1
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Garland W, Jensen TH. Nuclear sorting of short RNA polymerase II transcripts. Mol Cell 2024; 84:3644-3655. [PMID: 39366352 DOI: 10.1016/j.molcel.2024.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 10/06/2024]
Abstract
Mammalian genomes produce an abundance of short RNA. This is, to a large extent, due to the genome-wide and spurious activity of RNA polymerase II (RNAPII). However, it is also because the vast majority of initiating RNAPII, regardless of the transcribed DNA unit, terminates within a ∼3-kb early "pausing zone." Given that the resultant RNAs constitute both functional and non-functional species, their proper sorting is critical. One way to think about such quality control (QC) is that transcripts, from their first emergence, are relentlessly targeted by decay factors, which may only be avoided by engaging protective processing pathways. In a molecular materialization of this concept, recent progress has found that both "destructive" and "productive" RNA effectors assemble at the 5' end of capped RNA, orchestrated by the essential arsenite resistance protein 2 (ARS2) protein. Based on this principle, we here discuss early QC mechanisms and how these might sort short RNAs to their final fates.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus, Denmark.
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2
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Xu C, Chen G, Yu B, Sun B, Zhang Y, Zhang M, Yang Y, Xiao Y, Cheng S, Li Y, Feng H. TRIM24 Cooperates with Ras Mutation to Drive Glioma Progression through snoRNA Recruitment of PHAX and DNA-PKcs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400023. [PMID: 38828688 PMCID: PMC11304257 DOI: 10.1002/advs.202400023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/16/2024] [Indexed: 06/05/2024]
Abstract
The factors driving glioma progression remain poorly understood. Here, the epigenetic regulator TRIM24 is identified as a driver of glioma progression, where TRIM24 overexpression promotes HRasV12 anaplastic astrocytoma (AA) progression into epithelioid GBM (Ep-GBM)-like tumors. Co-transfection of TRIM24 with HRasV12 also induces Ep-GBM-like transformation of human neural stem cells (hNSCs) with tumor protein p53 gene (TP53) knockdown. Furthermore, TRIM24 is highly expressed in clinical Ep-GBM specimens. Using single-cell RNA-sequencing (scRNA-Seq), the authors show that TRIM24 overexpression impacts both intratumoral heterogeneity and the tumor microenvironment. Mechanically, HRasV12 activates phosphorylated adaptor for RNA export (PHAX) and upregulates U3 small nucleolar RNAs (U3 snoRNAs) to recruit Ku-dependent DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Overexpressed TRIM24 is also recruited by PHAX to U3 snoRNAs, thereby facilitating DNA-PKcs phosphorylation of TRIM24 at S767/768 residues. Phosphorylated TRIM24 induces epigenome and transcription factor network reprogramming and promotes Ep-GBM-like transformation. Targeting DNA-PKcs with the small molecule inhibitor NU7441 synergizes with temozolomide to reduce Ep-GBM tumorigenicity and prolong animal survival. These findings provide new insights into the epigenetic regulation of Ep-GBM-like transformation and suggest a potential therapeutic strategy for patients with Ep-GBM.
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Affiliation(s)
- Chenxin Xu
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Guoyu Chen
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Bo Yu
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Bowen Sun
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yingwen Zhang
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Mingda Zhang
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yi Yang
- Pediatric Translational Medicine InstituteDepartment of Hematology & OncologyShanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityNational Health Committee Key Laboratory of Pediatric Hematology & OncologyShanghai200127China
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Shi‐Yuan Cheng
- Department of NeurologyLou and Jean Malnati Brain Tumor InstituteThe Robert H. Lurie Comprehensive Cancer CenterSimpson Querrey Institute for EpigeneticsNorthwestern University Feinberg School of MedicineChicagoIL60611USA
| | - Yanxin Li
- Pediatric Translational Medicine InstituteDepartment of Hematology & OncologyShanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityNational Health Committee Key Laboratory of Pediatric Hematology & OncologyShanghai200127China
| | - Haizhong Feng
- State Key Laboratory of Systems Medicine for CancerRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
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3
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Dubiez E, Pellegrini E, Finderup Brask M, Garland W, Foucher AE, Huard K, Heick Jensen T, Cusack S, Kadlec J. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. Cell Rep 2024; 43:113639. [PMID: 38175753 DOI: 10.1016/j.celrep.2023.113639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
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Affiliation(s)
- Etienne Dubiez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Erika Pellegrini
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Maja Finderup Brask
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | | | - Karine Huard
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
| | - Jan Kadlec
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
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4
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Böğürcü-Seidel N, Ritschel N, Acker T, Németh A. Beyond ribosome biogenesis: noncoding nucleolar RNAs in physiology and tumor biology. Nucleus 2023; 14:2274655. [PMID: 37906621 PMCID: PMC10730139 DOI: 10.1080/19491034.2023.2274655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The nucleolus, the largest subcompartment of the nucleus, stands out from the nucleoplasm due to its exceptionally high local RNA and low DNA concentrations. Within this central hub of nuclear RNA metabolism, ribosome biogenesis is the most prominent ribonucleoprotein (RNP) biogenesis process, critically determining the structure and function of the nucleolus. However, recent studies have shed light on other roles of the nucleolus, exploring the interplay with various noncoding RNAs that are not directly involved in ribosome synthesis. This review focuses on this intriguing topic and summarizes the techniques to study and the latest findings on nucleolar long noncoding RNAs (lncRNAs) as well as microRNAs (miRNAs) in the context of nucleolus biology beyond ribosome biogenesis. We particularly focus on the multifaceted roles of the nucleolus and noncoding RNAs in physiology and tumor biology.
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Affiliation(s)
| | - Nadja Ritschel
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Attila Németh
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
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Staněk D. Coilin and Cajal bodies. Nucleus 2023; 14:2256036. [PMID: 37682044 PMCID: PMC10494742 DOI: 10.1080/19491034.2023.2256036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
The nucleus of higher eukaryotes contains a number of structures that concentrate specific biomolecules and play distinct roles in nuclear metabolism. In recent years, the molecular mechanisms controlling their formation have been intensively studied. In this brief review, I focus on coilin and Cajal bodies. Coilin is a key scaffolding protein of Cajal bodies that is evolutionarily conserved in metazoans. Cajal bodies are thought to be one of the archetypal nuclear structures involved in the metabolism of several short non-coding nuclear RNAs. Yet surprisingly little is known about the structure and function of coilin, and a comprehensive model to explain the origin of Cajal bodies is also lacking. Here, I summarize recent results on Cajal bodies and coilin and discuss them in the context of the last three decades of research in this field.
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Affiliation(s)
- David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
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6
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Mghezzi-Habellah M, Prochasson L, Jalinot P, Mocquet V. Viral Subversion of the Chromosome Region Maintenance 1 Export Pathway and Its Consequences for the Cell Host. Viruses 2023; 15:2218. [PMID: 38005895 PMCID: PMC10674744 DOI: 10.3390/v15112218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
In eukaryotic cells, the spatial distribution between cytoplasm and nucleus is essential for cell homeostasis. This dynamic distribution is selectively regulated by the nuclear pore complex (NPC), which allows the passive or energy-dependent transport of proteins between these two compartments. Viruses possess many strategies to hijack nucleocytoplasmic shuttling for the benefit of their viral replication. Here, we review how viruses interfere with the karyopherin CRM1 that controls the nuclear export of protein cargoes. We analyze the fact that the viral hijacking of CRM1 provokes are-localization of numerous cellular factors in a suitable place for specific steps of viral replication. While CRM1 emerges as a critical partner for viruses, it also takes part in antiviral and inflammatory response regulation. This review also addresses how CRM1 hijacking affects it and the benefits of CRM1 inhibitors as antiviral treatments.
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Affiliation(s)
| | | | | | - Vincent Mocquet
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure-Lyon, Université Claude Bernard Lyon, U1293, UMR5239, 69364 Lyon, France; (M.M.-H.); (L.P.); (P.J.)
