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Mattijssen S, Kerkhofs K, Stephen J, Yang A, Han CG, Tadafumi Y, Iben JR, Mishra S, Sakhawala RM, Ranjan A, Gowda M, Gahl WA, Gu S, Malicdan MC, Maraia RJ. A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.577363. [PMID: 38410490 PMCID: PMC10896340 DOI: 10.1101/2024.02.05.577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.
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Affiliation(s)
- Sandy Mattijssen
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kyra Kerkhofs
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - Chen G. Han
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yokoyama Tadafumi
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James R. Iben
- Molecular Genetics Core, NICHD, NIH, Bethesda, MD 20892, USA
| | - Saurabh Mishra
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amitabh Ranjan
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mamatha Gowda
- Department of Obstetrics & Gynaecology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Puducherry, India
| | - William A. Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - May C. Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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Sterrett MC, Cureton LA, Cohen LN, van Hoof A, Khoshnevis S, Fasken MB, Corbett AH, Ghalei H. Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562946. [PMID: 37904946 PMCID: PMC10614903 DOI: 10.1101/2023.10.18.562946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The RNA exosome is an evolutionarily conserved exoribonuclease complex that consists of a 3-subunit cap, a 6-subunit barrel-shaped core, and a catalytic base subunit. Missense mutations in genes encoding structural subunits of the RNA exosome cause a growing family of diseases with diverse pathologies, collectively termed RNA exosomopathies. The disease symptoms vary and can manifest as neurological defects or developmental disorders. The diversity of the RNA exosomopathy pathologies suggests that the different missense mutations in structural genes result in distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models using budding yeast by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant models rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome, EXOSC2, EXOSC3 and EXOSC5 showed the largest transcriptomic differences. Further analyses revealed shared increased transcripts enriched in translation or ribosomal RNA modification/processing pathways across the three mutant models. Studies of the impact of the mutations on translation revealed shared defects in ribosome biogenesis but distinct impacts on translation. Collectively, our results provide the first comparative analysis of several RNA exosomopathy mutant models and suggest that different RNA exosomopathy mutations result in in vivo consequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.
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Affiliation(s)
- Maria C. Sterrett
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Lauryn A. Cureton
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lauren N. Cohen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Sohail Khoshnevis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Milo B. Fasken
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | | | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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Sterrett MC, Farchi D, Strassler SE, Boise LH, Fasken MB, Corbett AH. In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:jkad049. [PMID: 36861343 PMCID: PMC10411580 DOI: 10.1093/g3journal/jkad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
The RNA exosome is a conserved molecular machine that processes/degrades numerous coding and non-coding RNAs. The 10-subunit complex is composed of three S1/KH cap subunits (human EXOSC2/3/1; yeast Rrp4/40/Csl4), a lower ring of six PH-like subunits (human EXOSC4/7/8/9/5/6; yeast Rrp41/42/43/45/46/Mtr3), and a singular 3'-5' exo/endonuclease DIS3/Rrp44. Recently, several disease-linked missense mutations have been identified in structural cap and core RNA exosome genes. In this study, we characterize a rare multiple myeloma patient missense mutation that was identified in the cap subunit gene EXOSC2. This missense mutation results in a single amino acid substitution, p.Met40Thr, in a highly conserved domain of EXOSC2. Structural studies suggest that this Met40 residue makes direct contact with the essential RNA helicase, MTR4, and may help stabilize the critical interaction between the RNA exosome complex and this cofactor. To assess this interaction in vivo, we utilized the Saccharomyces cerevisiae system and modeled the EXOSC2 patient mutation into the orthologous yeast gene RRP4, generating the variant rrp4-M68T. The rrp4-M68T cells show accumulation of certain RNA exosome target RNAs and show sensitivity to drugs that impact RNA processing. We also identified robust negative genetic interactions between rrp4-M68T and specific mtr4 mutants. A complementary biochemical approach revealed that Rrp4 M68T shows decreased interaction with Mtr4, consistent with these genetic results. This study suggests that the EXOSC2 mutation identified in a multiple myeloma patient impacts the function of the RNA exosome and provides functional insight into a critical interface between the RNA exosome and Mtr4.
