1
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Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 2024; 15:2425. [PMID: 38499544 PMCID: PMC10948791 DOI: 10.1038/s41467-024-46596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Siyan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Wujian Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Qiao Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Ping Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Di Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Simeng He
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jiayi Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China.
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2
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Pederiva C, Trevisan DM, Peirasmaki D, Chen S, Savage SA, Larsson O, Ule J, Baranello L, Agostini F, Farnebo M. Control of protein synthesis through mRNA pseudouridylation by dyskerin. SCIENCE ADVANCES 2023; 9:eadg1805. [PMID: 37506213 PMCID: PMC10381945 DOI: 10.1126/sciadv.adg1805] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Posttranscriptional modifications of mRNA have emerged as regulators of gene expression. Although pseudouridylation is the most abundant, its biological role remains poorly understood. Here, we demonstrate that the pseudouridine synthase dyskerin associates with RNA polymerase II, binds to thousands of mRNAs, and is responsible for their pseudouridylation, an action that occurs in chromatin and does not appear to require a guide RNA with full complementarity. In cells lacking dyskerin, mRNA pseudouridylation is reduced, while at the same time, de novo protein synthesis is enhanced, indicating that this modification interferes with translation. Accordingly, mRNAs with fewer pseudouridines due to knockdown of dyskerin are translated more efficiently. Moreover, mRNA pseudouridylation is severely reduced in patients with dyskeratosis congenita caused by inherited mutations in the gene encoding dyskerin (i.e., DKC1). Our findings demonstrate that pseudouridylation by dyskerin modulates mRNA translatability, with important implications for both normal development and disease.
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Affiliation(s)
- Chiara Pederiva
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
| | - Davide M. Trevisan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14152, Sweden
| | - Dimitra Peirasmaki
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
| | - Shan Chen
- Department of Oncology and Pathology, Karolinska Institutet, Solna 17165, Sweden
- Science for Life Laboratory, Stockholm 17165, Sweden
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20852, USA
| | - Ola Larsson
- Department of Oncology and Pathology, Karolinska Institutet, Solna 17165, Sweden
- Science for Life Laboratory, Stockholm 17165, Sweden
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK
- UK Dementia Research Institute, King’s College London, London W1T 7NF, UK
- National Institute of Chemistry, 1001 Ljubljana, Slovenia
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Stockholm 17165, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna 17165, Sweden
| | - Marianne Farnebo
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14152, Sweden
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3
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Goodier JL, Wan H, Soares AO, Sanchez L, Selser JM, Pereira GC, Karma S, García-Pérez JL, Kazazian HH, García Cañadas MM. ZCCHC3 is a stress granule zinc knuckle protein that strongly suppresses LINE-1 retrotransposition. PLoS Genet 2023; 19:e1010795. [PMID: 37405998 DOI: 10.1371/journal.pgen.1010795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023] Open
Abstract
Retrotransposons have generated about half of the human genome and LINE-1s (L1s) are the only autonomously active retrotransposons. The cell has evolved an arsenal of defense mechanisms to protect against retrotransposition with factors we are only beginning to understand. In this study, we investigate Zinc Finger CCHC-Type Containing 3 (ZCCHC3), a gag-like zinc knuckle protein recently reported to function in the innate immune response to infecting viruses. We show that ZCCHC3 also severely restricts human retrotransposons and associates with the L1 ORF1p ribonucleoprotein particle. We identify ZCCHC3 as a bona fide stress granule protein, and its association with LINE-1 is further supported by colocalization with L1 ORF1 protein in stress granules, dense cytoplasmic aggregations of proteins and RNAs that contain stalled translation pre-initiation complexes and form when the cell is under stress. Our work also draws links between ZCCHC3 and the anti-viral and retrotransposon restriction factors Mov10 RISC Complex RNA Helicase (MOV10) and Zinc Finger CCCH-Type, Antiviral 1 (ZC3HAV1, also called ZAP). Furthermore, collective evidence from subcellular localization, co-immunoprecipitation, and velocity gradient centrifugation connects ZCCHC3 with the RNA exosome, a multi-subunit ribonuclease complex capable of degrading various species of RNA molecules and that has previously been linked with retrotransposon control.