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7
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Katahira J, Ohmae T, Yasugi M, Sasaki R, Itoh Y, Kohda T, Hieda M, Yokota Hirai M, Okamoto T, Miyamoto Y. Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex. Nucleic Acids Res 2023; 51:7602-7618. [PMID: 37260089 PMCID: PMC10415132 DOI: 10.1093/nar/gkad483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
To facilitate selfish replication, viruses halt host gene expression in various ways. The nuclear export of mRNA is one such process targeted by many viruses. SARS-CoV-2, the etiological agent of severe acute respiratory syndrome, also prevents mRNA nuclear export. In this study, Nsp14, a bifunctional viral replicase subunit, was identified as a novel inhibitor of mRNA nuclear export. Nsp14 induces poly(A)+ RNA nuclear accumulation and the dissolution/coalescence of nuclear speckles. Genome-wide gene expression analysis revealed the global dysregulation of splicing and 3'-end processing defects of replication-dependent histone mRNAs by Nsp14. These abnormalities were also observed in SARS-CoV-2-infected cells. A mutation introduced at the guanine-N7-methyltransferase active site of Nsp14 diminished these inhibitory activities. Targeted capillary electrophoresis-mass spectrometry analysis (CE-MS) unveiled the production of N7-methyl-GTP in Nsp14-expressing cells. Association of the nuclear cap-binding complex (NCBC) with the mRNA cap and subsequent recruitment of U1 snRNP and the stem-loop binding protein (SLBP) were impaired by Nsp14. These data suggest that the defects in mRNA processing and export arise from the compromise of NCBC function by N7-methyl-GTP, thus exemplifying a novel viral strategy to block host gene expression.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Tatsuya Ohmae
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Mayo Yasugi
- Laboratory of Veterinary Public Health, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoko Kohda
- Laboratory of Veterinary Epidemiology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Miki Hieda
- Department of Medical Technology, Ehime Prefectural University of Health Sciences, 543 Tobe-Cho Takaoda, Iyo, Ehime791-2102, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085, Japan
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8
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Yuan L, Jiang X, Gong Q, Gao N. Arsenic resistance protein 2 and microRNA biogenesis: Biological implications in cancer development. Pharmacol Ther 2023; 244:108386. [PMID: 36933704 DOI: 10.1016/j.pharmthera.2023.108386] [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: 01/01/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Arsenic resistance protein 2 (Ars2) is a nuclear protein that plays a critical role in the regulation of microRNA (miRNA) biogenesis. Ars2 is required for cell proliferation and for the early stages of mammalian development through a possible effect on miRNA processing. Increasing evidence reveal that Ars2 is highly expressed in proliferating cancer cells, suggesting that Ars2 may be a potential therapeutic target for cancer. Therefore, development of the novel Ars2 inhibitors could represent the novel therapeutic strategies for treatment of cancer. In this review, we briefly discuss the mechanisms by which Ars2 regulates miRNA biogenesis and its impact on cell proliferation and cancer development. Particularly, we mainly discuss the role of Ars2 in the regulation of cancer development and highlight pharmacological targeting of Ars2 as a promising cancer therapeutic strategy.
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Affiliation(s)
- Liang Yuan
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China
| | - Xiuxing Jiang
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
| | - Ning Gao
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
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9
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Shepelev N, Dontsova O, Rubtsova M. Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:5027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [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: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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Affiliation(s)
- Nikita Shepelev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Olga Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maria Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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10
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [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] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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11
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Thalalla Gamage S, Bortolin-Cavaillé ML, Link C, Bryson K, Sas-Chen A, Schwartz S, Cavaillé J, Meier JL. Antisense pairing and SNORD13 structure guide RNA cytidine acetylation. RNA (NEW YORK, N.Y.) 2022; 28:1582-1596. [PMID: 36127124 PMCID: PMC9670809 DOI: 10.1261/rna.079254.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023]
Abstract
N4-acetylcytidine (ac4C) is an RNA nucleobase found in all domains of life. The establishment of ac4C in helix 45 (h45) of human 18S ribosomal RNA (rRNA) requires the combined activity of the acetyltransferase NAT10 and the box C/D snoRNA SNORD13. However, the molecular mechanisms governing RNA-guided nucleobase acetylation in humans remain unexplored. After applying comparative sequence analysis and site-directed mutagenesis to provide evidence that SNORD13 folds into three main RNA helices, we report two assays that enable the study of SNORD13-dependent RNA acetylation in human cells. First, we demonstrate that ectopic expression of SNORD13 rescues h45 in a SNORD13 knockout cell line. Next, we show that mutant snoRNAs can be used in combination with nucleotide resolution ac4C sequencing to define structure and sequence elements critical for SNORD13 function. Finally, we develop a second method that reports on the substrate specificity of endogenous NAT10-SNORD13 via mutational analysis of an ectopically expressed pre-rRNA substrate. By combining mutational analysis of these reconstituted systems with nucleotide resolution ac4C sequencing, our studies reveal plasticity in the molecular determinants underlying RNA-guided cytidine acetylation that is distinct from deposition of other well-studied rRNA modifications (e.g., pseudouridine). Overall, our studies provide a new approach to reconstitute RNA-guided cytidine acetylation in human cells as well as nucleotide resolution insights into the mechanisms governing this process.
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Affiliation(s)
| | - Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Courtney Link
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Keri Bryson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Aldema Sas-Chen
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6195001 Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jérôme Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
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12
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Rubtsova M, Dontsova O. How Structural Features Define Biogenesis and Function of Human Telomerase RNA Primary Transcript. Biomedicines 2022; 10:biomedicines10071650. [PMID: 35884955 PMCID: PMC9313293 DOI: 10.3390/biomedicines10071650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022] Open
Abstract
Telomerase RNA has been uncovered as a component of the telomerase enzyme, which acts as a reverse transcriptase and maintains the length of telomeres in proliferated eukaryotic cells. Telomerase RNA is considered to have major functions as a template for telomeric repeat synthesis and as a structural scaffold for telomerase. However, investigations of its biogenesis and turnover, as well as structural data, have provided evidence of functions of telomerase RNA that are not associated with telomerase activity. The primary transcript produced from the human telomerase RNA gene encodes for the hTERP protein, which presents regulatory functions related to autophagy, cellular proliferation, and metabolism. This review focuses on the specific features relating to the biogenesis and structure of human telomerase RNA that support the existence of an isoform suitable for functioning as an mRNA. We believe that further investigation into human telomerase RNA biogenesis mechanisms will provide more levels for manipulating cellular homeostasis, survival, and transformation mechanisms, and may contribute to a deeper understanding of the mechanisms of aging.
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Affiliation(s)
- Maria Rubtsova
- Department of Chemistry, A.N. Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence:
| | - Olga Dontsova
- Department of Chemistry, A.N. Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia
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13
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Pakhomova T, Moshareva M, Vasilkova D, Zatsepin T, Dontsova O, Rubtsova M. Role of RNA Biogenesis Factors in the Processing and Transport of Human Telomerase RNA. Biomedicines 2022; 10:biomedicines10061275. [PMID: 35740297 PMCID: PMC9219725 DOI: 10.3390/biomedicines10061275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Telomerase RNA has long been considered to be a noncoding component of telomerase. However, the expression of the telomerase RNA gene is not always associated with telomerase activity. The existence of distinct TERC gene expression products possessing different functions were demonstrated recently. During biogenesis, hTR is processed by distinct pathways and localized in different cell compartments, depending on whether it functions as a telomerase complex component or facilitates antistress activities as a noncoding RNA, in which case it is either processed in the mitochondria or translated. In order to identify the factors responsible for the appearance and localization of the exact isoform of hTR, we investigated the roles of the factors regulating transcription DSIF (Spt5) and NELF-E; exosome-attracting factors ZCCHC7, ZCCHC8, and ZFC3H1; ARS2, which attracts processing and transport factors; and transport factor PHAX during the biogenesis of hTR. The data obtained revealed that ZFC3H1 participates in hTR biogenesis via pathways related to the polyadenylated RNA degradation mechanism. The data revealed essential differences that are important for understanding hTR biogenesis and that are interesting for further investigations of new, therapeutically significant targets.
