatidylinositol (3,4,5)-trisphosphate (PIP3), an IPMK product, restores ALY recognition in IPMK-depleted cell extracts, suggesting a mechanism underlying transcript selection. Our findings implicate IPMK in a transcript-selective mRNA export pathway controlled by phosphoinositide turnover that preserves genome integrity in humans.
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Affiliation(s)
- Vihandha O Wickramasinghe
- The Medical Research Council Cancer Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
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43
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Yang H, Lowenson JD, Clarke S, Zubarev RA. Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice. J Proteome Res 2013; 12:4566-76. [PMID: 23947766 DOI: 10.1021/pr400688r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein l-isoaspartyl methyltransferase (PIMT) repairs the isoaspartyl residues (isoAsp) that originate from asparagine deamidation and aspartic acid (Asp) isomerization to Asp residues. Deletion of the gene encoding PIMT in mice (Pcmt1) leads to isoAsp accumulation in all tissues measured, especially in the brain. These PIMT-knockout (PIMT-KO) mice have perturbed glutamate metabolism and die prematurely of epileptic seizures. To elucidate the role of PIMT further, brain proteomes of PIMT-KO mice and controls were analyzed. The isoAsp levels from two of the detected 67 isoAsp sites (residue 98 from calmodulin and 68 from glyceraldehyde-3-phosphate dehydrogenase) were quantified and found to be significantly increased in PIMT-KO mice (p < 0.01). Additionally, the abundance of at least 151 out of the 1017 quantified proteins was found to be altered in PIMT-KO mouse brains. Gene ontology analysis revealed that many down-regulated proteins are involved in cellular amino acid biosynthesis. For example, the serine synthesis pathway was suppressed, possibly leading to reduced serine production in PIMT-KO mice. Additionally, the abundances of enzymes in the glutamate-glutamine cycle were altered toward the accumulation of glutamate. These findings support the involvement of PIMT in glutamate metabolism and suggest that the absence of PIMT also affects other processes involving amino acid synthesis and metabolism.
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Affiliation(s)
- Hongqian Yang
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Scheeles väg 2, SE-17 177 Stockholm, Sweden
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Caporilli S, Yu Y, Jiang J, White-Cooper H. The RNA export factor, Nxt1, is required for tissue specific transcriptional regulation. PLoS Genet 2013; 9:e1003526. [PMID: 23754955 PMCID: PMC3674997 DOI: 10.1371/journal.pgen.1003526] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 04/08/2013] [Indexed: 01/19/2023] Open
Abstract
The highly conserved, Nxf/Nxt (TAP/p15) RNA nuclear export pathway is important for export of most mRNAs from the nucleus, by interacting with mRNAs and promoting their passage through nuclear pores. Nxt1 is essential for viability; using a partial loss of function allele, we reveal a role for this gene in tissue specific transcription. We show that many Drosophila melanogaster testis-specific mRNAs require Nxt1 for their accumulation. The transcripts that require Nxt1 also depend on a testis-specific transcription complex, tMAC. We show that loss of Nxt1 leads to reduced transcription of tMAC targets. A reporter transcript from a tMAC-dependent promoter is under-expressed in Nxt1 mutants, however the same transcript accumulates in mutants if driven by a tMAC-independent promoter. Thus, in Drosophila primary spermatocytes, the transcription factor used to activate expression of a transcript, rather than the RNA sequence itself or the core transcription machinery, determines whether this expression requires Nxt1. We additionally find that transcripts from intron-less genes are more sensitive to loss of Nxt1 function than those from intron-containing genes and propose a mechanism in which transcript processing feeds back to increase activity of a tissue specific transcription complex.
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Affiliation(s)
- Simona Caporilli
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Yachuan Yu
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Jianqiao Jiang
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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45
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Muerdter F, Guzzardo PM, Gillis J, Luo Y, Yu Y, Chen C, Fekete R, Hannon GJ. A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol Cell 2013; 50:736-48. [PMID: 23665228 DOI: 10.1016/j.molcel.2013.04.006] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/19/2023]
Abstract
A large fraction of our genome consists of mobile genetic elements. Governing transposons in germ cells is critically important, and failure to do so compromises genome integrity, leading to sterility. In animals, the piRNA pathway is the key to transposon constraint, yet the precise molecular details of how piRNAs are formed and how the pathway represses mobile elements remain poorly understood. In an effort to identify general requirements for transposon control and components of the piRNA pathway, we carried out a genome-wide RNAi screen in Drosophila ovarian somatic sheet cells. We identified and validated 87 genes necessary for transposon silencing. Among these were several piRNA biogenesis factors. We also found CG3893 (asterix) to be essential for transposon silencing, most likely by contributing to the effector step of transcriptional repression. Asterix loss leads to decreases in H3K9me3 marks on certain transposons but has no effect on piRNA levels.
