101
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Bizarro J, Deryusheva S, Wacheul L, Gupta V, Ernst FGM, Lafontaine DLJ, Gall JG, Meier UT. Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity. Genes Dev 2021; 35:1123-1141. [PMID: 34301768 PMCID: PMC8336889 DOI: 10.1101/gad.348660.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
In this study, Bizarro et al. sought to understand the function and subcellular site of snRNA modification, and found that Cajal body (CB) localization of the protein Nopp140 is essential for concentration of small Cajal body-specific ribonucleoproteins (scaRNPs) in nuclear condensate and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB)-specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
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Affiliation(s)
| | | | - Ludivine Wacheul
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Varun Gupta
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Felix G M Ernst
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Joseph G Gall
- Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - U Thomas Meier
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
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102
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Martin K, Musaus M, Navabpour S, Gustin A, Ray WK, Helm RF, Jarome TJ. Females, but not males, require protein degradation in the hippocampus for contextual fear memory formation. ACTA ACUST UNITED AC 2021; 28:248-253. [PMID: 34266989 PMCID: PMC8284313 DOI: 10.1101/lm.053429.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022]
Abstract
Strong evidence supports a role for protein degradation in fear memory formation. However, these data have been largely done in only male animals. Here, we found that following contextual fear conditioning, females, but not males, had increased levels of proteasome activity and K48 polyubiquitin protein targeting in the dorsal hippocampus, the latter of which occurred at chaperones or RNA processing proteins. In vivo CRISPR–dCas9-mediated repression of protein degradation in the dorsal hippocampus impaired contextual fear memory in females, but not males. These results suggest a sex-specific role for protein degradation in the hippocampus during the consolidation of a contextual fear memory.
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Affiliation(s)
- Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Department of Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, Virginia 24016, USA
| | - Aspen Gustin
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Timothy J Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.,Fralin Biomedical Research Institute, Department of Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, Virginia 24016, USA.,Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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103
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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104
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The anti-oxidative effect of Lingzhi protein hydrolysates on lipopolysaccharide-stimulated A549 cells. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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105
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Cerezo EL, Houles T, Lié O, Sarthou MK, Audoynaud C, Lavoie G, Halladjian M, Cantaloube S, Froment C, Burlet-Schiltz O, Henry Y, Roux PP, Henras AK, Romeo Y. RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit. PLoS Genet 2021; 17:e1009583. [PMID: 34125833 PMCID: PMC8224940 DOI: 10.1371/journal.pgen.1009583] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/24/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
Ribosome biogenesis lies at the nexus of various signaling pathways coordinating protein synthesis with cell growth and proliferation. This process is regulated by well-described transcriptional mechanisms, but a growing body of evidence indicates that other levels of regulation exist. Here we show that the Ras/mitogen-activated protein kinase (MAPK) pathway stimulates post-transcriptional stages of human ribosome synthesis. We identify RIOK2, a pre-40S particle assembly factor, as a new target of the MAPK-activated kinase RSK. RIOK2 phosphorylation by RSK stimulates cytoplasmic maturation of late pre-40S particles, which is required for optimal protein synthesis and cell proliferation. RIOK2 phosphorylation facilitates its release from pre-40S particles and its nuclear re-import, prior to completion of small ribosomal subunits. Our results bring a detailed mechanistic link between the Ras/MAPK pathway and the maturation of human pre-40S particles, which opens a hitherto poorly explored area of ribosome biogenesis.
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Affiliation(s)
- Emilie L. Cerezo
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thibault Houles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec, Canada
| | - Oriane Lié
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Kerguelen Sarthou
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Charlotte Audoynaud
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Geneviève Lavoie
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec, Canada
| | - Maral Halladjian
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Yves Henry
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Anthony K. Henras
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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106
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Wang Y, Yu Y, Pang Y, Yu H, Zhang W, Zhao X, Yu J. The distinct roles of zinc finger CCHC-type (ZCCHC) superfamily proteins in the regulation of RNA metabolism. RNA Biol 2021; 18:2107-2126. [PMID: 33787465 DOI: 10.1080/15476286.2021.1909320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The zinc finger CCHC-type (ZCCHC) superfamily proteins, characterized with the consensus sequence C-X2-C-X4-H-X4-C, are accepted to have high-affinity binding to single-stranded nucleic acids, especially single-stranded RNAs. In human beings 25 ZCCHC proteins have been annotated in the HGNC database. Of interest is that among the family, most members are involved in the multiple steps of RNA metabolism. In this review, we focus on the diverged roles of human ZCCHC proteins on RNA transcription, biogenesis, splicing, as well as translation and degradation.
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Affiliation(s)
- Yishu Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Yu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yidan Pang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haojun Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqi Zhang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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107
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G-patch domain-containing protein 4 localizes to both the nucleoli and Cajal bodies and regulates cell growth and nucleolar structure. Biochem Biophys Res Commun 2021; 559:99-105. [PMID: 33933995 DOI: 10.1016/j.bbrc.2021.04.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/20/2022]
Abstract
Ribosome formation occurs in the nucleolus through interaction with various trans-acting factors. Therefore, hundreds of nucleolar proteins have a function in ribosome formation, although the precise function of each nucleolar protein in ribosome formation is largely unclear. We have previously identified an uncharacterized protein, G-patch domain-containing protein 4 (GPATCH4 or G4), as a component of the pre-ribosomes purified with either nucleolin (NCL) or NPM1. In this present study, we sought to clarify the localization and function of G4. We identified that G4 localizes to both the nucleolus and the Cajal body. Although knockdown of G4 did not have a significant effect on pre-ribosomal RNA processing, cell growth did decrease. Interestingly, G4 knockdown also decreased the number of fibrillar center and dense fibrillar component regions inside the nucleolus. This data has identified G4 as a novel nucleolar protein involved in the regulation of cell growth and nucleolar structure.
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108
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Bizarro J, Deryusheva S, Wacheul L, Gupta V, Ernst FGM, Lafontaine DLJ, Gall JG, Meier UT. Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.29.441821. [PMID: 33948588 PMCID: PMC8095195 DOI: 10.1101/2021.04.29.441821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB) specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at some 80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2'-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
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109
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Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock. eLife 2021; 10:61254. [PMID: 33908345 PMCID: PMC8112863 DOI: 10.7554/elife.61254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.
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Affiliation(s)
- Laura Plassart
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ramtin Shayan
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | | | - Dana Rinaldi
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Natacha Larburu
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carole Pichereaux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ulrike Kutay
- Institut für Biochemie, ETH Zürich, Zurich, Switzerland
| | - Julien Marcoux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Celia Plisson-Chastang
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
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110
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Ryu H, Sun XX, Chen Y, Li Y, Wang X, Dai RS, Zhu HM, Klimek J, David L, Fedorov LM, Azuma Y, Sears RC, Dai MS. The deubiquitinase USP36 promotes snoRNP group SUMOylation and is essential for ribosome biogenesis. EMBO Rep 2021; 22:e50684. [PMID: 33852194 DOI: 10.15252/embr.202050684] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
SUMOylation plays a crucial role in regulating diverse cellular processes including ribosome biogenesis. Proteomic analyses and experimental evidence showed that a number of nucleolar proteins involved in ribosome biogenesis are modified by SUMO. However, how these proteins are SUMOylated in cells is less understood. Here, we report that USP36, a nucleolar deubiquitinating enzyme (DUB), promotes nucleolar SUMOylation. Overexpression of USP36 enhances nucleolar SUMOylation, whereas its knockdown or genetic deletion reduces the levels of SUMOylation. USP36 interacts with SUMO2 and Ubc9 and directly mediates SUMOylation in cells and in vitro. We show that USP36 promotes the SUMOylation of the small nucleolar ribonucleoprotein (snoRNP) components Nop58 and Nhp2 in cells and in vitro and their binding to snoRNAs. It also promotes the SUMOylation of snoRNP components Nop56 and DKC1. Functionally, we show that knockdown of USP36 markedly impairs rRNA processing and translation. Thus, USP36 promotes snoRNP group SUMOylation and is critical for ribosome biogenesis and protein translation.