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Affiliation(s)
- Tatiana Pakhomova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
| | - Maria Moshareva
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
| | - Daria Vasilkova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
| | - Timofey Zatsepin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
| | - Olga Dontsova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow 121205, Russia
| | - Maria Rubtsova
- Department of Chemistry, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (T.P.); (M.M.); (D.V.); (O.D.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
- Correspondence:
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14
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Boris-Lawrie K, Singh G, Osmer PS, Zucko D, Staller S, Heng X. Anomalous HIV-1 RNA, How Cap-Methylation Segregates Viral Transcripts by Form and Function. Viruses 2022; 14:935. [PMID: 35632676 PMCID: PMC9145092 DOI: 10.3390/v14050935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022] Open
Abstract
The acquisition of m7G-cap-binding proteins is now recognized as a major variable driving the form and function of host RNAs. This manuscript compares the 5'-cap-RNA binding proteins that engage HIV-1 precursor RNAs, host mRNAs, small nuclear (sn)- and small nucleolar (sno) RNAs and sort into disparate RNA-fate pathways. Before completion of the transcription cycle, the transcription start site of nascent class II RNAs is appended to a non-templated guanosine that is methylated (m7G-cap) and bound by hetero-dimeric CBP80-CBP20 cap binding complex (CBC). The CBC is a nexus for the co-transcriptional processing of precursor RNAs to mRNAs and the snRNA and snoRNA of spliceosomal and ribosomal ribonucleoproteins (RNPs). Just as sn/sno-RNAs experience hyper-methylation of m7G-cap to trimethylguanosine (TMG)-cap, so do select HIV RNAs and an emerging cohort of mRNAs. TMG-cap is blocked from Watson:Crick base pairing and disqualified from participating in secondary structure. The HIV TMG-cap has been shown to license select viral transcripts for specialized cap-dependent translation initiation without eIF4E that is dependent upon CBP80/NCBP3. The exceptional activity of HIV precursor RNAs secures their access to maturation pathways of sn/snoRNAs, canonical and non-canonical host mRNAs in proper stoichiometry to execute the retroviral replication cycle.
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Affiliation(s)
- Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Seth Staller
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
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15
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Kumar AV, Lapierre LR. Location, location, location: subcellular protein partitioning in proteostasis and aging. Biophys Rev 2021; 13:931-941. [PMID: 35047088 PMCID: PMC8724496 DOI: 10.1007/s12551-021-00890-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022] Open
Abstract
Somatic maintenance and cell survival rely on proper protein homeostasis to ensure reliable functions across the cell and to prevent proteome collapse. Maintaining protein folding and solubility is central to proteostasis and is coordinated by protein synthesis, chaperoning, and degradation capacities. An emerging aspect that influences proteostasis is the dynamic protein partitioning across different subcellular structures and compartments. Here, we review recent literature related to nucleocytoplasmic partitioning of proteins, nuclear and cytoplasmic quality control mechanisms, and their impact on the development of age-related diseases. We also highlight new points of entry to modulate spatially-regulated proteostatic mechanisms to delay aging.
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Affiliation(s)
- Anita V. Kumar
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912 USA
| | - Louis R. Lapierre
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912 USA
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16
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Abstract
Herculean efforts by the Wellcome Sanger Institute, the National Cancer Institute, and the National Human Genome Research Institute to sequence thousands of tumors representing all major cancer types have yielded more than 700 genes that contribute to neoplastic growth when mutated, amplified, or deleted. While some of these genes (now included in the COSMIC Cancer Gene Census) encode proteins previously identified in hypothesis-driven experiments (oncogenic transcription factors, protein kinases, etc.), additional classes of cancer drivers have emerged, perhaps none more surprisingly than RNA-binding proteins (RBPs). Over 40 RBPs responsible for virtually all aspects of RNA metabolism, from synthesis to degradation, are recurrently mutated in cancer, and just over a dozen are considered major cancer drivers. This Review investigates whether and how their RNA-binding activities pertain to their oncogenic functions. Focusing on several well-characterized steps in RNA metabolism, we demonstrate that for virtually all cancer-driving RBPs, RNA processing activities are either abolished (the loss-of-function phenotype) or carried out with low fidelity (the LoFi phenotype). Conceptually, this suggests that in normal cells, RBPs act as gatekeepers maintaining proper RNA metabolism and the "balanced" proteome. From the practical standpoint, at least some LoFi phenotypes create therapeutic vulnerabilities, which are beginning to be exploited in the clinic.
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17
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Maturation and shuttling of the yeast telomerase RNP: assembling something new using recycled parts. Curr Genet 2021; 68:3-14. [PMID: 34476547 PMCID: PMC8801399 DOI: 10.1007/s00294-021-01210-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022]
Abstract
As the limiting component of the budding yeast telomerase, the Tlc1 RNA must undergo multiple consecutive modifications and rigorous quality checks throughout its lifecycle. These steps will ensure that only correctly processed and matured molecules are assembled into telomerase complexes that subsequently act at telomeres. The complex pathway of Tlc1 RNA maturation, involving 5'- and 3'-end processing, stabilisation and assembly with the protein subunits, requires at least one nucleo-cytoplasmic passage. Furthermore, it appears that the pathway is tightly coordinated with the association of various and changing proteins, including the export factor Xpo1, the Mex67/Mtr2 complex, the Kap122 importin, the Sm7 ring and possibly the CBC and TREX-1 complexes. Although many of these maturation processes also affect other RNA species, the Tlc1 RNA exploits them in a new combination and, therefore, ultimately follows its own and unique pathway. In this review, we highlight recent new insights in maturation and subcellular shuttling of the budding yeast telomerase RNA and discuss how these events may be fine-tuned by the biochemical characteristics of the varying processing and transport factors as well as the final telomerase components. Finally, we indicate outstanding questions that we feel are important to be addressed for a complete understanding of the telomerase RNA lifecycle and that could have implications for the human telomerase as well.
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18
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Galloway A, Kaskar A, Ditsova D, Atrih A, Yoshikawa H, Gomez-Moreira C, Suska O, Warminski M, Grzela R, Lamond AI, Darzynkiewicz E, Jemielity J, Cowling V. Upregulation of RNA cap methyltransferase RNMT drives ribosome biogenesis during T cell activation. Nucleic Acids Res 2021; 49:6722-6738. [PMID: 34125914 PMCID: PMC8266598 DOI: 10.1093/nar/gkab465] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023] Open
Abstract
The m7G cap is ubiquitous on RNAPII-transcribed RNA and has fundamental roles in eukaryotic gene expression, however its in vivo role in mammals has remained unknown. Here, we identified the m7G cap methyltransferase, RNMT, as a key mediator of T cell activation, which specifically regulates ribosome production. During T cell activation, induction of mRNA expression and ribosome biogenesis drives metabolic reprogramming, rapid proliferation and differentiation generating effector populations. We report that RNMT is induced by T cell receptor (TCR) stimulation and co-ordinates the mRNA, snoRNA and rRNA production required for ribosome biogenesis. Using transcriptomic and proteomic analyses, we demonstrate that RNMT selectively regulates the expression of terminal polypyrimidine tract (TOP) mRNAs, targets of the m7G-cap binding protein LARP1. The expression of LARP1 targets and snoRNAs involved in ribosome biogenesis is selectively compromised in Rnmt cKO CD4 T cells resulting in decreased ribosome synthesis, reduced translation rates and proliferation failure. By enhancing ribosome abundance, upregulation of RNMT co-ordinates mRNA capping and processing with increased translational capacity during T cell activation.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dimitrinka Ditsova
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Abdelmadjid Atrih
- FingerPrints Proteomics Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Carolina Gomez-Moreira
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Marcin Warminski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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19
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ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control. Biochem Soc Trans 2021; 49:1325-1336. [PMID: 34060620 DOI: 10.1042/bst20201008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/26/2023]
Abstract
ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.
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20
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Baldini L, Charpentier B, Labialle S. Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs. Noncoding RNA 2021; 7:ncrna7020030. [PMID: 34066559 PMCID: PMC8162545 DOI: 10.3390/ncrna7020030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.
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Affiliation(s)
| | - Bruno Charpentier
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| | - Stéphane Labialle
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
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21
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Ding B, Sepehrimanesh M. Nucleocytoplasmic Transport: Regulatory Mechanisms and the Implications in Neurodegeneration. Int J Mol Sci 2021; 22:4165. [PMID: 33920577 PMCID: PMC8072611 DOI: 10.3390/ijms22084165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleocytoplasmic transport (NCT) across the nuclear envelope is precisely regulated in eukaryotic cells, and it plays critical roles in maintenance of cellular homeostasis. Accumulating evidence has demonstrated that dysregulations of NCT are implicated in aging and age-related neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), and Huntington disease (HD). This is an emerging research field. The molecular mechanisms underlying impaired NCT and the pathogenesis leading to neurodegeneration are not clear. In this review, we comprehensively described the components of NCT machinery, including nuclear envelope (NE), nuclear pore complex (NPC), importins and exportins, RanGTPase and its regulators, and the regulatory mechanisms of nuclear transport of both protein and transcript cargos. Additionally, we discussed the possible molecular mechanisms of impaired NCT underlying aging and neurodegenerative diseases, such as ALS/FTD, HD, and AD.