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Affiliation(s)
- Maria C Sterrett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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Study on differential gene expression profile of serum exosomes in patients with acute cerebral infarction. DIGITAL CHINESE MEDICINE 2021. [DOI: 10.1016/j.dcmed.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Sterrett MC, Enyenihi L, Leung SW, Hess L, Strassler SE, Farchi D, Lee RS, Withers ES, Kremsky I, Baker RE, Basrai MA, van Hoof A, Fasken MB, Corbett AH. A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex. RNA (NEW YORK, N.Y.) 2021; 27:1046-1067. [PMID: 34162742 PMCID: PMC8370739 DOI: 10.1261/rna.078618.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
RNA exosomopathies, a growing family of diseases, are linked to missense mutations in genes encoding structural subunits of the evolutionarily conserved, 10-subunit exoribonuclease complex, the RNA exosome. This complex consists of a three-subunit cap, a six-subunit, barrel-shaped core, and a catalytic base subunit. While a number of mutations in RNA exosome genes cause pontocerebellar hypoplasia, mutations in the cap subunit gene EXOSC2 cause an apparently distinct clinical presentation that has been defined as a novel syndrome SHRF (short stature, hearing loss, retinitis pigmentosa, and distinctive facies). We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by modeling pathogenic EXOSC2 missense mutations (p.Gly30Val and p.Gly198Asp) in the orthologous S. cerevisiae gene RRP4 The resulting rrp4 mutant cells show defects in cell growth and RNA exosome function. Consistent with altered RNA exosome function, we detect significant transcriptomic changes in both coding and noncoding RNAs in rrp4-G226D cells that model EXOSC2 p.Gly198Asp, suggesting defects in nuclear surveillance. Biochemical and genetic analyses suggest that the Rrp4 G226D variant subunit shows impaired interactions with key RNA exosome cofactors that modulate the function of the complex. These results provide the first in vivo evidence that pathogenic missense mutations present in EXOSC2 impair the function of the RNA exosome. This study also sets the stage to compare exosomopathy models to understand how defects in RNA exosome function underlie distinct pathologies.
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Affiliation(s)
- Maria C Sterrett
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Laurie Hess
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Richard S Lee
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Elise S Withers
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Isaac Kremsky
- Loma Linda University School of Medicine, Loma Linda, California 92350, USA
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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Tossberg JT, Heinrich RM, Farley VM, Crooke PS, Aune TM. Adenosine-to-Inosine RNA Editing of Alu Double-Stranded (ds)RNAs Is Markedly Decreased in Multiple Sclerosis and Unedited Alu dsRNAs Are Potent Activators of Proinflammatory Transcriptional Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:2606-2617. [PMID: 33046502 PMCID: PMC7872017 DOI: 10.4049/jimmunol.2000384] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022]
Abstract
Sensors that detect dsRNA stimulate IFN responses as a defense against viral infection. IFN responses are also well documented in a variety of human autoimmune diseases, including relapsing-remitting multiple sclerosis (MS), in which increased IFN responses result from increased levels of double-stranded endogenous Alu RNAs. Mechanisms underlying increases in double-stranded Alu RNAs in MS are obscure. We find widespread loss of adenosine-to-inosine editing of Alu RNAs in MS. Unedited Alu RNAs are potent activators of both IFN and NF-κB responses via the dsRNA sensors, RIG-I, and TLR3. Minor editing of highly active Alu elements abrogates the ability to activate both transcriptional responses. Thus, adenosine-to-inosine editing may also represent an important defense against autoimmune diseases such as MS.
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Affiliation(s)
- John T Tossberg
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Rachel M Heinrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Virginia M Farley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Philip S Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN 37212; and
| | - Thomas M Aune
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212;
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212
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Choi JH, Burke JM, Szymanik KH, Nepal U, Battenhouse A, Lau JT, Stark A, Lam V, Sullivan CS. DUSP11-mediated control of 5'-triphosphate RNA regulates RIG-I sensitivity. Genes Dev 2020; 34:1697-1712. [PMID: 33184222 PMCID: PMC7706711 DOI: 10.1101/gad.340604.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
In this study, Choi et al. set out to elucidate the physiological role of RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) in the innate immune response. Using in vivo and in vitro experiments, the authors describe the importance of controlling 5′-triphosphate RNA levels to prevent aberrant RIG-I signaling and demonstrate DUSP11 as a key effector of this mechanism. Deciphering the mechanisms that regulate the sensitivity of pathogen recognition receptors is imperative to understanding infection and inflammation. Here we demonstrate that the RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) acts on both host and virus-derived 5′-triphosphate RNAs rendering them less active in inducing a RIG-I-mediated immune response. Reducing DUSP11 levels alters host triphosphate RNA packaged in extracellular vesicles and induces enhanced RIG-I activation in cells exposed to extracellular vesicles. Virus infection of cells lacking DUSP11 results in a higher proportion of triphosphorylated viral transcripts and attenuated virus replication, which is rescued by reducing RIG-I expression. Consistent with the activity of DUSP11 in the cellular RIG-I response, mice lacking DUSP11 display lower viral loads, greater sensitivity to triphosphorylated RNA, and a signature of enhanced interferon activity in select tissues. Our results reveal the importance of controlling 5′-triphosphate RNA levels to prevent aberrant RIG-I signaling and demonstrate DUSP11 as a key effector of this mechanism.