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Affiliation(s)
- John L Goodier
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Han Wan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alisha O Soares
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Laura Sanchez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - John Michael Selser
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gavin C Pereira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sadik Karma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jose Luis García-Pérez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Haig H Kazazian
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marta M García Cañadas
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
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4
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Yin W, Song X, Xiang Y. WDR79 promotes aerobic glycolysis of pancreatic ductal adenocarcinoma (PDAC) by the suppression of SIRT4. Open Med (Wars) 2023; 18:20220624. [PMID: 36712589 PMCID: PMC9843230 DOI: 10.1515/med-2022-0624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 01/17/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive malignant disease. Pancreatic ductal adenocarcinoma (PDAC) is a main type of PDAC. The inhibition of aerobic glycolysis in PC cells is one of the approaches to treat PDAC. WD repeat protein 79 (WDR79) acts as a scaffold protein and is involved in several physiological processes. Since WDR79 affects the progression of several types of cancers, whereas its role in PDAC remains unclear. This study was aimed to investigate the role of WDR79 in the progression of PDAC and clarify the mechanism. We found that WDR79 was highly expressed in PDAC cells. Knockdown of WDR79 inhibited the growth as well as the motility of PDAC cells, while overexpression of WDR79 contributed to the growth and motility. The ablation of WDR79 restrained aerobic glycolysis of PDAC cells. Mechanically, we found that WDR79 depletion increased SIRT4 expression by suppressing UHRF1 expression, which counteracted the function of WDR79 in PDAC. We thought that WDR79 could serve as a target for treating PDAC.
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Affiliation(s)
- Wenke Yin
- Department of Pathology, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, No. 55 Dongshun Road, Gaoping District, Nanchong, Sichuan, 637100, China,Department of Pathology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Xiaoyan Song
- Ultrasonography Lab, Nanchong Oriental Hospital, Nanchong, Sichuan, 637000, China
| | - Yue Xiang
- Department of Pathology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, China
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5
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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6
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Aune TM, Tossberg JT, Heinrich RM, Porter KP, Crooke PS. Alu RNA Structural Features Modulate Immune Cell Activation and A-to-I Editing of Alu RNAs Is Diminished in Human Inflammatory Bowel Disease. Front Immunol 2022; 13:818023. [PMID: 35126398 PMCID: PMC8813004 DOI: 10.3389/fimmu.2022.818023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Alu retrotransposons belong to the class of short interspersed nuclear elements (SINEs). Alu RNA is abundant in cells and its repetitive structure forms double-stranded RNAs (dsRNA) that activate dsRNA sensors and trigger innate immune responses with significant pathological consequences. Mechanisms to prevent innate immune activation include deamination of adenosines to inosines in dsRNAs, referred to as A-to-I editing, degradation of Alu RNAs by endoribonucleases, and sequestration of Alu RNAs by RNA binding proteins. We have previously demonstrated that widespread loss of Alu RNA A-to-I editing is associated with diverse human diseases including viral (COVID-19, influenza) and autoimmune diseases (multiple sclerosis). Here we demonstrate loss of A-to-I editing in leukocytes is also associated with inflammatory bowel diseases. Our structure-function analysis demonstrates that ability to activate innate immune responses resides in the left arm of Alu RNA, requires a 5’-PPP, RIG-I is the major Alu dsRNA sensor, and A-to-I editing disrupts both structure and function. Further, edited Alu RNAs inhibit activity of unedited Alu RNAs. Altering Alu RNA nucleotide sequence increases biological activity. Two classes of Alu RNAs exist, one class stimulates both IRF and NF-kB transcriptional activity and a second class only stimulates IRF transcriptional activity. Thus, Alu RNAs play important roles in human disease but may also have therapeutic potential.