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Affiliation(s)
- Baojin Ding
- Department of Biology, University of Louisiana at Lafayette, 410 East Saint Mary Boulevard, Lafayette, LA 70503, USA;
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22
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Chen L, Roake CM, Galati A, Bavasso F, Micheli E, Saggio I, Schoeftner S, Cacchione S, Gatti M, Artandi SE, Raffa GD. Loss of Human TGS1 Hypermethylase Promotes Increased Telomerase RNA and Telomere Elongation. Cell Rep 2021; 30:1358-1372.e5. [PMID: 32023455 PMCID: PMC7156301 DOI: 10.1016/j.celrep.2020.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/09/2019] [Accepted: 12/31/2019] [Indexed: 02/08/2023] Open
Abstract
Biogenesis of the human telomerase RNA (hTR) involves a complex series of posttranscriptional modifications, including hypermethylation of the 5' mono-methylguanosine cap to a tri-methylguanosine cap (TMG). How the TMG cap affects hTR maturation is unknown. Here, we show that depletion of trimethylguanosine synthase 1 (TGS1), the enzyme responsible for cap hypermethylation, increases levels of hTR and telomerase. Diminished trimethylation increases hTR association with the cap-binding complex (CBC) and with Sm chaperone proteins. Loss of TGS1 causes an increase in accumulation of mature hTR in both the nucleus and the cytoplasm compared with controls. In TGS1 mutant cells, increased hTR assembles with telomerase reverse transcriptase (TERT) protein to yield elevated active telomerase complexes and increased telomerase activity, resulting in telomere elongation in cultured human cells. Our results show that TGS1-mediated hypermethylation of the hTR cap inhibits hTR accumulation, restrains levels of assembled telomerase, and limits telomere elongation.
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Affiliation(s)
- Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caitlin M Roake
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Emanuela Micheli
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Stefan Schoeftner
- Cancer Epigenetic Group, Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy; Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Roma, Italy
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Grazia D Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Roma, Italy.
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23
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Qin J, Autexier C. Regulation of human telomerase RNA biogenesis and localization. RNA Biol 2021; 18:305-315. [PMID: 32813614 PMCID: PMC7954027 DOI: 10.1080/15476286.2020.1809196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/16/2022] Open
Abstract
Maintenance of telomeres is essential for genome integrity and replicative capacity in eukaryotic cells. Telomerase, the ribonucleoprotein complex that catalyses telomere synthesis is minimally composed of a reverse transcriptase and an RNA component. The sequence and structural domains of human telomerase RNA (hTR) have been extensively characterized, while the regulation of hTR transcription, maturation, and localization, is not fully understood. Here, we provide an up-to-date review of hTR, with an emphasis on current breakthroughs uncovering the mechanisms of hTR maturation and localization.
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Affiliation(s)
- Jian Qin
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, Canada
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24
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Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Res 2020; 48:10413-10427. [PMID: 32960271 PMCID: PMC7544205 DOI: 10.1093/nar/gkaa744] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear Cap-Binding Complex (CBC), consisting of Nuclear Cap-Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5′cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein–protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association in vitro and in vivo requires EJC core integrity and the in vivo RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting mRNA expression.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Isabelle Barbosa
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Claudia Iasillo
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wiebke Manuela Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
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25
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Dou Y, Kalmykova S, Pashkova M, Oghbaie M, Jiang H, Molloy KR, Chait BT, Rout MP, Fenyö D, Jensen TH, Altukhov I, LaCava J. Affinity proteomic dissection of the human nuclear cap-binding complex interactome. Nucleic Acids Res 2020; 48:10456-10469. [PMID: 32960270 PMCID: PMC7544204 DOI: 10.1093/nar/gkaa743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
A 5′,7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative CBC together with NCBP1, and to interact with the canonical CBC along with the protein SRRT. The theme of post-transcriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly, is abundant with complicated, ambiguous, and likely incomplete models. In an effort to clarify the compositions of NCBP1-, 2- and 3-related macromolecular assemblies, we have applied an affinity capture-based interactome screen where the experimental design and data processing have been modified to quantitatively identify interactome differences between targets under a range of experimental conditions. This study generated a comprehensive view of NCBP-protein interactions in the ribonucleoprotein context and demonstrates the potential of our approach to benefit the interpretation of complex biological pathways.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Maria Pashkova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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26
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Machitani M, Taniguchi I, McCloskey A, Suzuki T, Ohno M. The RNA transport factor PHAX is required for proper histone H2AX expression and DNA damage response. RNA (NEW YORK, N.Y.) 2020; 26:1716-1725. [PMID: 32759388 PMCID: PMC7566570 DOI: 10.1261/rna.074625.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
PHAX (phosphorylated adaptor for RNA export) promotes nuclear export of short transcripts of RNA polymerase II such as spliceosomal U snRNA precursors, as well as intranuclear transport of small nucleolar RNAs (snoRNAs). However, it remains unknown whether PHAX has other critical functions. Here we show that PHAX is required for efficient DNA damage response (DDR) via regulation of phosphorylated histone variant H2AX (γH2AX), a key factor for DDR. Knockdown of PHAX led to a significant reduction of H2AX mRNA levels, through inhibition of both transcription of the H2AX gene and nuclear export of H2AX mRNA, one of the shortest mRNAs in the cell. As a result, PHAX-knockdown cells become more sensitive to DNA damage due to a shortage of γH2AX. These results reveal a novel function of PHAX, which secures efficient DDR and hence genome stability.
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Affiliation(s)
- Mitsuhiro Machitani
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ichiro Taniguchi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Asako McCloskey
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tatsuya Suzuki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mutsuhito Ohno
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
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27
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Verbeke D, Demeyer S, Prieto C, de Bock CE, De Bie J, Gielen O, Jacobs K, Mentens N, Verhoeven BM, Uyttebroeck A, Boeckx N, De Keersmaecker K, Maertens J, Segers H, Cools J. The XPO1 Inhibitor KPT-8602 Synergizes with Dexamethasone in Acute Lymphoblastic Leukemia. Clin Cancer Res 2020; 26:5747-5758. [PMID: 32826328 DOI: 10.1158/1078-0432.ccr-20-1315] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/20/2020] [Accepted: 08/18/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE KPT-8602 (Eltanexor) is a second-generation exportin-1 (XPO1) inhibitor with potent activity against acute lymphoblastic leukemia (ALL) in preclinical models and with minimal effects on normal cells. In this study, we evaluated whether KPT-8602 would synergize with dexamethasone, vincristine, or doxorubicin, three drugs currently used for the treatment of ALL. EXPERIMENTAL DESIGN First, we searched for the most synergistic combination of KPT-8602 with dexamethasone, vincristine, or doxorubicin in vitro in both B-ALL and T-ALL cell lines using proliferation and apoptosis as a readout. Next, we validated this synergistic effect by treatment of clinically relevant B- and T-ALL patient-derived xenograft models in vivo. Finally, we performed RNA-sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to determine the mechanism of synergy. RESULTS KPT-8602 showed strong synergism with dexamethasone on human B-ALL and T-ALL cell lines as well as in vivo in three patient-derived ALL xenografts. Compared with single-drug treatment, the drug combination caused increased apoptosis and led to histone depletion. Mechanistically, integration of ChIP-seq and RNA-seq data revealed that addition of KPT-8602 to dexamethasone enhanced the activity of the glucocorticoid receptor (NR3C1) and led to increased inhibition of E2F-mediated transcription. We observed strong inhibition of E2F target genes related to cell cycle, DNA replication, and transcriptional regulation. CONCLUSIONS Our preclinical study demonstrates that KPT-8602 enhances the effects of dexamethasone to inhibit B-ALL and T-ALL cells via NR3C1- and E2F-mediated transcriptional complexes, allowing to achieve increased dexamethasone effects for patients.