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Affiliation(s)
- Hyunju Ryu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiao-Xin Sun
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yingxiao Chen
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yanping Li
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiaoyan Wang
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Roselyn S Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Hong-Ming Zhu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - John Klimek
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Larry David
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Lev M Fedorov
- OHSU Transgenic Mouse Models Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Rosalie C Sears
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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111
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Das M, Zattas D, Zinder JC, Wasmuth EV, Henri J, Lima CD. Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome. Proc Natl Acad Sci U S A 2021; 118:e2024846118. [PMID: 33782132 PMCID: PMC8040639 DOI: 10.1073/pnas.2024846118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quality control requires discrimination between functional and aberrant species to selectively target aberrant substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation followed by helicase-dependent 3' to 5' degradation by the RNA exosome. Using reconstitution biochemistry, we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to protect stable RNA from degradation while selectively targeting and degrading less stable RNA. Substrate discrimination is lost when the distributive exoribonuclease activity of Rrp6 is inactivated, leading to degradation of stable and unstable RNA species. These data support a proofreading mechanism in which deadenylation by Rrp6 competes with Mtr4-dependent degradation to protect stable RNA while selectively targeting and degrading unstable RNA.
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Affiliation(s)
- Mom Das
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Dimitrios Zattas
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - John C Zinder
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elizabeth V Wasmuth
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Julien Henri
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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112
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Ladelfa MF, Peche LY, Amato GE, Escalada MC, Zampieri S, Pascucci FA, Benevento AF, Do Porto DF, Dardis A, Schneider C, Monte M. Expression of the tumor-expressed protein MageB2 enhances rRNA transcription. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119015. [PMID: 33741433 DOI: 10.1016/j.bbamcr.2021.119015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022]
Abstract
An essential requirement for cells to sustain a high proliferating rate is to be paired with enhanced protein synthesis through the production of ribosomes. For this reason, part of the growth-factor signaling pathways, are devoted to activate ribosome biogenesis. Enhanced production of ribosomes is a hallmark in cancer cells, which is boosted by different mechanisms. Here we report that the nucleolar tumor-protein MageB2, whose expression is associated with cell proliferation, also participates in ribosome biogenesis. Studies carried out in both siRNA-mediated MageB2 silenced cells and CRISPR/CAS9-mediated MageB2 knockout (KO) cells showed that its expression is linked to rRNA transcription increase independently of the cell proliferation status. Mechanistically, MageB2 interacts with phospho-UBF, a protein which causes the recruitment of RNA Pol I pre-initiation complex required for rRNA transcription. In addition, cells expressing MageB2 displays enhanced phospho-UBF occupancy at the rDNA gene promoter. Proteomic studies performed in MageB2 KO cells revealed impairment in ribosomal protein (RPs) content. Functionally, enhancement in rRNA production in MageB2 expressing cells, was directly associated with an increased dynamic in protein synthesis. Altogether our results unveil a novel function for a tumor-expressed protein from the MAGE-I family. Findings reported here suggest that nucleolar MageB2 might play a role in enhancing ribosome biogenesis as part of its repertoire to support cancer cell proliferation.
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Affiliation(s)
- María Fátima Ladelfa
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leticia Yamila Peche
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Area Science Park, Trieste, Italy
| | - Gastón Ezequiel Amato
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Micaela Carolina Escalada
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Stefania Zampieri
- Centro di Coordinamento Regionale per le Malattie Rare, Ospedale Universitario Santa Maria Della Misericordia, Udine, Italy
| | - Franco Andrés Pascucci
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andres Fernandez Benevento
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Pabellón 2, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Dario Fernandez Do Porto
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Pabellón 2, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Andrea Dardis
- Centro di Coordinamento Regionale per le Malattie Rare, Ospedale Universitario Santa Maria Della Misericordia, Udine, Italy
| | - Claudio Schneider
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Area Science Park, Trieste, Italy; Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, p.le Kolbe 4, Udine, Italy
| | - Martin Monte
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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113
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Ogawa LM, Buhagiar AF, Abriola L, Leland BA, Surovtseva YV, Baserga SJ. Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription. Mol Biol Cell 2021; 32:956-973. [PMID: 33689394 PMCID: PMC8108525 DOI: 10.1091/mbc.e20-10-0670] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nucleoli are dynamic nuclear condensates in eukaryotic cells that originate through ribosome biogenesis at loci that harbor the ribosomal DNA. These loci are known as nucleolar organizer regions (NORs), and there are 10 in a human diploid genome. While there are 10 NORs, however, the number of nucleoli observed in cells is variable. Furthermore, changes in number are associated with disease, with increased numbers and size common in aggressive cancers. In the near-diploid human breast epithelial cell line, MCF10A, the most frequently observed number of nucleoli is two to three per cell. Here, to identify novel regulators of ribosome biogenesis we used high-throughput quantitative imaging of MCF10A cells to identify proteins that, when depleted, increase the percentage of nuclei with ≥5 nucleoli. Unexpectedly, this unique screening approach led to identification of proteins associated with the cell cycle. Functional analysis on a subset of hits further revealed not only proteins required for progression through the S and G2/M phase, but also proteins required explicitly for the regulation of RNA polymerase I transcription and protein synthesis. Thus, results from this screen for increased nucleolar number highlight the significance of the nucleolus in human cell cycle regulation, linking RNA polymerase I transcription to cell cycle progression.
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Affiliation(s)
- Lisa M Ogawa
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06520
| | - Amber F Buhagiar
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06520
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516
| | - Bryan A Leland
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516
| | - Susan J Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT 06520.,Department of Genetics, Yale University School of Medicine, New Haven, CT 06520.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520
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114
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Liu K, Santos DA, Hussmann JA, Wang Y, Sutter BM, Weissman JS, Tu BP. Regulation of translation by methylation multiplicity of 18S rRNA. Cell Rep 2021; 34:108825. [PMID: 33691096 PMCID: PMC8063911 DOI: 10.1016/j.celrep.2021.108825] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/04/2021] [Accepted: 02/12/2021] [Indexed: 02/01/2023] Open
Abstract
N6-methyladenosine (m6A) is a conserved ribonucleoside modification that regulates many facets of RNA metabolism. Using quantitative mass spectrometry, we find that the universally conserved tandem adenosines at the 3' end of 18S rRNA, thought to be constitutively di-methylated (m62A), are also mono-methylated (m6A). Although present at substoichiometric amounts, m6A at these positions increases significantly in response to sulfur starvation in yeast cells and mammalian cell lines. Combining yeast genetics and ribosome profiling, we provide evidence to suggest that m6A-bearing ribosomes carry out translation distinctly from m62A-bearing ribosomes, featuring a striking specificity for sulfur metabolism genes. Our work thus reveals methylation multiplicity as a mechanism to regulate translation.
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Affiliation(s)
- Kuanqing Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Santos
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin M Sutter
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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115
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Bury M, Le Calvé B, Ferbeyre G, Blank V, Lessard F. New Insights into CDK Regulators: Novel Opportunities for Cancer Therapy. Trends Cell Biol 2021; 31:331-344. [PMID: 33676803 DOI: 10.1016/j.tcb.2021.01.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022]
Abstract
Cyclins and their catalytic partners, the cyclin-dependent kinases (CDKs), control the transition between different phases of the cell cycle. CDK/cyclin activity is regulated by CDK inhibitors (CKIs), currently comprising the CDK-interacting protein/kinase inhibitory protein (CIP/KIP) family and the inhibitor of kinase (INK) family. Recent studies have identified a third group of CKIs, called ribosomal protein-inhibiting CDKs (RPICs). RPICs were discovered in the context of cellular senescence, a stable cell cycle arrest with tumor-suppressing abilities. RPICs accumulate in the nonribosomal fraction of senescent cells due to a decrease in rRNA biogenesis. Accordingly, RPICs are often downregulated in human cancers together with other ribosomal proteins, the tumor-suppressor functions of which are still under study. In this review, we discuss unique therapies that have been developed to target CDK activity in the context of cancer treatment or senescence-associated pathologies, providing novel tools for precision medicine.