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Affiliation(s)
- Thomas M. Aune
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- *Correspondence: Thomas M. Aune,
| | - John T. Tossberg
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rachel M. Heinrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Krislyn P. Porter
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Philip S. Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN, United States
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7
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Bogard B, Francastel C, Hubé F. Systematic Identification and Functional Validation of New snoRNAs in Human Muscle Progenitors. Noncoding RNA 2021; 7:ncrna7030056. [PMID: 34564318 PMCID: PMC8482216 DOI: 10.3390/ncrna7030056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Small non-coding RNAs (sncRNAs) represent an important class of regulatory RNAs involved in the regulation of transcription, RNA splicing or translation. Among these sncRNAs, small nucleolar RNAs (snoRNAs) mostly originate from intron splicing in humans and are central to posttranscriptional regulation of gene expression. However, the characterization of the complete repertoire of sncRNAs in a given cellular context and the functional annotation of the human transcriptome are far from complete. Here, we report the large-scale identification of sncRNAs in the size range of 50 to 200 nucleotides without a priori on their biogenesis, structure and genomic origin in the context of normal human muscle cells. We provided a complete set of experimental validation of novel candidate snoRNAs by evaluating the prerequisites for their biogenesis and functionality, leading to their validation as genuine snoRNAs. Interestingly, we also found intergenic snoRNAs, which we showed are in fact integrated into candidate introns of unannotated transcripts or degraded by the Nonsense Mediated Decay pathway. Hence, intergenic snoRNAs represent a new type of landmark for the identification of new transcripts that have gone undetected because of low abundance or degradation after the release of the snoRNA.
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8
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Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans 2021; 48:645-656. [PMID: 32267490 PMCID: PMC7200641 DOI: 10.1042/bst20191046] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
Identified five decades ago amongst the most abundant cellular RNAs, small nucleolar RNAs (snoRNAs) were initially described as serving as guides for the methylation and pseudouridylation of ribosomal RNA through direct base pairing. In recent years, however, increasingly powerful high-throughput genomic approaches and strategies have led to the discovery of many new members of the family and surprising diversity in snoRNA functionality and mechanisms of action. SnoRNAs are now known to target RNAs of many biotypes for a wider range of modifications, interact with diverse binding partners, compete with other binders for functional interactions, recruit diverse players to targets and affect protein function and accessibility through direct interaction. This mini-review presents the continuing characterization of the snoRNome through the identification of new snoRNA members and the discovery of their mechanisms of action, revealing a highly versatile noncoding family playing central regulatory roles and connecting the main cellular processes.
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9
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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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10
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Boivin V, Reulet G, Boisvert O, Couture S, Elela SA, Scott MS. Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA. Nucleic Acids Res 2020; 48:2271-2286. [PMID: 31980822 PMCID: PMC7049693 DOI: 10.1093/nar/gkaa028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/08/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 111 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new snoRNA and tRNA-like genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distorts the perceived architecture of the human transcriptome.
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Affiliation(s)
- Vincent Boivin
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Gaspard Reulet
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Olivier Boisvert
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sonia Couture
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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11
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Nostramo RT, Hopper AK. Beyond rRNA and snRNA: tRNA as a 2'-O-methylation target for nucleolar and Cajal body box C/D RNPs. Genes Dev 2020; 33:739-740. [PMID: 31262844 PMCID: PMC6601515 DOI: 10.1101/gad.328443.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This Outlook discusses Vitali and Kiss's finding that uncovers a new role for SNORD97 and SCARNA97 in tRF biogenesis, which modulates a diverse set of cellular functions in human health and disease. Box C/D small nucleolar RNAs (snoRNAs) and small Cajal body (CB) RNAs (scaRNAs) form ribonucleoprotein (RNP) complexes to mediate 2′-O-methylation of rRNAs and small nuclear RNAs (snRNAs), respectively. The site of methylation is determined by antisense elements in the box C/D RNAs that are complementary to sequences in target RNAs. However, numerous box C/D RNAs in mammalian cells lack antisense elements to rRNAs or snRNAs; thus, their targets remain unknown. In this issue of Genes & Development, Vitali and Kiss (pp. 741–746) demonstrate that “orphan” nucleolar box C/D snoRNA SNORD97 and CB box C/D scaRNA SCARNA97 contain antisense elements that target the wobble cytidine at position 34 of human elongator tRNAMet(CAT) for 2′-O-methylation (C34m). C34m is jointly mediated by SNORD97 and SCARNA97 despite their apparently different intranuclear locations. Furthermore, the investigators demonstrate that C34m prohibits site-specific cleavage of tRNAMet (CAT) into tRNA fragments (tRFs) by the stress-responsive endoribonuclease angiogenin, thereby uncovering a role for SNORD97 and SCARNA97 in the biogenesis of tRFs, which modulate a diverse set of cellular functions in human health and disease.