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Affiliation(s)
- Delphine Verbeke
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Cristina Prieto
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales, Australia
| | - Jolien De Bie
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Nicole Mentens
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Bronte Manouk Verhoeven
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Pediatric Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Johan Maertens
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Hematology, UZ Leuven, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Pediatric Oncology, UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
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28
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Lemus-Diaz N, Ferreira RR, Bohnsack KE, Gruber J, Bohnsack MT. The human box C/D snoRNA U3 is a miRNA source and miR-U3 regulates expression of sortin nexin 27. Nucleic Acids Res 2020; 48:8074-8089. [PMID: 32609813 PMCID: PMC7430653 DOI: 10.1093/nar/gkaa549] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression and their dysfunction is often associated with cancer. Alongside the canonical miRNA biogenesis pathway involving stepwise processing and export of pri- and pre-miRNA transcripts by the microprocessor complex, Exportin 5 and Dicer, several alternative mechanisms of miRNA production have been described. Here, we reveal that the atypical box C/D snoRNA U3, which functions as a scaffold during early ribosome assembly, is a miRNA source. We show that a unique stem-loop structure in the 5' domain of U3 is processed to form short RNA fragments that associate with Argonaute. miR-U3 production is independent of Drosha, and an increased amount of U3 in the cytoplasm in the absence of Dicer suggests that a portion of the full length snoRNA is exported to the cytoplasm where it is efficiently processed into miRNAs. Using reporter assays, we demonstrate that miR-U3 can act as a low proficiency miRNA in vivo and our data support the 3' UTR of the sortin nexin SNX27 mRNA as an endogenous U3-derived miRNA target. We further reveal that perturbation of U3 snoRNP assembly induces miR-U3 production, highlighting potential cross-regulation of target mRNA expression and ribosome production.
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Affiliation(s)
- Nicolas Lemus-Diaz
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Rafael Rinaldi Ferreira
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jens Gruber
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Justus-von-Liebig-Weg 11, 37077 Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)
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29
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Al-Lamki RS, Hudson NJ, Bradley JR, Warren AY, Eisen T, Welsh SJ, Riddick ACP, O’Mahony FC, Turnbull A, Powles T, Reverter A, Harrison DJ, Stewart GD. The Efficacy of Sunitinib Treatment of Renal Cancer Cells Is Associated with the Protein PHAX In Vitro. BIOLOGY 2020; 9:E74. [PMID: 32272660 PMCID: PMC7236799 DOI: 10.3390/biology9040074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 02/02/2023]
Abstract
Anti-angiogenic agents, such as the multi-tyrosine kinase inhibitor sunitinib, are key first line therapies for metastatic clear cell renal cell carcinoma (ccRCC), but their mechanism of action is not fully understood. Here, we take steps towards validating a computational prediction based on differential transcriptome network analysis that phosphorylated adapter RNA export protein (PHAX) is associated with sunitinib drug treatment. The regulatory impact factor differential network algorithm run on patient tissue samples suggests PHAX is likely an important regulator through changes in genome-wide network connectivity. Immunofluorescence staining of patient tumours showed strong localisation of PHAX to the microvasculature consistent with the anti-angiogenic effect of sunitinib. In normal kidney tissue, PHAX protein abundance was low but increased with tumour grade (G1 vs. G3/4; p < 0.01), consistent with a possible role in cancer progression. In organ culture, ccRCC cells had higher levels of PHAX protein expression than normal kidney cells, and sunitinib increased PHAX protein expression in a dose dependent manner (untreated vs. 100 µM; p < 0.05). PHAX knockdown in a ccRCC organ culture model impacted the ability of sunitinib to cause cancer cell death (p < 0.0001 untreated vs. treated), suggesting a role for PHAX in mediating the efficacy of sunitinib.
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Affiliation(s)
- Rafia S. Al-Lamki
- Department of Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (R.S.A.-L.); (J.R.B.)
| | - Nicholas J. Hudson
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD 4343, Australia;
| | - John R. Bradley
- Department of Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (R.S.A.-L.); (J.R.B.)
| | - Anne Y. Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Tim Eisen
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah J. Welsh
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Antony C. P. Riddick
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Fiach C. O’Mahony
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Arran Turnbull
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Thomas Powles
- Bart’s Cancer Institute, Charterhouse Square, London EC1M 6BE, UK;
| | - SCOTRRCC Collaborative
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia;
| | - David J. Harrison
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
- School of Medicine, University of St. Andrews, St. Andrews KY16 9TF, UK
| | - Grant D. Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
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30
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Hutten S, Dormann D. Nucleocytoplasmic transport defects in neurodegeneration — Cause or consequence? Semin Cell Dev Biol 2020; 99:151-162. [DOI: 10.1016/j.semcdb.2019.05.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022]
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31
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Lee H, Kim J, Weber JA, Chung O, Cho YS, Jho S, Jun J, Kim HM, Lim J, Choi JP, Jeon S, Blazyte A, Edwards JS, Paek WK, Bhak J. Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. Mol Cells 2020; 43:86-95. [PMID: 31940721 PMCID: PMC6999708 DOI: 10.14348/molcells.2019.0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified redcrowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH , RPA1, PHAX, HNMT , HS2ST1 , PPCDC , PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species.
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Affiliation(s)
- HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Jungeun Kim
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Jessica A. Weber
- Department of Genetics, Harvard Medical School, Boston, MA 02115,
USA
| | | | | | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | | | - Hak-Min Kim
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Jeongheui Lim
- National Science Museum, Ministry of Science and ICT, Daejeon 34143,
Korea
| | - Jae-Pil Choi
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Sungwon Jeon
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Asta Blazyte
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Jeremy S. Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131,
USA
| | - Woon Kee Paek
- National Science Museum, Ministry of Science and ICT, Daejeon 34143,
Korea
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
- Clinomics, Ulsan 44919,
Korea
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
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32
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Silla T, Karadoulama E, Mąkosa D, Lubas M, Jensen TH. The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts. Cell Rep 2019; 23:2199-2210. [PMID: 29768216 PMCID: PMC5972229 DOI: 10.1016/j.celrep.2018.04.061] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Accepted: 04/15/2018] [Indexed: 12/31/2022] Open
Abstract
Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short lived due to their nuclear degradation by the ribonucleolytic RNA exosome. Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA+) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA+ RNA foci with “pA-tail exosome targeting (PAXT) connection” components MTR4, ZFC3H1, and PABPN1 but no overlap with known nuclear structures such as Cajal bodies, speckles, paraspeckles, or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence, selected pA+ RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear pA+ RNA retention factor, counteracting nuclear export activity. Abolished RNA exosome function leads to pA+ RNA accumulation in nuclear foci pA+ RNA foci are enriched with various transcripts and exosome adaptor proteins The exosome adaptor protein ZFC3H1 is required for pA+ RNA foci formation ZFC3H1 functionally counteracts the mRNA export factor AlyREF
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Affiliation(s)
- Toomas Silla
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Evdoxia Karadoulama
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark; The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, 2200 Copenhagen, Denmark
| | - Dawid Mąkosa
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Michal Lubas
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark.
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33
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Garland W, Jensen TH. Nuclear sorting of RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1572. [PMID: 31713323 DOI: 10.1002/wrna.1572] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/27/2022]
Abstract
The majority of the mammalian genome is transcribed by RNA polymerase II, yielding a vast amount of noncoding RNA (ncRNA) in addition to the standard production of mRNA. The typical nuclear biogenesis of mRNA relies on the tightly controlled coupling of co- and post-transcriptional processing events, which ultimately results in the export of transcripts into the cytoplasm. These processes are subject to surveillance by nuclear RNA decay pathways to prevent the export of aberrant, or otherwise "non-optimal," transcripts. However, unlike mRNA, many long ncRNAs are nuclear retained and those that maintain enduring functions must employ precautions to evade decay. Proper sorting and localization of RNA is therefore an essential activity in eukaryotic cells and the formation of ribonucleoprotein complexes during early stages of RNA synthesis is central to deciding such transcript fate. This review details our current understanding of the pathways and factors that direct RNAs towards a particular destiny and how transcripts combat the adverse conditions of the nucleus. 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)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
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34
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Michalski D, Ontiveros JG, Russo J, Charley PA, Anderson JR, Heck AM, Geiss BJ, Wilusz J. Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection. J Biol Chem 2019; 294:16282-16296. [PMID: 31519749 DOI: 10.1074/jbc.ra119.009129] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Insect-borne flaviviruses produce a 300-500-base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5'-3'-exoribonuclease 1 (XRN1) via structures located in their 3' UTRs. In this study, we demonstrate that sfRNA production by Zika virus represses XRN1 analogous to what we have previously shown for other flaviviruses. Using protein-RNA reconstitution and a stringent RNA pulldown assay with human choriocarcinoma (JAR) cells, we demonstrate that the sfRNAs from both dengue type 2 and Zika viruses interact with a common set of 21 RNA-binding proteins that contribute to the regulation of post-transcriptional processes in the cell, including splicing, RNA stability, and translation. We found that four of these sfRNA-interacting host proteins, DEAD-box helicase 6 (DDX6) and enhancer of mRNA decapping 3 (EDC3) (two RNA decay factors), phosphorylated adaptor for RNA export (a regulator of the biogenesis of the splicing machinery), and apolipoprotein B mRNA-editing enzyme catalytic subunit 3C (APOBEC3C, a nucleic acid-editing deaminase), inherently restrict Zika virus infection. Furthermore, we demonstrate that the regulations of cellular mRNA decay and RNA splicing are compromised by Zika virus infection as well as by sfRNA alone. Collectively, these results reveal the large extent to which Zika virus-derived sfRNAs interact with cellular RNA-binding proteins and highlight the potential for widespread dysregulation of post-transcriptional control that likely limits the effective response of these cells to viral infection.