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Affiliation(s)
- Marina Bury
- De Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | | | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.
| | - Volker Blank
- Lady Davis Institute for Medical Research, Departments of Medicine and Physiology, McGill University, Montreal, QC, H3T 1E2, Canada.
| | - Frédéric Lessard
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.
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116
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Stuparević I, Novačić A, Rahmouni AR, Fernandez A, Lamb N, Primig M. Regulation of the conserved 3'-5' exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev Camb Philos Soc 2021; 96:1092-1113. [PMID: 33599082 DOI: 10.1111/brv.12693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 processes and degrades RNA, regulates gene expression and participates in DNA double-strand break repair and control of telomere maintenance via degradation of the telomerase RNA component. EXOSC10/Rrp6 is part of the multimeric nuclear RNA exosome and interacts with numerous proteins. Previous clinical, genetic, biochemical and genomic studies revealed the protein's essential functions in cell division and differentiation, its RNA substrates and its relevance to autoimmune disorders and oncology. However, little is known about the regulatory mechanisms that control the transcription, translation and stability of EXOSC10/Rrp6 during cell growth, development and disease and how these mechanisms evolved from yeast to human. Herein, we provide an overview of the RNA- and protein expression profiles of EXOSC10/Rrp6 during cell division, development and nutritional stress, and we summarize interaction networks and post-translational modifications across species. Additionally, we discuss how known and predicted protein interactions and post-translational modifications influence the stability of EXOSC10/Rrp6. Finally, we explore the idea that different EXOSC10/Rrp6 alleles, which potentially alter cellular protein levels or affect protein function, might influence human development and disease progression. In this review we interpret information from the literature together with genomic data from knowledgebases to inspire future work on the regulation of this essential protein's stability in normal and malignant cells.
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Affiliation(s)
- Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR4301 du CNRS, Orléans, 45071, France
| | - Anne Fernandez
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Ned Lamb
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, 35000, France
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117
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Li M, Geng R, Li C, Meng F, Zhao H, Liu J, Dai J, Wang X. Dysregulated gene-associated biomarkers for Alzheimer's disease and aging. Transl Neurosci 2021; 12:83-95. [PMID: 33623715 PMCID: PMC7885957 DOI: 10.1515/tnsci-2021-0009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/20/2020] [Accepted: 01/18/2021] [Indexed: 01/03/2023] Open
Abstract
Alzheimer’s disease (AD), the most common type of dementia, is a neurodegenerative disorder with a hidden onset, including difficult early detection and diagnosis. Nevertheless, the new crucial biomarkers for the diagnosis and pathogenesis of AD need to be explored further. Here, the common differentially expressed genes (DEGs) were identified through a comprehensive analysis of gene expression profiles from the Gene Expression Omnibus (GEO) database. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these DEGs were mainly associated with biological processes, cellular components, and molecular functions, which are involved in multiple cellular functions. Next, we found that 9 of the 24 genes showed the same regulatory changes in the blood of patients with AD compared to those in the GEO database, and 2 of the 24 genes showed a significant correlation with Montreal Cognitive Assessment scores. Finally, we determined that mice with AD and elderly mice had the same regulatory changes in the identified DEGs in both the blood and hippocampus. Our study identified several potential core biomarkers of AD and aging, which could contribute to the early detection, differential diagnosis, treatment, and pathological analysis of AD.
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Affiliation(s)
- Min Li
- Department of Neurology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Binzhou, Shandong, 256603, China
| | - Rongxin Geng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430000, China
| | - Chen Li
- Institute for Metabolic & Neuropsychiatric Disorders, Binzhou Medical University Hospital, Binzhou, Shandong, 256603, China
| | - Fantao Meng
- Institute for Metabolic & Neuropsychiatric Disorders, Binzhou Medical University Hospital, Binzhou, Shandong, 256603, China
| | - Hongwei Zhao
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, Shandong, 256603, China
| | - Jing Liu
- Institute for Metabolic & Neuropsychiatric Disorders, Binzhou Medical University Hospital, Binzhou, Shandong, 256603, China
| | - Juanjuan Dai
- Cancer Research Institute, Binzhou Medical University Hospital, Binzhou, Shandong, 256603, China
| | - Xuezhen Wang
- Department of Neurology, Binzhou Medical University Hospital, No. 661 Huanghe 2nd Road, Binzhou, Shandong, 256603, China
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118
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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning. Sci Rep 2021; 11:2997. [PMID: 33542373 PMCID: PMC7862453 DOI: 10.1038/s41598-021-82565-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.
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119
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Ye C, Liu B, Lu H, Liu J, Rabson AB, Jacinto E, Pestov DG, Shen Z. BCCIP is required for nucleolar recruitment of eIF6 and 12S pre-rRNA production during 60S ribosome biogenesis. Nucleic Acids Res 2021; 48:12817-12832. [PMID: 33245766 PMCID: PMC7736804 DOI: 10.1093/nar/gkaa1114] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 01/25/2023] Open
Abstract
Ribosome biogenesis is a fundamental process required for cell proliferation. Although evolutionally conserved, the mammalian ribosome assembly system is more complex than in yeasts. BCCIP was originally identified as a BRCA2 and p21 interacting protein. A partial loss of BCCIP function was sufficient to trigger genomic instability and tumorigenesis. However, a complete deletion of BCCIP arrested cell growth and was lethal in mice. Here, we report that a fraction of mammalian BCCIP localizes in the nucleolus and regulates 60S ribosome biogenesis. Both abrogation of BCCIP nucleolar localization and impaired BCCIP-eIF6 interaction can compromise eIF6 recruitment to the nucleolus and 60S ribosome biogenesis. BCCIP is vital for a pre-rRNA processing step that produces 12S pre-rRNA, a precursor to the 5.8S rRNA. However, a heterozygous Bccip loss was insufficient to impair 60S biogenesis in mouse embryo fibroblasts, but a profound reduction of BCCIP was required to abrogate its function in 60S biogenesis. These results suggest that BCCIP is a critical factor for mammalian pre-rRNA processing and 60S generation and offer an explanation as to why a subtle dysfunction of BCCIP can be tumorigenic but a complete depletion of BCCIP is lethal.
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Affiliation(s)
- Caiyong Ye
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Bochao Liu
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Huimei Lu
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Jingmei Liu
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Arnold B Rabson
- Department of Pharmacology, and The Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Estela Jacinto
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
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120
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Ishida YI, Miyao S, Saito M, Hiraishi N, Nagahama M. Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2. Int J Biochem Cell Biol 2021; 132:105919. [PMID: 33422691 DOI: 10.1016/j.biocel.2021.105919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022]
Abstract
The AAA-ATPase NVL2 associates with an RNA helicase MTR4 and the nuclear RNA exosome in the course of ribosome biogenesis. In our proteomic screen, we had identified a ribosome biogenesis factor WDR74 as a MTR4-interacting partner, whose dissociation is stimulated by the ATP hydrolysis of NVL2. In this study, we report the identification of splicing factor 30 (SPF30), another MTR4-interacting protein with a similar regulatory mechanism. SPF30 is a pre-mRNA splicing factor harboring a Tudor domain in its central region, which regulates various cellular events by binding to dimethylarginine-modified proteins. The interaction between SPF30 and the exosome core is mediated by MTR4 and RRP6, a catalytic component of the nuclear exosome. The N- and C-terminal regions, but not the Tudor domain, of SPF30 are involved in the association with MTR4 and the exosome. The knockdown of SPF30 caused subtle delay in the 12S pre-rRNA processing to mature 5.8S rRNA, even though no obvious effect was observed on the ribosome subunit profile in the cells. Shotgun proteomic analysis to search for SPF30-interacting proteins indicated its role in ribosome biogenesis, pre-mRNA splicing, and box C/D snoRNA biogenesis. These results suggest that SPF30 collaborates with the MTR4-exosome machinery to play a functional role in multiple RNA metabolic pathways, some of which may be regulated by the ATP hydrolysis of NVL2.