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Affiliation(s)
- Regina T Nostramo
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anita K Hopper
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA.,The Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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12
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Persson H, Søkilde R, Häkkinen J, Vallon-Christersson J, Mitelman F, Borg Å, Höglund M, Rovira C. Analysis of fusion transcripts indicates widespread deregulation of snoRNAs and their host genes in breast cancer. Int J Cancer 2020; 146:3343-3353. [PMID: 32067223 DOI: 10.1002/ijc.32927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022]
Abstract
Genomic rearrangements in cancer can join the sequences of two separate genes. Studies of such gene fusion events have mainly focused on identification of fusion proteins from the chimeric transcripts. We have previously investigated how fusions instead can affect the expression of intronic microRNA (miRNA) genes that are encoded within fusion gene partners. Here, we extend our analysis to small nucleolar RNAs (snoRNAs) that also are embedded within protein-coding or noncoding host genes. We found that snoRNA hosts are selectively enriched in fusion transcripts, like miRNA host genes, and that this enrichment is associated with all snoRNA classes. These structural changes may have functional consequences for the cell; proteins involved in the protein translation machinery are overrepresented among snoRNA host genes, a gene architecture assumed to be needed for closely coordinated expression of snoRNAs and host proteins. Our data indicate that this structure is frequently disrupted in cancer. We furthermore observed that snoRNA genes involved in fusions tend to associate with stronger promoters than the natural host, suggesting a mechanism that selects for snoRNA overexpression. In summary, we highlight a previously unexplored frequent structural change in cancer that affects important components of cellular physiology.
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Affiliation(s)
- Helena Persson
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden
| | - Rolf Søkilde
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Jari Häkkinen
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden
| | | | - Felix Mitelman
- Department of Laboratory Medicine, Clinical Genetics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden.,CREATE Health, Strategic Centre for Translational Cancer Research, Lund, Sweden
| | - Mattias Höglund
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden
| | - Carlos Rovira
- Department of Clinical Sciences Lund, Oncology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
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13
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Deryusheva S, Talhouarne GJS, Gall JG. "Lost and Found": snoRNA Annotation in the Xenopus Genome and Implications for Evolutionary Studies. Mol Biol Evol 2020; 37:149-166. [PMID: 31553476 PMCID: PMC6984369 DOI: 10.1093/molbev/msz209] [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] [Indexed: 12/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) function primarily as guide RNAs for posttranscriptional modification of rRNAs and spliceosomal snRNAs, both of which are functionally important and evolutionarily conserved molecules. It is commonly believed that snoRNAs and the modifications they mediate are highly conserved across species. However, most relevant data on snoRNA annotation and RNA modification are limited to studies on human and yeast. Here, we used RNA-sequencing data from the giant oocyte nucleus of the frog Xenopus tropicalis to annotate a nearly complete set of snoRNAs. We compared the frog data with snoRNA sets from human and other vertebrate genomes, including mammals, birds, reptiles, and fish. We identified many Xenopus-specific (or nonhuman) snoRNAs and Xenopus-specific domains in snoRNAs from conserved RNA families. We predicted that some of these nonhuman snoRNAs and domains mediate modifications at unexpected positions in rRNAs and snRNAs. These modifications were mapped as predicted when RNA modification assays were applied to RNA from nine vertebrate species: frogs X. tropicalis and X. laevis, newt Notophthalmus viridescens, axolotl Ambystoma mexicanum, whiptail lizard Aspidoscelis neomexicana, zebrafish Danio rerio, chicken, mouse, and human. This analysis revealed that only a subset of RNA modifications is evolutionarily conserved and that modification patterns may vary even between closely related species. We speculate that each functional domain in snoRNAs (half of an snoRNA) may evolve independently and shuffle between different snoRNAs.