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Affiliation(s)
- Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - J Gustavo Ontiveros
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
| | - Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Adam M Heck
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523 .,Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
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35
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Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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36
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Gaviraghi M, Vivori C, Pareja Sanchez Y, Invernizzi F, Cattaneo A, Santoliquido BM, Frenquelli M, Segalla S, Bachi A, Doglioni C, Pelechano V, Cittaro D, Tonon G. Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus. EMBO J 2018; 37:embj.201899179. [PMID: 30373810 DOI: 10.15252/embj.201899179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
Focal deletions occur frequently in the cancer genome. However, the putative tumor-suppressive genes residing within these regions have been difficult to pinpoint. To robustly identify these genes, we implemented a computational approach based on non-negative matrix factorization, NMF, and interrogated the TCGA dataset. This analysis revealed a metagene signature including a small subset of genes showing pervasive hemizygous deletions, reduced expression in cancer patient samples, and nucleolar function. Amid the genes belonging to this signature, we have identified PNRC1, a nuclear receptor coactivator. We found that PNRC1 interacts with the cytoplasmic DCP1α/DCP2 decapping machinery and hauls it inside the nucleolus. PNRC1-dependent nucleolar translocation of the decapping complex is associated with a decrease in the 5'-capped U3 and U8 snoRNA fractions, hampering ribosomal RNA maturation. As a result, PNRC1 ablates the enhanced proliferation triggered by established oncogenes such as RAS and MYC These observations uncover a previously undescribed mechanism of tumor suppression, whereby the cytoplasmic decapping machinery is hauled within nucleoli, tightly regulating ribosomal RNA maturation.
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Affiliation(s)
- Marco Gaviraghi
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Vivori
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Yerma Pareja Sanchez
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Francesca Invernizzi
- Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Angela Cattaneo
- Functional Proteomics Program, Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Benedetta Maria Santoliquido
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Michela Frenquelli
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Simona Segalla
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Angela Bachi
- Functional Proteomics Program, Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Vicent Pelechano
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy .,Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
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37
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Williams T, Ngo LH, Wickramasinghe VO. Nuclear export of RNA: Different sizes, shapes and functions. Semin Cell Dev Biol 2018; 75:70-77. [DOI: 10.1016/j.semcdb.2017.08.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 01/08/2023]
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38
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Hayes KE, Barr JA, Xie M, Steitz JA, Martinez I. Immunoprecipitation of Tri-methylated Capped RNA. Bio Protoc 2018. [PMID: 29527542 DOI: 10.21769/bioprotoc.2717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Cellular quiescence (also known as G0 arrest) is characterized by reduced DNA replication, increased autophagy, and increased expression of cyclin-dependent kinase p27Kip1. Quiescence is essential for wound healing, organ regeneration, and preventing neoplasia. Previous findings indicate that microRNAs (miRNAs) play an important role in regulating cellular quiescence. Our recent publication demonstrated the existence of an alternative miRNA biogenesis pathway in primary human foreskin fibroblast (HFF) cells during quiescence. Indeed, we have identified a group of pri-miRNAs (whose mature miRNAs were found induced during quiescence) modified with a 2,2,7-trimethylguanosine (TMG)-cap by the trimethylguanosine synthase 1 (TGS1) protein and transported to the cytoplasm by the Exportin-1 (XPO1) protein. We used an antibody against (TMG)-caps (which does not cross-react with the (m7G)-caps that most pri-miRNAs or mRNAs contain [Luhrmann et al., 1982]) to perform RNA immunoprecipitations from total RNA extracts of proliferating or quiescent HFFs. The novelty of this assay is the specific isolation of pri-miRNAs as well as other non-coding RNAs containing a TMG-cap modification.
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Affiliation(s)
- Karen E Hayes
- Department of Microbiology, Program in Cancer Cell Biology, WVU Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Jamie A Barr
- Department of Microbiology, Program in Cancer Cell Biology, WVU Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Mingyi Xie
- Department of Biochemistry & Molecular Biology, U.F. Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Joan A Steitz
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.,Yale Cancer Center, New Haven, CT, USA
| | - Ivan Martinez
- Department of Microbiology, Program in Cancer Cell Biology, WVU Cancer Institute, West Virginia University, Morgantown, WV, USA
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39
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Li MW, Sletten AC, Lee J, Pyles KD, Matkovich SJ, Ory DS, Schaffer JE. Nuclear export factor 3 regulates localization of small nucleolar RNAs. J Biol Chem 2017; 292:20228-20239. [PMID: 29021253 PMCID: PMC5724009 DOI: 10.1074/jbc.m117.818146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/05/2017] [Indexed: 01/04/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) guide chemical modifications of ribosomal and small nuclear RNAs, functions that are carried out in the nucleus. Although most snoRNAs reside in the nucleolus, a growing body of evidence indicates that snoRNAs are also present in the cytoplasm and that snoRNAs move between the nucleus and cytoplasm by a mechanism that is regulated by lipotoxic and oxidative stress. Here, in a genome-wide shRNA-based screen, we identified nuclear export factor 3 (NXF3) as a transporter that alters the nucleocytoplasmic distribution of box C/D snoRNAs from the ribosomal protein L13a (Rpl13a) locus. Using RNA-sequencing analysis, we show that NXF3 associates not only with Rpl13a snoRNAs, but also with a broad range of box C/D and box H/ACA snoRNAs. Under homeostatic conditions, gain- or loss-of-function of NXF3, but not related family member NXF1, decreases or increases cytosolic Rpl13a snoRNAs, respectively. Furthermore, treatment with the adenylyl cyclase activator forskolin diminishes cytosolic localization of the Rpl13a snoRNAs through a mechanism that is dependent on NXF3 but not NXF1. Our results provide evidence of a new role for NXF3 in regulating the distribution of snoRNAs between the nuclear and cytoplasmic compartments.
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Affiliation(s)
- Melissa W Li
- Diabetes Research Center, Department of Medicine, St. Louis, Missouri 63110
| | - Arthur C Sletten
- Diabetes Research Center, Department of Medicine, St. Louis, Missouri 63110
| | - Jiyeon Lee
- Diabetes Research Center, Department of Medicine, St. Louis, Missouri 63110
| | - Kelly D Pyles
- Diabetes Research Center, Department of Medicine, St. Louis, Missouri 63110
| | - Scot J Matkovich
- Center for Cardiovascular Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Daniel S Ory
- Diabetes Research Center, Department of Medicine, St. Louis, Missouri 63110
| | - Jean E Schaffer
- Diabetes Research Center, Department of Medicine, St. Louis, Missouri 63110.