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Affiliation(s)
- Yo-Ichi Ishida
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Sotaro Miyao
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Mitsuaki Saito
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Nobuhiro Hiraishi
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan.
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121
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Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
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Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
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122
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Madrid FF, Grossman LI, Aras S. Mitochondria Autoimmunity and MNRR1 in Breast Carcinogenesis: A Review. JOURNAL OF CANCER IMMUNOLOGY 2020; 2:138-158. [PMID: 33615312 PMCID: PMC7894625 DOI: 10.33696/cancerimmunol.2.027] [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] [Indexed: 01/11/2023]
Abstract
We review here the evidence for participation of mitochondrial autoimmunity in BC inception and progression and propose a new paradigm that may challenge the prevailing thinking in oncogenesis by suggesting that mitochondrial autoimmunity is a major contributor to breast carcinogenesis and probably to the inception and progression of other solid tumors. It has been shown that MNRR1 mediated mitochondrial-nuclear function promotes BC cell growth and migration and the development of metastasis and constitutes a proof of concept supporting the participation of mitochondrial autoimmunity in breast carcinogenesis. The resemblance of the autoantibody profile in BC detected by IFA with that in the rheumatic autoimmune diseases suggested that studies on the autoantibody response to tumor associated antigens and the characterization of the mtDNA- and nDNA-encoded antigens may provide functional data on breast carcinogenesis. We also review the studies supporting the view that a panel of autoreactive nDNA-encoded mitochondrial antigens in addition to MNRR1 may be involved in breast carcinogenesis. These include GAPDH, PKM2, GSTP1, SPATA5, MFF, ncRNA PINK1-AS/DDOST as probably contributing to BC progression and metastases and the evidence suggesting that DDX21 orchestrates a complex signaling network with participation of JUND and ATF3 driving chronic inflammation and breast tumorigenesis. We suggest that the widespread autoreactivity of mtDNA- and nDNA-encoded mitochondrial proteins found in BC sera may be the reflection of autoimmunity triggered by mitochondrial and non-mitochondrial tumor associated antigens involved in multiple tumorigenic pathways. Furthermore, we suggest that mitochondrial proteins may contribute to mitochondrial dysfunction in BC even if mitochondrial respiration is found to be within normal limits. However, although the studies show that mitochondrial autoimmunity is a major factor in breast cancer inception and progression, it is not the only factor since there is a multiplex autoantibody profile targeting centrosome and stem cell antigens as well as anti-idiotypic antibodies, revealing the complex signaling network involved in breast carcinogenesis. In summary, the studies reviewed here open new, unexpected therapeutic avenues for cancer prevention and treatment of patients with cancer derived from an entirely new perspective of breast carcinogenesis.
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Affiliation(s)
- Félix Fernández Madrid
- Department of Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Siddhesh Aras
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
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123
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Farooq M, Lindbæk L, Krogh N, Doganli C, Keller C, Mönnich M, Gonçalves AB, Sakthivel S, Mang Y, Fatima A, Andersen VS, Hussain MS, Eiberg H, Hansen L, Kjaer KW, Gopalakrishnan J, Pedersen LB, Møllgård K, Nielsen H, Baig SM, Tommerup N, Christensen ST, Larsen LA. RRP7A links primary microcephaly to dysfunction of ribosome biogenesis, resorption of primary cilia, and neurogenesis. Nat Commun 2020; 11:5816. [PMID: 33199730 PMCID: PMC7670429 DOI: 10.1038/s41467-020-19658-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/26/2020] [Indexed: 12/25/2022] Open
Abstract
Primary microcephaly (MCPH) is characterized by reduced brain size and intellectual disability. The exact pathophysiological mechanism underlying MCPH remains to be elucidated, but dysfunction of neuronal progenitors in the developing neocortex plays a major role. We identified a homozygous missense mutation (p.W155C) in Ribosomal RNA Processing 7 Homolog A, RRP7A, segregating with MCPH in a consanguineous family with 10 affected individuals. RRP7A is highly expressed in neural stem cells in developing human forebrain, and targeted mutation of Rrp7a leads to defects in neurogenesis and proliferation in a mouse stem cell model. RRP7A localizes to centrosomes, cilia and nucleoli, and patient-derived fibroblasts display defects in ribosomal RNA processing, primary cilia resorption, and cell cycle progression. Analysis of zebrafish embryos supported that the patient mutation in RRP7A causes reduced brain size, impaired neurogenesis and cell proliferation, and defective ribosomal RNA processing. These findings provide novel insight into human brain development and MCPH. The RRP7A a gene is involved in ribosome biogenesis. Here the authors report a homozygous missense mutation segregating with primary microcephaly, and show that this occurs via functional defects in both nucleoli and primary cilia disrupting cell proliferation and neurogenesis.
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Affiliation(s)
- Muhammad Farooq
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark.,Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Baghdad ul Jadeed Campus, 63100, Bahawalpur, Punjab, Pakistan
| | - Louise Lindbæk
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Canan Doganli
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Cecilie Keller
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Maren Mönnich
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - André Brás Gonçalves
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Srinivasan Sakthivel
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Yuan Mang
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Ambrin Fatima
- Human Molecular Genetics Laboratory; Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering PIEAS, Jhang Road, 38000, Faisalabad, Punjab, Pakistan
| | - Vivi Søgaard Andersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Muhammad S Hussain
- Institute of Biochemistry I, University of Cologne, Joseph-Stelzmann-Strasse 52, D50931, Cologne, Germany.,Cologne Center for Genomics and Center for Molecular Medicine Cologne, University of Cologne, Robert-Koch-Strasse 21, D50931, Cologne, Germany
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Lars Hansen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Klaus Wilbrandt Kjaer
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Jay Gopalakrishnan
- Institute of Human Genetics, Universitätsstrasse 1, Heinrich-Heine-University, D-40225, Düsseldorf, Germany
| | - Lotte Bang Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Kjeld Møllgård
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Shahid M Baig
- Human Molecular Genetics Laboratory; Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering PIEAS, Jhang Road, 38000, Faisalabad, Punjab, Pakistan
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Søren Tvorup Christensen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark.
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark.
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124
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Akef A, McGraw K, Cappell SD, Larson DR. Ribosome biogenesis is a downstream effector of the oncogenic U2AF1-S34F mutation. PLoS Biol 2020; 18:e3000920. [PMID: 33137094 PMCID: PMC7660540 DOI: 10.1371/journal.pbio.3000920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/12/2020] [Accepted: 09/22/2020] [Indexed: 01/05/2023] Open
Abstract
U2 Small Nuclear RNA Auxiliary Factor 1 (U2AF1) forms a heterodimeric complex with U2AF2 that is primarily responsible for 3' splice site selection. U2AF1 mutations have been identified in most cancers but are prevalent in Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML), and the most common mutation is a missense substitution of serine-34 to phenylalanine (S34F). The U2AF heterodimer also has a noncanonical function as a translational regulator. Here, we report that the U2AF1-S34F mutation results in specific misregulation of the translation initiation and ribosome biogenesis machinery. The net result is an increase in mRNA translation at the single-cell level. Among the translationally up-regulated targets of U2AF1-S34F is Nucleophosmin 1 (NPM1), which is a major driver of myeloid malignancy. Depletion of NPM1 impairs the viability of the U2AF1-S34F mutant cells and causes ribosomal RNA (rRNA) processing defects, thus indicating an unanticipated synthetic interaction between U2AF1, NPM1, and ribosome biogenesis. Our results establish a unique molecular phenotype for the U2AF1 mutation that recapitulates translational misregulation in myeloid disease.