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Affiliation(s)
| | | | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
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14
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Vitali P, Kiss T. Cooperative 2'-O-methylation of the wobble cytidine of human elongator tRNA Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP. Genes Dev 2019; 33:741-746. [PMID: 31171702 PMCID: PMC6601510 DOI: 10.1101/gad.326363.119] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 04/17/2019] [Indexed: 12/22/2022]
Abstract
Site-specific 2'-O-ribose methylation of mammalian rRNAs and RNA polymerase II-synthesized spliceosomal small nuclear RNAs (snRNAs) is mediated by small nucleolar and small Cajal body (CB)-specific box C/D ribonucleoprotein particles (RNPs) in the nucleolus and the nucleoplasmic CBs, respectively. Here, we demonstrate that 2'-O-methylation of the C34 wobble cytidine of human elongator tRNAMet(CAT) is achieved by collaboration of a nucleolar and a CB-specific box C/D RNP carrying the SNORD97 and SCARNA97 box C/D 2'-O-methylation guide RNAs. Methylation of C34 prevents site-specific cleavage of tRNAMet(CAT) by the stress-induced endoribonuclease angiogenin, implicating box C/D guide RNPs in controlling stress-responsive production of putative regulatory tRNA fragments.
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Affiliation(s)
- Patrice Vitali
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, Centre National de la Recherche Scientifique, Centre de Biologie Intégrative, Université Paul Sabatier, 31062 Toulouse Cedex 9, France
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, Centre National de la Recherche Scientifique, Centre de Biologie Intégrative, Université Paul Sabatier, 31062 Toulouse Cedex 9, France.,Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary
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15
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Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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16
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Guide snoRNAs: Drivers or Passengers in Human Disease? BIOLOGY 2018; 8:biology8010001. [PMID: 30577491 PMCID: PMC6466398 DOI: 10.3390/biology8010001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 01/17/2023]
Abstract
In every domain of life, RNA-protein interactions play a significant role in co- and post-transcriptional modifications and mRNA translation. RNA performs diverse roles inside the cell, and therefore any aberrancy in their function can cause various diseases. During maturation from its primary transcript, RNA undergoes several functionally important post-transcriptional modifications including pseudouridylation and ribose 2′-O-methylation. These modifications play a critical role in the stability of the RNA. In the last few decades, small nucleolar RNAs (snoRNAs) were revealed to be one of the main components to guide these modifications. Due to their active links to the nucleoside modification, deregulation in the snoRNA expressions can cause multiple disorders in humans. Additionally, host genes carrying snoRNA-encoding sequences in their introns also show differential expression in disease. Although few reports support a causal link between snoRNA expression and disease manifestation, this emerging field will have an impact on the way we think about biomarkers or identify novel targets for therapy. This review focuses on the intriguing aspect of snoRNAs that function as a guide in post-transcriptional RNA modification, and regulation of their host genes in human disease.