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40
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Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate. Cell Rep 2017; 18:2635-2650. [PMID: 28297668 PMCID: PMC5368414 DOI: 10.1016/j.celrep.2017.02.046] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/13/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3′-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3′-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport. Surprisingly, these proteins all bind capped RNAs without strong preferences for given transcripts, and their steady-state binding correlates poorly with their function. Despite this, PHAX and ZC3H18 compete for CBC binding and we demonstrate that this competitive binding is functionally relevant. We further show that CBC-containing complexes are short lived in vivo, and we therefore suggest that RNA fate involves the transient formation of mutually exclusive CBC complexes, which may only be consequential at particular checkpoints during RNA biogenesis. PHAX and ZC3H18 compete for binding to the nuclear CBC PHAX and ZC3H18 have opposite effects on the fate of snRNA precursors and other RNAs PHAX, ARS2, and ZC3H18 bind capped RNAs without strong preference for given transcripts CBC-containing complexes are short lived in vivo, with a lifetime of a few seconds
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41
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Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2. Nat Commun 2017; 8:1302. [PMID: 29101316 PMCID: PMC5670239 DOI: 10.1038/s41467-017-01402-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022] Open
Abstract
Pol II transcribes diverse classes of RNAs that need to be directed into the appropriate nuclear maturation pathway. All nascent Pol II transcripts are 5′-capped and the cap is immediately sequestered by the nuclear cap-binding complex (CBC). Mutually exclusive interactions of CBC with different partner proteins have been implicated in transcript fate determination. Here, we characterise the direct interactions between CBC and NELF-E, a subunit of the negative elongation factor complex, ARS2 and PHAX. Our biochemical and crystal structure results show that the homologous C-terminal peptides of NELF-E and ARS2 bind identically to CBC and in each case the affinity is enhanced when CBC is bound to a cap analogue. Furthermore, whereas PHAX forms a complex with CBC and ARS2, NELF-E binding to CBC is incompatible with PHAX binding. We thus define two mutually exclusive complexes CBC–NELF–E and CBC–ARS2–PHAX, which likely act in respectively earlier and later phases of transcription. The nuclear cap-binding complex (CBC) binds to the 5′-cap structure of Pol II transcripts. Here, the authors give structural insights into CBC-mediated transcript processing and show that CBC forms mutual exclusive complexes with NELF and ARS2, which might act in earlier and later phases of transcription, respectively.
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42
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Tapia O, Narcís JO, Riancho J, Tarabal O, Piedrafita L, Calderó J, Berciano MT, Lafarga M. Cellular bases of the RNA metabolism dysfunction in motor neurons of a murine model of spinal muscular atrophy: Role of Cajal bodies and the nucleolus. Neurobiol Dis 2017; 108:83-99. [PMID: 28823932 DOI: 10.1016/j.nbd.2017.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/01/2017] [Accepted: 08/16/2017] [Indexed: 02/06/2023] Open
Abstract
Spinal muscular atrophy (SMA) is caused by a homozygous deletion or mutation in the survival motor neuron 1 (SMN1) gene that leads to reduced levels of SMN protein resulting in degeneration of motor neurons (MNs). The best known functions of SMN is the biogenesis of spliceosomal snRNPs. Linked to this function, Cajal bodies (CBs) are involved in the assembly of spliceosomal (snRNPs) and nucleolar (snoRNPs) ribonucleoproteins required for pre-mRNA and pre-rRNA processing. Recent studies support that the interaction between CBs and nucleoli, which are especially prominent in neurons, is essential for the nucleolar rRNA homeostasis. We use the SMN∆7 murine model of type I SMA to investigate the cellular basis of the dysfunction of RNA metabolism in MNs. SMN deficiency in postnatal MNs produces a depletion of functional CBs and relocalization of coilin, which is a scaffold protein of CBs, in snRNP-free perinucleolar caps or within the nucleolus. Disruption of CBs is the earliest nuclear sign of MN degeneration. We demonstrate that depletion of CBs, with loss of CB-nucleolus interactions, induces a progressive nucleolar dysfunction in ribosome biogenesis. It includes reorganization and loss of nucleolar transcription units, segregation of dense fibrillar and granular components, retention of SUMO-conjugated proteins in intranucleolar bodies and a reactive, compensatory, up-regulation of mature 18S rRNA and genes encoding key nucleolar proteins, such as upstream binding factor, fibrillarin, nucleolin and nucleophosmin. We propose that CB depletion and nucleolar alterations are essential components of the dysfunction of RNA metabolism in SMA.
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Affiliation(s)
- Olga Tapia
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Santander, Spain
| | - Josep Oriol Narcís
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Santander, Spain
| | - Javier Riancho
- Service of Neurology, University Hospital Marqués de Valdecilla-IDIVAL-CIBERNED, Santander, Spain
| | - Olga Tarabal
- Department of Experimental Medicine, School of Medicine, University of Lleida and "Institut de Recerca Biomèdica de Lleida" (IRBLLEIDA), Lleida, Spain
| | - Lídia Piedrafita
- Department of Experimental Medicine, School of Medicine, University of Lleida and "Institut de Recerca Biomèdica de Lleida" (IRBLLEIDA), Lleida, Spain
| | - Jordi Calderó
- Department of Experimental Medicine, School of Medicine, University of Lleida and "Institut de Recerca Biomèdica de Lleida" (IRBLLEIDA), Lleida, Spain
| | - Maria T Berciano
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Santander, Spain
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Santander, Spain.
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43
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Martinez I, Hayes KE, Barr JA, Harold AD, Xie M, Bukhari SIA, Vasudevan S, Steitz JA, DiMaio D. An Exportin-1-dependent microRNA biogenesis pathway during human cell quiescence. Proc Natl Acad Sci U S A 2017; 114:E4961-E4970. [PMID: 28584122 PMCID: PMC5488920 DOI: 10.1073/pnas.1618732114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The reversible state of proliferative arrest known as "cellular quiescence" plays an important role in tissue homeostasis and stem cell biology. By analyzing the expression of miRNAs and miRNA-processing factors during quiescence in primary human fibroblasts, we identified a group of miRNAs that are induced during quiescence despite markedly reduced expression of Exportin-5, a protein required for canonical miRNA biogenesis. The biogenesis of these quiescence-induced miRNAs is independent of Exportin-5 and depends instead on Exportin-1. Moreover, these quiescence-induced primary miRNAs (pri-miRNAs) are modified with a 2,2,7-trimethylguanosine (TMG)-cap, which is known to bind Exportin-1, and knockdown of Exportin-1 or trimethylguanosine synthase 1, responsible for (TMG)-capping, inhibits their biogenesis. Surprisingly, in quiescent cells Exportin-1-dependent pri-miR-34a is present in the cytoplasm together with a small isoform of Drosha, implying the existence of a different miRNA processing pathway in these cells. Our findings suggest that during quiescence the canonical miRNA biogenesis pathway is down-regulated and specific miRNAs are generated by an alternative pathway to regulate genes involved in cellular growth arrest.
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Affiliation(s)
- Ivan Martinez
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506;
| | - Karen E Hayes
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506
| | - Jamie A Barr
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506
| | - Abby D Harold
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610
| | - Syed I A Bukhari
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Shobha Vasudevan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536;
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06536
- Yale Cancer Center, New Haven, CT 06520
| | - Daniel DiMaio
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536
- Yale Cancer Center, New Haven, CT 06520
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06510
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44
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Brun S, Abella N, Berciano MT, Tapia O, Jaumot M, Freire R, Lafarga M, Agell N. SUMO regulates p21Cip1 intracellular distribution and with p21Cip1 facilitates multiprotein complex formation in the nucleolus upon DNA damage. PLoS One 2017; 12:e0178925. [PMID: 28582471 PMCID: PMC5459497 DOI: 10.1371/journal.pone.0178925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/22/2017] [Indexed: 01/06/2023] Open
Abstract
We previously showed that p21Cip1 transits through the nucleolus on its way from the nucleus to the cytoplasm and that DNA damage inhibits this transit and induces the formation of p21Cip1-containing intranucleolar bodies (INoBs). Here, we demonstrate that these INoBs also contain SUMO-1 and UBC9, the E2 SUMO-conjugating enzyme. Furthermore, whereas wild type SUMO-1 localized in INoBs, a SUMO-1 mutant, which is unable to conjugate with proteins, does not, suggesting the presence of SUMOylated proteins at INoBs. Moreover, depletion of the SUMO-conjugating enzyme UBC9 or the sumo hydrolase SENP2 changed p21Cip1 intracellular distribution. In addition to SUMO-1 and p21Cip1, cell cycle regulators and DNA damage checkpoint proteins, including Cdk2, Cyclin E, PCNA, p53 and Mdm2, and PML were also detected in INoBs. Importantly, depletion of UBC9 or p21Cip1 impacted INoB biogenesis and the nucleolar accumulation of the cell cycle regulators and DNA damage checkpoint proteins following DNA damage. The impact of p21Cip1 and SUMO-1 on the accumulation of proteins in INoBs extends also to CRM1, a nuclear exportin that is also important for protein translocation from the cytoplasm to the nucleolus. Thus, SUMO and p21Cip1 regulate the transit of proteins through the nucleolus, and that disruption of nucleolar export by DNA damage induces SUMO and p21Cip1 to act as hub proteins to form a multiprotein complex in the nucleolus.