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MESH Headings
- Amino Acid Substitution
- Animals
- Cell Cycle Checkpoints/genetics
- Cell Line
- Eukaryotic Initiation Factors/genetics
- Eukaryotic Initiation Factors/metabolism
- Gene Silencing
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mice, Transgenic
- Mutation
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/metabolism
- Myeloid Progenitor Cells/metabolism
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- Abdalla Akef
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathy McGraw
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Steven D. Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel R. Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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125
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Dong HJ, Zhang R, Kuang Y, Wang XJ. Selective regulation in ribosome biogenesis and protein production for efficient viral translation. Arch Microbiol 2020; 203:1021-1032. [PMID: 33124672 PMCID: PMC7594972 DOI: 10.1007/s00203-020-02094-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022]
Abstract
As intracellular parasites, viruses depend heavily on host cell structures and their functions to complete their life cycle and produce new viral particles. Viruses utilize or modulate cellular translational machinery to achieve efficient replication; the role of ribosome biogenesis and protein synthesis in viral replication particularly highlights the importance of the ribosome quantity and/or quality in controlling viral protein synthesis. Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Here we summarize the recent literature on RBFs and RPs and their association with subcellular redistribution, post-translational modification, enzyme catalysis, and direct interaction with viral proteins. The advances described in this literature establish a rationale for targeting ribosome production and function in the design of the next generation of antiviral agents.
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Affiliation(s)
- Hui-Jun Dong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Rui Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Yu Kuang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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126
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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127
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Besic V, Habibolahi F, Noël B, Rupp S, Genovesio A, Lebreton A. Coordination of transcriptional and translational regulations in human epithelial cells infected by Listeria monocytogenes. RNA Biol 2020; 17:1492-1507. [PMID: 32584699 PMCID: PMC7549700 DOI: 10.1080/15476286.2020.1777380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
The invasion of mammalian cells by intracellular bacterial pathogens reshuffles their gene expression and functions; however, we lack dynamic insight into the distinct control levels that shape the host response. Here, we have addressed the respective contribution of transcriptional and translational regulations during a time-course of infection of human intestinal epithelial cells by an epidemic strain of Listeria monocytogenes, using transcriptome analysis paralleled with ribosome profiling. Upregulations were dominated by early transcriptional activation of pro-inflammatory genes, whereas translation inhibition appeared as the major driver of downregulations. Instead of a widespread but transient shutoff, translation inhibition affected specifically and durably transcripts encoding components of the translation machinery harbouring a 5'-terminal oligopyrimidine motif. Pre-silencing the most repressed target gene (PABPC1) slowed down the intracellular multiplication of Listeria monocytogenes, suggesting that the infected host cell can benefit from the repression of genes involved in protein synthesis and thereby better control infection.
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Affiliation(s)
- Vinko Besic
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fatemeh Habibolahi
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benoît Noël
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sebastian Rupp
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Auguste Genovesio
- Computational Biology and Bioinformatics Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Alice Lebreton
- Bacterial Infection & RNA Destiny Group, Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- INRAE, IBENS, Paris, France
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128
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Bursać S, Prodan Y, Pullen N, Bartek J, Volarević S. Dysregulated Ribosome Biogenesis Reveals Therapeutic Liabilities in Cancer. Trends Cancer 2020; 7:57-76. [PMID: 32948502 DOI: 10.1016/j.trecan.2020.08.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Ribosome biogenesis (RiBi) is one of the most complex and energy demanding processes in human cells, critical for cell growth and proliferation. Strong causal links between inherited and acquired impairment in RiBi with cancer pathogenesis are emerging, pointing to RiBi as an attractive therapeutic target for cancer. Here, we will highlight new knowledge about causes of excessive or impaired RiBi and the impact of these changes on protein synthesis. We will also discuss how new knowledge about secondary consequences of dysregulated RiBi and protein synthesis, including proteotoxic stress, metabolic alterations, adaptive transcriptional and translational programs, and the impaired ribosome biogenesis checkpoint (IRBC) provide a foundation for the development of new anticancer therapies.
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Affiliation(s)
- Slađana Bursać
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Ylenia Prodan
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Nick Pullen
- Bristol Myers Squibb, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, 171 76, Stockholm, Sweden; The Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Siniša Volarević
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia.
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129
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Sorino C, Catena V, Bruno T, De Nicola F, Scalera S, Bossi G, Fabretti F, Mano M, De Smaele E, Fanciulli M, Iezzi S. Che-1/AATF binds to RNA polymerase I machinery and sustains ribosomal RNA gene transcription. Nucleic Acids Res 2020; 48:5891-5906. [PMID: 32421830 PMCID: PMC7293028 DOI: 10.1093/nar/gkaa344] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Originally identified as an RNA polymerase II interactor, Che-1/AATF (Che-1) has now been recognized as a multifunctional protein involved in cell-cycle regulation and cancer progression, as well as apoptosis inhibition and response to stress. This protein displays a peculiar nucleolar localization and it has recently been implicated in pre-rRNA processing and ribosome biogenesis. Here, we report the identification of a novel function of Che-1 in the regulation of ribosomal RNA (rRNA) synthesis, in both cancer and normal cells. We demonstrate that Che-1 interacts with RNA polymerase I and nucleolar upstream binding factor (UBF) and promotes RNA polymerase I-dependent transcription. Furthermore, this protein binds to the rRNA gene (rDNA) promoter and modulates its epigenetic state by contrasting the recruitment of HDAC1. Che-1 downregulation affects RNA polymerase I and UBF recruitment on rDNA and leads to reducing rDNA promoter activity and 47S pre-rRNA production. Interestingly, Che-1 depletion induces abnormal nucleolar morphology associated with re-distribution of nucleolar proteins. Finally, we show that upon DNA damage Che-1 re-localizes from rDNA to TP53 gene promoter to induce cell-cycle arrest. This previously uncharacterized function of Che-1 confirms the important role of this protein in the regulation of ribosome biogenesis, cellular proliferation and response to stress.
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Affiliation(s)
- Cristina Sorino
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.,Department of Experimental Medicine, Sapienza-University of Rome, 00161 Rome, Italy
| | - Valeria Catena
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Tiziana Bruno
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Stefano Scalera
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Gianluca Bossi
- Oncogenomic and Epigenetic Unit, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany.,CECAD, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany
| | - Miguel Mano
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra 3060 197, Portugal
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza-University of Rome, 00161 Rome, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Simona Iezzi
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
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130
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Farley-Barnes KI, Deniz E, Overton MM, Khokha MK, Baserga SJ. Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development. PLoS Genet 2020; 16:e1008967. [PMID: 32813698 PMCID: PMC7437866 DOI: 10.1371/journal.pgen.1008967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022] Open
Abstract
Dysregulation of ribosome production can lead to a number of developmental disorders called ribosomopathies. Despite the ubiquitous requirement for these cellular machines used in protein synthesis, ribosomopathies manifest in a tissue-specific manner, with many affecting the development of the face. Here we reveal yet another connection between craniofacial development and making ribosomes through the protein Paired Box 9 (PAX9). PAX9 functions as an RNA Polymerase II transcription factor to regulate the expression of proteins required for craniofacial and tooth development in humans. We now expand this function of PAX9 by demonstrating that PAX9 acts outside of the cell nucleolus to regulate the levels of proteins critical for building the small subunit of the ribosome. This function of PAX9 is conserved to the organism Xenopus tropicalis, an established model for human ribosomopathies. Depletion of pax9 leads to craniofacial defects due to abnormalities in neural crest development, a result consistent with that found for depletion of other ribosome biogenesis factors. This work highlights an unexpected layer of how the making of ribosomes is regulated in human cells and during embryonic development.
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Affiliation(s)
- Katherine I. Farley-Barnes
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Maya M. Overton
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Susan J. Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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131
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Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Tanaka Hall TM. Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA. RNA (NEW YORK, N.Y.) 2020; 26:1049-1059. [PMID: 32371454 PMCID: PMC7373996 DOI: 10.1261/rna.075416.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/29/2020] [Indexed: 05/04/2023]
Abstract
Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA-Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.