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Affiliation(s)
- Felix Muerdter
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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TREX exposes the RNA-binding domain of Nxf1 to enable mRNA export. Nat Commun 2013; 3:1006. [PMID: 22893130 PMCID: PMC3654228 DOI: 10.1038/ncomms2005] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 07/11/2012] [Indexed: 12/03/2022] Open
Abstract
The metazoan TREX complex is recruited to mRNA during nuclear RNA processing and functions in exporting mRNA to the cytoplasm. Nxf1 is an mRNA export receptor, which binds processed mRNA and transports it through the nuclear pore complex. At present, the relationship between TREX and Nxf1 is not understood. Here we show that Nxf1 uses an intramolecular interaction to inhibit its own RNA binding activity. When the TREX subunits Aly and Thoc5 make contact with Nxf1, Nxf1 is driven into an open conformation, exposing its RNA binding domain, allowing RNA binding. Moreover, the combined knockdown of Aly and Thoc5 drastically reduces the amount of Nxf1 bound to mRNA in vivo and also causes a severe mRNA export block. Together, our data indicate that TREX provides a license for mRNA export by driving Nxf1 into a conformation capable of binding mRNA.
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Chtop is a component of the dynamic TREX mRNA export complex. EMBO J 2013; 32:473-86. [PMID: 23299939 PMCID: PMC3567497 DOI: 10.1038/emboj.2012.342] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 12/03/2012] [Indexed: 11/08/2022] Open
Abstract
The TREX complex couples nuclear pre-mRNA processing with mRNA export and contains multiple protein components, including Uap56, Alyref, Cip29 and the multi-subunit THO complex. Here, we have identified Chtop as a novel TREX component. We show that both Chtop and Alyref activate the ATPase and RNA helicase activities of Uap56 and that Uap56 functions to recruit both Alyref and Chtop onto mRNA. As observed with the THO complex subunit Thoc5, Chtop binds to the NTF2-like domain of Nxf1, and this interaction requires arginine methylation of Chtop. Using RNAi, we show that co-knockdown of Alyref and Chtop results in a potent mRNA export block. Chtop binds to Uap56 in a mutually exclusive manner with Alyref, and Chtop binds to Nxf1 in a mutually exclusive manner with Thoc5. However, Chtop, Thoc5 and Nxf1 exist in a single complex in vivo. Together, our data indicate that TREX and Nxf1 undergo dynamic remodelling, driven by the ATPase cycle of Uap56 and post-translational modifications of Chtop.
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Mamon LA, Kliver SF, Golubkova EV. Evolutionarily conserved features of the retained intron in alternative transcripts of the <i>nxf1</i> (nuclear export factor) genes in different organisms. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojgen.2013.33018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pan H, Liu S, Tang D. HPR1, a component of the THO/TREX complex, plays an important role in disease resistance and senescence in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:831-843. [PMID: 22035198 DOI: 10.1111/j.1365-313x.2011.04835.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
ENHANCED DISEASE RESISTANCE 1 (EDR1) is a negative regulator of powdery mildew resistance, cell death and ethylene-induced senescence. To identify components involved in EDR1 signaling, we performed a forward genetic screen for edr1 suppressors. In this screen, we identified the hpr1-4 mutation, which partially suppresses edr1-mediated resistance to the powdery mildew pathogen Golovinomyces cichoracearum and mildew-induced cell death. However, the hpr1-4 mutation enhanced the ethylene-induced senescence phenotype of edr1. The hpr1-4 single mutant displayed enhanced susceptibility to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 and the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Arabidopsis HPR1 encodes a homolog of human HPR1, a component of the conserved THO/transcription export (THO/TREX) complex that is required for mRNA export in yeast and humans. HPR1 is expressed in various organs and throughout all developmental stages. HPR1 localizes to the nucleus, and, significantly, mRNA export is compromised in the hpr1-4 mutant. Taken together, these data demonstrate that HPR1 plays an important role in disease resistance in plants, and that the THO/TREX complex is functionally conserved among plants, yeast and humans. Our data indicate a general link between mRNA export, defense responses and ethylene signaling in plants.
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Affiliation(s)
- Huairong Pan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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50
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Xiong F, Lin Y, Han Z, Shi G, Tian L, Wu X, Zeng Q, Zhou Y, Deng J, Chen H. Plk1-mediated phosphorylation of UAP56 regulates the stability of UAP56. Mol Biol Rep 2012; 39:1935-42. [PMID: 21637952 DOI: 10.1007/s11033-011-0940-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
Polo-like kinase 1 (Plk1) is a conserved serine/threonine protein kinase that plays pivotal roles during the cell cycle and cell proliferation. Although a number of important targets have been identified, the mechanism of Plk1-regulated pathways and the bulk of the Plk1 interactome are largely unknown. Here, we demonstrate that Plk1 interacts with the DExH/D RNA helicase, UAP56. The protein levels of UAP56 and Plk1 are inversely correlated during the cell cycle. We also show that Plk1 phosphorylates UAP56 in vitro and in vivo and that Plk1-dependent phosphorylation of UAP56 triggers ubiquitination and degradation of UAP56 through proteasomes. This result suggests that Plk1-mediated phosphorylation of UAP56 regulates the stability of UAP56. Our results will be helpful in further understanding mRNA metabolism, cell cycle progression, and the link between mRNA metabolism and cellular function.
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Affiliation(s)
- Fuyin Xiong
- Beijing Institute of Biotechnology, Beijing 100071, People's Republic of China
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