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Affiliation(s)
- Sonia Brun
- Departament Biomedicina, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Neus Abella
- Departament Biomedicina, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Maria T. Berciano
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IDIVAL, Santander, Spain
| | - Olga Tapia
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IDIVAL, Santander, Spain
| | - Montserrat Jaumot
- Departament Biomedicina, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Tenerife, Spain
| | - Miguel Lafarga
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IDIVAL, Santander, Spain
| | - Neus Agell
- Departament Biomedicina, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
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45
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Raimer AC, Gray KM, Matera AG. SMN - A chaperone for nuclear RNP social occasions? RNA Biol 2017; 14:701-711. [PMID: 27648855 PMCID: PMC5519234 DOI: 10.1080/15476286.2016.1236168] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/01/2016] [Accepted: 09/09/2016] [Indexed: 12/24/2022] Open
Abstract
Survival Motor Neuron (SMN) protein localizes to both the nucleus and the cytoplasm. Cytoplasmic SMN is diffusely localized in large oligomeric complexes with core member proteins, called Gemins. Biochemical and cell biological studies have demonstrated that the SMN complex is required for the cytoplasmic assembly and nuclear transport of Sm-class ribonucleoproteins (RNPs). Nuclear SMN accumulates with spliceosomal small nuclear (sn)RNPs in Cajal bodies, sub-domains involved in multiple facets of snRNP maturation. Thus, the SMN complex forms stable associations with both nuclear and cytoplasmic snRNPs, and plays a critical role in their biogenesis. In this review, we focus on potential functions of the nuclear SMN complex, with particular emphasis on its role within the Cajal body.
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Affiliation(s)
- Amanda C. Raimer
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kelsey M. Gray
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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46
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Massenet S, Bertrand E, Verheggen C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol 2017; 14:680-692. [PMID: 27715451 PMCID: PMC5519232 DOI: 10.1080/15476286.2016.1243646] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022] Open
Abstract
Box C/D and box H/ACA snoRNAs are abundant non-coding RNAs that localize in the nucleolus and mostly function as guides for nucleotide modifications. While a large pool of snoRNAs modifies rRNAs, an increasing number of snoRNAs could also potentially target mRNAs. ScaRNAs belong to a family of specific RNAs that localize in Cajal bodies and that are structurally similar to snoRNAs. Most scaRNAs are involved in snRNA modification, while telomerase RNA, which contains H/ACA motifs, functions in telomeric DNA synthesis. In this review, we describe how box C/D and H/ACA snoRNAs are processed and assembled with core proteins to form functional RNP particles. Their biogenesis involve several transport factors that first direct pre-snoRNPs to Cajal bodies, where some processing steps are believed to take place, and then to nucleoli. Assembly of core proteins involves the HSP90/R2TP chaperone-cochaperone system for both box C/D and H/ACA RNAs, but also several factors specific for each family. These assembly factors chaperone unassembled core proteins, regulate the formation and disassembly of pre-snoRNP intermediates, and control the activity of immature particles. The AAA+ ATPase RUVBL1 and RUVBL2 belong to the R2TP co-chaperones and play essential roles in snoRNP biogenesis, as well as in the formation of other macro-molecular complexes. Despite intensive research, their mechanisms of action are still incompletely understood.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS, 9 Avenue de la forêt de Haye, 54505 Vandoeuvre-les-Nancy Cedex, France, Université de Lorraine, Campus Biologie –Santé, CS 50184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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47
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Staněk D, Fox AH. Nuclear bodies: news insights into structure and function. Curr Opin Cell Biol 2017; 46:94-101. [PMID: 28577509 DOI: 10.1016/j.ceb.2017.05.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/20/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023]
Abstract
The cell nucleus contains a number of different dynamic bodies that are variously composed of proteins and generally, but not always, specific RNA molecules. Recent studies have revealed new understanding about nuclear body formation and function in different aspects of nuclear metabolism. Here, we focus on findings describing the role of nuclear bodies in the biogenesis of specific ribonucleoprotein complexes, processing of key mRNAs, and subnuclear sequestration of protein factors. We highlight how nuclear bodies are involved in stress responses, innate immunity and tumorigenesis. We further review organization of nuclear bodies and principles that govern their assembly, highlighting the pivotal role of scaffolding noncoding RNAs, and liquid-liquid phase separation, which are transforming our picture of nuclear body formation.
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Affiliation(s)
- David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Archa H Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Crawley, 6009 Western Australia, Australia.
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48
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Heyn P, Salmonowicz H, Rodenfels J, Neugebauer KM. Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos. RNA Biol 2016; 14:752-760. [PMID: 27858508 DOI: 10.1080/15476286.2016.1255397] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Nuclear bodies are cellular compartments that lack lipid bilayers and harbor specific RNAs and proteins. Recent proposals that nuclear bodies form through liquid-liquid phase separation leave the question of how different nuclear bodies maintain their distinct identities unanswered. Here we investigate Cajal bodies (CBs), histone locus bodies (HLBs) and nucleoli - involved in assembly of the splicing machinery, histone mRNA 3' end processing, and rRNA processing, respectively - in the embryos of the zebrafish, Danio rerio. We take advantage of the transcriptional silence of the 1-cell embryo and follow nuclear body appearance as zygotic transcription becomes activated. CBs are present from fertilization onwards, while HLB and nucleolar components formed foci several hours later when histone genes and rDNA became active. HLB formation was blocked by transcription inhibition, suggesting nascent histone transcripts recruit HLB components like U7 snRNP. Surprisingly, we found that U7 base-pairing with nascent histone transcripts was not required for localization to HLBs. Rather, the type of Sm ring assembled on U7 determined its targeting to HLBs or CBs; the spliceosomal Sm ring targeted snRNAs to CBs while the specialized U7 Sm-ring localized to HLBs, demonstrating the contribution of protein constituents to the distinction among nuclear bodies. Thus, nucleolar, HLB, and CB components can mix in early embryogenesis when transcription is naturally or artificially silenced. These data support a model in which transcription of specific gene loci nucleates nuclear body components with high specificity and fidelity to perform distinct regulatory functions.
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Affiliation(s)
- Patricia Heyn
- a Max Planck Institute of Molecular Cell Biology and Genetics , Dresden , Germany
| | - Hanna Salmonowicz
- a Max Planck Institute of Molecular Cell Biology and Genetics , Dresden , Germany
| | - Jonathan Rodenfels
- b Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
| | - Karla M Neugebauer
- b Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
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49
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Hebert MD, Poole AR. Towards an understanding of regulating Cajal body activity by protein modification. RNA Biol 2016; 14:761-778. [PMID: 27819531 DOI: 10.1080/15476286.2016.1243649] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The biogenesis of small nuclear ribonucleoproteins (snRNPs), small Cajal body-specific RNPs (scaRNPs), small nucleolar RNPs (snoRNPs) and the telomerase RNP involves Cajal bodies (CBs). Although many components enriched in the CB contain post-translational modifications (PTMs), little is known about how these modifications impact individual protein function within the CB and, in concert with other modified factors, collectively regulate CB activity. Since all components of the CB also reside in other cellular locations, it is also important that we understand how PTMs affect the subcellular localization of CB components. In this review, we explore the current knowledge of PTMs on the activity of proteins known to enrich in CBs in an effort to highlight current progress as well as illuminate paths for future investigation.
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Affiliation(s)
- Michael D Hebert
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Aaron R Poole
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
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50
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Trinkle-Mulcahy L, Sleeman JE. The Cajal body and the nucleolus: "In a relationship" or "It's complicated"? RNA Biol 2016; 14:739-751. [PMID: 27661468 DOI: 10.1080/15476286.2016.1236169] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
From their initial identification as 'nucleolar accessory bodies' more than a century ago, the relationship between Cajal bodies and nucleoli has been a subject of interest and controversy. In this review, we seek to place recent developments in the understanding of the physical and functional relationships between the 2 structures in the context of historical observations. Biophysical models of nuclear body formation, the molecular nature of CB/nucleolus interactions and the increasing list of joint roles for CBs and nucleoli, predominantly in assembling ribonucleoprotein (RNP) complexes, are discussed.
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Affiliation(s)
- Laura Trinkle-Mulcahy
- a Department of Cellular and Molecular Medicine , Ottawa Institute of Systems Biology, University of Ottawa , Ottawa , ON , Canada
| | - Judith E Sleeman
- b BSRC Complex, School of Biology, University of St Andrews , UK
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