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Affiliation(s)
- Jun Zhang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Takamasa Teramoto
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Lauren E Gonzalez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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132
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Ribosomes: An Exciting Avenue in Stem Cell Research. Stem Cells Int 2020; 2020:8863539. [PMID: 32695182 PMCID: PMC7362291 DOI: 10.1155/2020/8863539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Stem cell research has focused on genomic studies. However, recent evidence has indicated the involvement of epigenetic regulation in determining the fate of stem cells. Ribosomes play a crucial role in epigenetic regulation, and thus, we focused on the role of ribosomes in stem cells. Majority of living organisms possess ribosomes that are involved in the translation of mRNA into proteins and promote cellular proliferation and differentiation. Ribosomes are stable molecular machines that play a role with changes in the levels of RNA during translation. Recent research suggests that specific ribosomes actively regulate gene expression in multiple cell types, such as stem cells. Stem cells have the potential for self-renewal and differentiation into multiple lineages and, thus, require high efficiency of translation. Ribosomes induce cellular transdifferentiation and reprogramming, and disrupted ribosome synthesis affects translation efficiency, thereby hindering stem cell function leading to cell death and differentiation. Stem cell function is regulated by ribosome-mediated control of stem cell-specific gene expression. In this review, we have presented a detailed discourse on the characteristics of ribosomes in stem cells. Understanding ribosome biology in stem cells will provide insights into the regulation of stem cell function and cellular reprogramming.
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133
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Liang X, Zuo MQ, Zhang Y, Li N, Ma C, Dong MQ, Gao N. Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Nat Commun 2020; 11:3542. [PMID: 32669547 PMCID: PMC7363849 DOI: 10.1038/s41467-020-17237-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.
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MESH Headings
- Cell Nucleus/metabolism
- Cryoelectron Microscopy
- Humans
- Models, Molecular
- RNA, Ribosomal, 5S/isolation & purification
- RNA, Ribosomal, 5S/metabolism
- RNA, Ribosomal, 5S/ultrastructure
- RNA-Binding Proteins/isolation & purification
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Ribosomal Proteins/isolation & purification
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/ultrastructure
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
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Affiliation(s)
- Xiaomeng Liang
- State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, 100084, Beijing, China
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Mei-Qing Zuo
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Yunyang Zhang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Chengying Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
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134
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Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW. A large-scale binding and functional map of human RNA-binding proteins. Nature 2020; 583:711-719. [PMID: 32728246 PMCID: PMC7410833 DOI: 10.1038/s41586-020-2077-3] [Citation(s) in RCA: 525] [Impact Index Per Article: 131.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 07/10/2019] [Indexed: 11/09/2022]
Abstract
Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.
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Affiliation(s)
- Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peter Freese
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Xiaofeng Wang
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Rui Xiao
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Neal A L Cody
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Cassandra Bazile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Michael O Duff
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Keri E Garcia
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chelsea Gelboin-Burkhart
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Myles Hochman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole J Lambert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael P McGurk
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thai B Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tsultrim Palden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Stanton
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amanda Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ruth Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ashley L Louie
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
| | - Christopher B Burge
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
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135
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Carl PL, Fried HM, Cohen PL. Proteins in assemblages formed by phase separation possess properties that promote their transformation to autoantigens: Implications for autoimmunity. J Autoimmun 2020; 111:102471. [DOI: 10.1016/j.jaut.2020.102471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
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136
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Müller JS, Burns DT, Griffin H, Wells GR, Zendah RA, Munro B, Schneider C, Horvath R. RNA exosome mutations in pontocerebellar hypoplasia alter ribosome biogenesis and p53 levels. Life Sci Alliance 2020; 3:3/8/e202000678. [PMID: 32527837 PMCID: PMC7295610 DOI: 10.26508/lsa.202000678] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
The RNA exosome is a ubiquitously expressed complex of nine core proteins (EXOSC1-9) and associated nucleases responsible for RNA processing and degradation. Mutations in EXOSC3, EXOSC8, EXOSC9, and the exosome cofactor RBM7 cause pontocerebellar hypoplasia and motor neuronopathy. We investigated the consequences of exosome mutations on RNA metabolism and cellular survival in zebrafish and human cell models. We observed that levels of mRNAs encoding p53 and ribosome biogenesis factors are increased in zebrafish lines with homozygous mutations of exosc8 or exosc9, respectively. Consistent with higher p53 levels, mutant zebrafish have a reduced head size, smaller brain, and cerebellum caused by an increased number of apoptotic cells during development. Down-regulation of EXOSC8 and EXOSC9 in human cells leads to p53 protein stabilisation and G2/M cell cycle arrest. Increased p53 transcript levels were also observed in muscle samples from patients with EXOSC9 mutations. Our work provides explanation for the pathogenesis of exosome-related disorders and highlights the link between exosome function, ribosome biogenesis, and p53-dependent signalling. We suggest that exosome-related disorders could be classified as ribosomopathies.
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Affiliation(s)
- Juliane S Müller
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - David T Burns
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Griffin
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Graeme R Wells
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Romance A Zendah
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Benjamin Munro
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Claudia Schneider
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rita Horvath
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK .,Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge, UK
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137
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Kaiser RWJ, Erber J, Höpker K, Fabretti F, Müller RU. AATF/Che-1-An RNA Binding Protein at the Nexus of DNA Damage Response and Ribosome Biogenesis. Front Oncol 2020; 10:919. [PMID: 32587828 PMCID: PMC7298124 DOI: 10.3389/fonc.2020.00919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
The DNA damage response (DDR) is a complex signaling network that is activated upon genotoxic stress. It determines cellular fate by either activating cell cycle arrest or initiating apoptosis and thereby ensures genomic stability. The Apoptosis Antagonizing Transcription Factor (AATF/Che-1), an RNA polymerase II-interacting transcription factor and known downstream target of major DDR kinases, affects DDR signaling by inhibiting p53-mediated transcription of pro-apoptotic genes and promoting cell cycle arrest through various pathways instead. Specifically, AATF was shown to inhibit p53 expression at the transcriptional level and repress its pro-apoptotic activity by direct binding to p53 protein and transactivation of anti-apoptotic genes. Solid and hematological tumors of various organs exploit this function by overexpressing AATF. Both copy number gains and high expression levels of AATF were associated with worse prognosis or relapse of malignant tumors. Recently, a number of studies have enabled insights into the molecular mechanisms by which AATF affects both DDR and proliferation. AATF was found to directly localize to sites of DNA damage upon laser ablation and interact with DNA repair proteins. In addition, depletion of AATF resulted in increased DNA damage and decrease of both proliferative activity and genotoxic tolerance. Interestingly, considering the role of ribosomal stress in the regulation of p53, more recent work established AATF as ribosomal RNA binding protein and enabled insights into its role as an important factor for rRNA processing and ribosome biogenesis. This Mini Review summarizes recent findings on AATF and its important role in the DDR, malignancy, and ribosome biogenesis.
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Affiliation(s)
- Rainer W J Kaiser
- Medizinische Klinik und Poliklinik I, University Hospital Ludwig-Maximilian-University Munich, Munich, Germany.,Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Johanna Erber
- Department I of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Department of Medicine II, School of Medicine, Technical University of Munich, University Hospital Rechts der Isar, Munich, Germany
| | - Katja Höpker
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
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138
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Lingaraju M, Schuller JM, Falk S, Gerlach P, Bonneau F, Basquin J, Benda C, Conti E. To Process or to Decay: A Mechanistic View of the Nuclear RNA Exosome. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:155-163. [PMID: 32493762 DOI: 10.1101/sqb.2019.84.040295] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The RNA exosome was originally discovered in yeast as an RNA-processing complex required for the maturation of 5.8S ribosomal RNA (rRNA), one of the constituents of the large ribosomal subunit. The exosome is now known in eukaryotes as the major 3'-5' RNA degradation machine involved in numerous processing, turnover, and surveillance pathways, both in the nucleus and the cytoplasm. Yet its role in maturing the 5.8S rRNA in the pre-60S ribosomal particle remains probably the most intricate and emblematic among its functions, as it involves all the RNA unwinding, degradation, and trimming activities embedded in this macromolecular complex. Here, we propose a comprehensive mechanistic model, based on current biochemical and structural data, explaining the dual functions of the nuclear exosome-the constructive versus the destructive mode.