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Affiliation(s)
- Joon H Choi
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - James M Burke
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Kayla H Szymanik
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Upasana Nepal
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Justin T Lau
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Aaron Stark
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Victor Lam
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Christopher S Sullivan
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
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Abstract
Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several forms of environmental stress. Y RNAs are regulators that inhibit or allow the interactions of Ro60 with other proteins and RNAs. Studies of Ro60 RNPs in other bacteria hint at additional functions, since the most conserved Y RNA contains a domain that is a close tRNA mimic and Ro60 RNPs are often encoded adjacent to components of RNA repair systems.
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Affiliation(s)
- Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Kevin Hughes
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
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Stolyarenko AD. Nuclear Argonaute Piwi Gene Mutation Affects rRNA by Inducing rRNA Fragment Accumulation, Antisense Expression, and Defective Processing in Drosophila Ovaries. Int J Mol Sci 2020; 21:ijms21031119. [PMID: 32046213 PMCID: PMC7037970 DOI: 10.3390/ijms21031119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/26/2022] Open
Abstract
Drosophila key nuclear piRNA silencing pathway protein Piwi of the Argonaute family has been classically studied as a factor controlling transposable elements and fertility. Piwi has been shown to concentrate in the nucleolus for reasons largely unknown. Ribosomal RNA is the main component of the nucleolus. In this work the effect of a piwi mutation on rRNA is described. This work led to three important conclusions: A mutation in piwi induces antisense 5S rRNA expression, a processing defect of 2S rRNA orthologous to the 3′-end of eukaryotic 5.8S rRNA, and accumulation of fragments of all five rRNAs in Drosophilamelanogaster ovaries. Hypotheses to explain these phenomena are proposed, possibly involving the interaction of the components of the piRNA pathway with the RNA surveillance machinery.
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Affiliation(s)
- Anastasia D Stolyarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., Moscow 123182, Russia
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10
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Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery. Nat Rev Mol Cell Biol 2020; 21:123-136. [PMID: 32020081 DOI: 10.1038/s41580-019-0209-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2019] [Indexed: 02/07/2023]
Abstract
Much of the mammalian genome is transcribed, generating long non-coding RNAs (lncRNAs) that can undergo post-transcriptional surveillance whereby only a subset of the non-coding transcripts is allowed to attain sufficient stability to persist in the cellular milieu and control various cellular functions. Paralleling protein turnover by the proteasome complex, lncRNAs are also likely to exist in a dynamic equilibrium that is maintained through constant monitoring by the RNA surveillance machinery. In this Review, we describe the RNA surveillance factors and discuss the vital role of lncRNA surveillance in orchestrating various biological processes, including the protection of genome integrity, maintenance of pluripotency of embryonic stem cells, antibody-gene diversification, coordination of immune cell activation and regulation of heterochromatin formation. We also discuss examples of human diseases and developmental defects associated with the failure of RNA surveillance mechanisms, further highlighting the importance of lncRNA surveillance in maintaining cell and organism functions and health.
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Abstract
The numerous quality control pathways that target defective ribonucleic acids (RNAs) for degradation play key roles in shaping mammalian transcriptomes and preventing disease. These pathways monitor most steps in the biogenesis of both noncoding RNAs (ncRNAs) and protein-coding messenger RNAs (mRNAs), degrading ncRNAs that fail to form functional complexes with one or more proteins and eliminating mRNAs that encode abnormal, potentially toxic proteins. Mutations in components of diverse RNA surveillance pathways manifest as disease. Some mutations are characterized by increased interferon production, suggesting that a major role of these pathways is to prevent aberrant cellular RNAs from being recognized as "non-self." Other mutations are common in cancer, or result in developmental defects, revealing the importance of RNA surveillance to cell and organismal function.