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Affiliation(s)
- Mahesh Lingaraju
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Jan M Schuller
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Sebastian Falk
- Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, 1030, Vienna, Austria
| | - Piotr Gerlach
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Fabien Bonneau
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Jérôme Basquin
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Christian Benda
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
| | - Elena Conti
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried/Munich, Germany
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139
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Chi Y, Liang Z, Guo Y, Chen D, Lu L, Lin J, Qiu S, Wang X, Qiu E, Lin F, Chen J, Luo S, Zheng D, Xu X. WBSCR22 confers cell survival and predicts poor prognosis in glioma. Brain Res Bull 2020; 161:1-12. [PMID: 32380188 DOI: 10.1016/j.brainresbull.2020.04.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/19/2022]
Abstract
Human WBSCR22 is involved in cancer proliferation, invasion and metastasis; however, its function in glioma remains unexplored. In our research, we aimed to investigate the role of WBSCR22 in the development of glioma and its possible molecular mechanisms. Using bioinformatic analysis of public datasets, we determined that WBSCR22 overexpression in glioma specimens was correlated with an unfavorable patient prognosis. Our results revealed that WBSCR22 was highly expressed in glioma cell lines. The loss of WBSCR22 inhibited the growth, invasion and migration of glioma cells, while WBSCR22 overexpression produced the opposite effects. Moreover, we found that WBSCR22 downregulation reduced the phosphorylation of Akt and GSK3β and decreased the levels of β-catenin and CyclinD1 in glioma cells. The opposite effects were observed when WBSCR22 was overexpressed. Additionally, we verified with a dual-luciferase reporter assay that WBSCR22 was a direct target of miR-146b-5p. Furthermore, overexpression of miR-146b-5p suppressed WBSCR22 mRNA and protein expression. Notably, the restoration of WBSCR22 expression remarkably reversed the effects of miR-146b-5p overexpression on cell survival, apoptosis and the cell cycle in glioma cells. Collectively, our findings revealed a tumor-promoting role for WBSCR22 in glioma cells, thus providing molecular evidence for WBSCR22 as a novel therapeutic target in glioma.
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Affiliation(s)
- Yajie Chi
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Zi Liang
- Department of Neurosurgery, Lian Jiang People's Hospital, Zhanjiang 524400, Guangdong, China
| | - Yanwu Guo
- The National Key Clinic Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong, China
| | - Daliang Chen
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Lenian Lu
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Jiye Lin
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Shengcong Qiu
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Xiang Wang
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Erning Qiu
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Famu Lin
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Jianmin Chen
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Shi Luo
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China
| | - Dahai Zheng
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China.
| | - Xiaobing Xu
- Department of Neurosurgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528300, Guangdong, China.
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140
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Analysis of U8 snoRNA Variants in Zebrafish Reveals How Bi-allelic Variants Cause Leukoencephalopathy with Calcifications and Cysts. Am J Hum Genet 2020; 106:694-706. [PMID: 32359472 DOI: 10.1016/j.ajhg.2020.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
How mutations in the non-coding U8 snoRNA cause the neurological disorder leukoencephalopathy with calcifications and cysts (LCC) is poorly understood. Here, we report the generation of a mutant U8 animal model for interrogating LCC-associated pathology. Mutant U8 zebrafish exhibit defective central nervous system development, a disturbance of ribosomal RNA (rRNA) biogenesis and tp53 activation, which monitors ribosome biogenesis. Further, we demonstrate that fibroblasts from individuals with LCC are defective in rRNA processing. Human precursor-U8 (pre-U8) containing a 3' extension rescued mutant U8 zebrafish, and this result indicates conserved biological function. Analysis of LCC-associated U8 mutations in zebrafish revealed that one null and one functional allele contribute to LCC. We show that mutations in three nucleotides at the 5' end of pre-U8 alter the processing of the 3' extension, and we identify a previously unknown base-pairing interaction between the 5' end and the 3' extension of human pre-U8. Indeed, LCC-associated mutations in any one of seven nucleotides in the 5' end and 3' extension alter the processing of pre-U8, and these mutations are present on a single allele in almost all individuals with LCC identified to date. Given genetic data indicating that bi-allelic null U8 alleles are likely incompatible with human development, and that LCC is not caused by haploinsufficiency, the identification of hypomorphic misprocessing mutations that mediate viable embryogenesis furthers our understanding of LCC molecular pathology and cerebral vascular homeostasis.
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141
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Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY. The 18S ribosomal RNA m 6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep 2020; 21:e49443. [PMID: 32350990 DOI: 10.15252/embr.201949443] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently emerged as an important layer of gene regulation. N6-methyladenosine (m6 A) is the most prominent modification on eukaryotic messenger RNA and has also been found on noncoding RNA, including ribosomal and small nuclear RNA. Recently, several m6 A methyltransferases were identified, uncovering the specificity of m6 A deposition by structurally distinct enzymes. In order to discover additional m6 A enzymes, we performed an RNAi screen to deplete annotated orthologs of human methyltransferase-like proteins (METTLs) in Drosophila cells and identified CG9666, the ortholog of human METTL5. We show that CG9666 is required for specific deposition of m6 A on 18S ribosomal RNA via direct interaction with the Drosophila ortholog of human TRMT112, CG12975. Depletion of CG9666 yields a subsequent loss of the 18S rRNA m6 A modification, which lies in the vicinity of the ribosome decoding center; however, this does not compromise rRNA maturation. Instead, a loss of CG9666-mediated m6 A impacts fly behavior, providing an underlying molecular mechanism for the reported human phenotype in intellectual disability. Thus, our work expands the repertoire of m6 A methyltransferases, demonstrates the specialization of these enzymes, and further addresses the significance of ribosomal RNA modifications in gene expression and animal behavior.
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Affiliation(s)
| | | | | | - Ludivine Wacheul
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Minh Anh Vu
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Pablo Mier
- Faculty of Biology, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Marc Graille
- BIOC, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Denis Lj Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Mainz, Germany.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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142
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Cherlin T, Magee R, Jing Y, Pliatsika V, Loher P, Rigoutsos I. Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. BMC Biol 2020; 18:38. [PMID: 32279660 PMCID: PMC7153239 DOI: 10.1186/s12915-020-0763-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 01/02/2023] Open
Abstract
Background The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously showed that the identities and abundances of microRNA isoforms (isomiRs) and transfer RNA-derived fragments (tRFs) are tightly regulated, and that they depend on a person’s sex and population origin, as well as on tissue type, tissue state, and disease type. Here, we characterize the regulation and distribution of fragments derived from ribosomal RNAs (rRNAs). rRNAs form a group that includes four (5S, 5.8S, 18S, 28S) rRNAs encoded by the human nuclear genome and two (12S, 16S) by the mitochondrial genome. rRNAs constitute the most abundant RNA type in eukaryotic cells. Results We analyzed rRNA-derived fragments (rRFs) across 434 transcriptomic datasets obtained from lymphoblastoid cell lines (LCLs) derived from healthy participants of the 1000 Genomes Project. The 434 datasets represent five human populations and both sexes. We examined each of the six rRNAs and their respective rRFs, and did so separately for each population and sex. Our analysis shows that all six rRNAs produce rRFs with unique identities, normalized abundances, and lengths. The rRFs arise from the 5′-end (5′-rRFs), the interior (i-rRFs), and the 3′-end (3′-rRFs) or straddle the 5′ or 3′ terminus of the parental rRNA (x-rRFs). Notably, a large number of rRFs are produced in a population-specific or sex-specific manner. Preliminary evidence suggests that rRF production is also tissue-dependent. Of note, we find that rRF production is not affected by the identity of the processing laboratory or the library preparation kit. Conclusions Our findings suggest that rRFs are produced in a regimented manner by currently unknown processes that are influenced by both ubiquitous as well as population-specific and sex-specific factors. The properties of rRFs mirror the previously reported properties of isomiRs and tRFs and have implications for the study of homeostasis and disease.