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Affiliation(s)
- Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
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Belair C, Sim S, Kim KY, Tanaka Y, Park IH, Wolin SL. The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. J Cell Biol 2019; 218:2564-2582. [PMID: 31308215 PMCID: PMC6683745 DOI: 10.1083/jcb.201811148] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/21/2019] [Accepted: 06/12/2019] [Indexed: 01/09/2023] Open
Abstract
This work shows that the exosome modulates the levels of LINE-1 retrotransposons and specific miRNAs, lncRNAs, and mRNAs that encode developmental regulators or affect their expression. The exosome restrains stem cell differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation. A defining feature of embryonic stem cells (ESCs) is the ability to differentiate into all three germ layers. Pluripotency is maintained in part by a unique transcription network that maintains expression of pluripotency-specific transcription factors and represses developmental genes. While the mechanisms that establish this transcription network are well studied, little is known of the posttranscriptional surveillance pathways that degrade differentiation-related RNAs. We report that the surveillance pathway mediated by the RNA exosome nuclease complex represses ESC differentiation. Depletion of the exosome expedites differentiation of human ESCs into all three germ layers. LINE-1 retrotransposons and specific miRNAs, lncRNAs, and mRNAs that encode developmental regulators or affect their expression are all bound by the exosome and increase in level upon exosome depletion. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation. Our studies establish the exosome as a regulator of human ESC differentiation and reveal the importance of RNA decay in maintaining pluripotency.
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Affiliation(s)
- Cedric Belair
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Soyeong Sim
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT
| | | | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT .,RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
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Heinrich MJ, Purcell CA, Pruijssers AJ, Zhao Y, Spurlock CF, Sriram S, Ogden KM, Dermody TS, Scholz MB, Crooke PS, Karijolich J, Aune TM. Endogenous double-stranded Alu RNA elements stimulate IFN-responses in relapsing remitting multiple sclerosis. J Autoimmun 2019; 100:40-51. [PMID: 30826177 DOI: 10.1016/j.jaut.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/22/2022]
Abstract
Various sensors that detect double-stranded RNA, presumably of viral origin, exist in eukaryotic cells and induce IFN-responses. Ongoing IFN-responses have also been documented in a variety of human autoimmune diseases including relapsing-remitting multiple sclerosis (RRMS) but their origins remain obscure. We find increased IFN-responses in leukocytes in relapsing-remitting multiple sclerosis at distinct stages of disease. Moreover, endogenous RNAs isolated from blood cells of these same patients recapitulate this IFN-response if transfected into naïve cells. These endogenous RNAs are double-stranded RNAs, contain Alu and Line elements and are transcribed from leukocyte transcriptional enhancers. Thus, transcribed endogenous retrotransposon elements can co-opt pattern recognition sensors to induce IFN-responses in RRMS.
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Affiliation(s)
- Maxwell J Heinrich
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Caroline A Purcell
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Andrea J Pruijssers
- Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Yang Zhao
- Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Charles F Spurlock
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Subramaniam Sriram
- Departments of Neurology, Vanderbilt University Medical Center, Nashville, TN, 37212, USA
| | - Kristen M Ogden
- Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Terence S Dermody
- Departments of Pediatrics and of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew B Scholz
- Vanderbilt Technologies for Advanced Genomics, Vanderbilt University Medical Center, Nashville, TN, 37212, USA
| | - Philip S Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN, 37212, USA
| | - John Karijolich
- Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Thomas M Aune
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
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14
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Abstract
RNA-binding proteins chaperone the biological functions of noncoding RNA by reducing RNA misfolding, improving matchmaking between regulatory RNA and targets, and exerting quality control over RNP biogenesis. Recent studies of Escherichia coli CspA, HIV NCp, and E. coli Hfq are beginning to show how RNA-binding proteins remodel RNA structures. These different protein families use common strategies for disrupting or annealing RNA double helices, which can be used to understand the mechanisms by which proteins chaperone RNA-dependent regulation in bacteria.
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15
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Gerlach P, Schuller JM, Bonneau F, Basquin J, Reichelt P, Falk S, Conti E. Distinct and evolutionary conserved structural features of the human nuclear exosome complex. eLife 2018; 7:38686. [PMID: 30047866 PMCID: PMC6072439 DOI: 10.7554/elife.38686] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.
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Affiliation(s)
- Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Jan M Schuller
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Peter Reichelt
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Sebastian Falk
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
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