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Affiliation(s)
- Tess Cherlin
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Rogan Magee
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Yi Jing
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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143
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Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu XD, Graveley BR, Yeo GW. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biol 2020; 21:90. [PMID: 32252787 PMCID: PMC7137325 DOI: 10.1186/s13059-020-01982-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/03/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types. RESULTS Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3' splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs. CONCLUSIONS This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.
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Affiliation(s)
- Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emily C Wheeler
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jasmine Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Samuel S Park
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Keri E Garcia
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chelsea Gelboin-Burkhart
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Thai B Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Stanton
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ruth Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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144
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Montellese C, van den Heuvel J, Ashiono C, Dörner K, Melnik A, Jonas S, Zemp I, Picotti P, Gillet LC, Kutay U. USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit. eLife 2020; 9:54435. [PMID: 32129764 PMCID: PMC7065907 DOI: 10.7554/elife.54435] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential connection between 40S maturation and protein synthesis.
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Affiliation(s)
| | - Jasmin van den Heuvel
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | | | - Kerstin Dörner
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - André Melnik
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ivo Zemp
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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145
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Full-length NF-κB repressing factor contains an XRN2 binding domain. Biochem J 2020; 477:773-786. [PMID: 32011671 PMCID: PMC7054742 DOI: 10.1042/bcj20190733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 11/28/2022]
Abstract
NF-κB repressing factor (NKRF) was recently identified as an RNA binding protein that together with its associated proteins, the 5′–3′ exonuclease XRN2 and the helicase DHX15, is required to process the precursor ribosomal RNA. XRN2 is a multi-functional ribonuclease that is also involved in processing mRNAs, tRNAs and lncRNAs. The activity and stability of XRN2 are controlled by its binding partners, PAXT-1, CDKN2AIP and CDKN2AIPNL. In each case, these proteins interact with XRN2 via an XRN2 binding domain (XTBD), the structure and mode of action of which is highly conserved. Rather surprisingly, although NKRF interacts directly with XRN2, it was not predicted to contain such a domain, and NKRF's interaction with XRN2 was therefore unexplained. We have identified an alternative upstream AUG start codon within the transcript that encodes NKRF and demonstrate that the full-length form of NKRF contains an XTBD that is conserved across species. Our data suggest that NKRF is tethered in the nucleolus by binding directly to rRNA and that the XTBD in the N-terminal extension of NKRF is essential for the retention of XRN2 in this sub-organelle. Thus, we propose NKRF regulates the early steps of pre-rRNA processing during ribosome biogenesis by controlling the spatial distribution of XRN2 and our data provide further support for the XTBD as an XRN2 interacting motif.
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146
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Cancer-associated mutations in the ribosomal protein L5 gene dysregulate the HDM2/p53-mediated ribosome biogenesis checkpoint. Oncogene 2020; 39:3443-3457. [PMID: 32108164 DOI: 10.1038/s41388-020-1231-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/05/2023]
Abstract
Perturbations in ribosome biogenesis have been associated with cancer. Such aberrations activate p53 through the RPL5/RPL11/5S rRNA complex-mediated inhibition of HDM2. Studies using animal models have suggested that this signaling pathway might constitute an important anticancer barrier. To gain a deeper insight into this issue in humans, here we analyze somatic mutations in RPL5 and RPL11 coding regions, reported in The Cancer Genome Atlas and International Cancer Genome Consortium databases. Using a combined computational and statistical approach, complemented by a range of biochemical and functional analyses in human cancer cell models, we demonstrate the existence of several mechanisms by which RPL5 mutations may impair wild-type p53 upregulation and ribosome biogenesis. Unexpectedly, the same approach provides only modest evidence for a similar role of RPL11, suggesting that RPL5 represents a preferred target during human tumorigenesis in cancers with wild-type p53. Furthermore, we find that several functional cancer-associated RPL5 somatic mutations occur as rare germline variants in general population. Our results shed light on the so-far enigmatic role of cancer-associated mutations in genes encoding ribosomal proteins, with implications for our understanding of the tumor suppressive role of the RPL5/RPL11/5S rRNA complex in human malignancies.
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147
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Li D, Kishta MS, Wang J. Regulation of pluripotency and reprogramming by RNA binding proteins. Curr Top Dev Biol 2020; 138:113-138. [PMID: 32220295 DOI: 10.1016/bs.ctdb.2020.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Embryonic stem cells have the capacities of self-renewal and pluripotency. Pluripotency establishment (somatic cell reprogramming), maintenance, and execution (differentiation) require orchestrated regulatory mechanisms of a cell's molecular machinery, including signaling pathways, epigenetics, transcription, translation, and protein degradation. RNA binding proteins (RBPs) take part in every process of RNA regulation and recent studies began to address their important functions in the regulation of pluripotency and reprogramming. Here, we discuss the roles of RBPs in key regulatory steps in the control of pluripotency and reprogramming. Among RNA binding proteins are a group of RNA helicases that are responsible for RNA structure remodeling with important functional implications. We highlight the largest family of RNA helicases, DDX (DEAD-box) helicase family and our current understanding of their functions specifically in the regulation of pluripotency and reprogramming.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mohamed S Kishta
- Hormones Department, Medical Research Division, National Research Centre, Cairo, Egypt; Stem Cell Lab., Center of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States.
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148
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Yao RW, Liu CX, Chen LL. Linking RNA Processing and Function. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:67-82. [PMID: 32019863 DOI: 10.1101/sqb.2019.84.039495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA processing is critical for eukaryotic mRNA maturation and function. It appears there is no exception for other types of RNAs. Long noncoding RNAs (lncRNAs) represent a subclass of noncoding RNAs, have sizes of >200 nucleotides (nt), and participate in various aspects of gene regulation. Although many lncRNAs are capped, polyadenylated, and spliced just like mRNAs, others are derived from primary transcripts of RNA polymerase II and stabilized by forming circular structures or by ending with small nucleolar RNA-protein complexes. Here we summarize the recent progress in linking the processing and function of these unconventionally processed lncRNAs; we also discuss how directional RNA movement is achieved using the radial flux movement of nascent precursor ribosomal RNA (pre-rRNA) in the human nucleolus as an example.
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Affiliation(s)
- Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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149
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Nieto B, Gaspar SG, Moriggi G, Pestov DG, Bustelo XR, Dosil M. Identification of distinct maturation steps involved in human 40S ribosomal subunit biosynthesis. Nat Commun 2020; 11:156. [PMID: 31919354 PMCID: PMC6952385 DOI: 10.1038/s41467-019-13990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/11/2019] [Indexed: 02/02/2023] Open
Abstract
Technical problems intrinsic to the purification of preribosome intermediates have limited our understanding of ribosome biosynthesis in humans. Addressing this issue is important given the implication of this biological process in human disease. Here we report a preribosome purification and tagging strategy that overcomes some of the existing technical difficulties. Using these tools, we find that the pre-40S precursors go through two distinct maturation phases inside the nucleolus and follow a regulatory step that precedes late maturation in the cytoplasm. This regulatory step entails the intertwined actions of both PARN (a metazoan-specific ribonuclease) and RRP12 (a phylogenetically conserved 40S biogenesis factor that has acquired additional functional features in higher eukaryotes). Together, these results demonstrate the usefulness of this purification method for the dissection of ribosome biogenesis in human cells. They also identify distinct maturation stages and metazoan-specific regulatory mechanisms involved in the generation of the human 40S ribosomal subunit. Ribosome synthesis is a complex multi-step process. Here the authors present a method that allows the efficient isolation and characterization of the preribosomal complexes formed along the entire ribosome synthesis pathway in human cells.
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Affiliation(s)
- Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Departamento de Bioquímica y Biología Molecular, University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.
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150
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Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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