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17
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Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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18
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Mafra FFP, Gattai PP, Macedo MM, Mori MA, Araujo RC. The angiotensin-I-converting enzyme insertion/deletion in polymorphic element codes for an AluYa5 RNA that downregulates gene expression. THE PHARMACOGENOMICS JOURNAL 2018; 18:517-527. [PMID: 29789676 DOI: 10.1038/s41397-018-0020-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 06/14/2017] [Accepted: 09/18/2017] [Indexed: 01/06/2023]
Abstract
Angiotensin-I-converting enzyme (ACE) is involved in the synthesis and degradation of important bioactive peptides. The ACE gene has a 287-bp insertion/deletion polymorphism that controls ACE expression through a mechanism that remains elusive. In this study, we found that the 287-bp polymorphic element of the ACE gene, a member of the AluYa5 sub-family of Alu elements, codes for an RNA molecule that controls the levels of ACE mRNA. Transient transfection of a plasmid containing a CMV promoter upstream of the ACE polymorphic element resulted in significant expression of an AluYa5 RNA and reduced ACE mRNA expression as well as ACE enzymatic activity in AD 293 cells. The AluYa5 element also independently reduced the expression of other genes, regardless of whether these genes harbored Alu elements within their genomic context. Interestingly, the CMV promoter was not required for the expression of the AluYa5 element in AD 293 cells. The 287-bp sequence was sufficient to produce AluYa5 RNA and led to a significant reduction in ACE gene expression. Moreover, the removal of an 11-bp fragment of the 3' end of the ACE polymorphic sequence, which is specific to this particular AluYa5 element, did not prevent this element from being expressed but did affect its ability to target ACE expression. Thus, the expression of the AluYa5 polymorphic element within the ACE gene could explain why patients carrying the ACE insertion polymorphism have reduced risk of developing several chronic diseases.
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Affiliation(s)
| | - Pedro P Gattai
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Michel M Macedo
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Marcelo A Mori
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Ronaldo C Araujo
- Dept. of Biophysics, Federal University of São Paulo, São Paulo, Brazil.
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19
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The role of Alu-derived RNAs in Alzheimer's and other neurodegenerative conditions. Med Hypotheses 2018; 115:29-34. [PMID: 29685192 DOI: 10.1016/j.mehy.2018.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 12/14/2022]
Abstract
Non-coding RNAs have emerged as essential contributors to neuroinflammation. The Alu element is the most abundant potential source of non-coding RNA in the human genome represented by over 1.1 million copies totaling ∼10% of the genome's mass. Accumulation of "Alu RNA" was observed in the brains of individuals with dementia and Creutzfeldt-Jakob disease - a degenerative brain disorder. "Alu RNAs" activate inflammatory pathways and apoptosis in the non-neural cells. In particular, the "Alu RNA" cytotoxicity is suggested as a mechanism in retinal pigment epithelium (RPE), a compartment damaged in the process of age-related macular degeneration. In RPE cells, the deficiency of Dicer is reported to lead to an accumulation of P3Alu transcripts, subsequent activation of the ERK1/2 signaling pathway, and the formation of NLRP3 inflammasome. In turn, these events result in RPE cell death by apoptosis. Importantly, RPE cells are of neuroectodermal origin, these cells display more similarity to neurons than to other epithelial cells. Thus, it is plausible that the mechanisms of "Alu RNA" cytotoxicity in brain neurons are similar to that in RPE. We hypothesize that accumulation of polymerase III-transcribed noncoding RNA of Alu (P3Alu) may contribute to both neuroinflammation and neurodegeneration associated with Alzheimer's disease (AD) and other degenerative brain disorders. This hypothesis points toward a novel molecular pathway not previously considered for the treatment of AD.
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20
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Massenet S, Bertrand E, Verheggen C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol 2017; 14:680-692. [PMID: 27715451 PMCID: PMC5519232 DOI: 10.1080/15476286.2016.1243646] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022] Open
Abstract
Box C/D and box H/ACA snoRNAs are abundant non-coding RNAs that localize in the nucleolus and mostly function as guides for nucleotide modifications. While a large pool of snoRNAs modifies rRNAs, an increasing number of snoRNAs could also potentially target mRNAs. ScaRNAs belong to a family of specific RNAs that localize in Cajal bodies and that are structurally similar to snoRNAs. Most scaRNAs are involved in snRNA modification, while telomerase RNA, which contains H/ACA motifs, functions in telomeric DNA synthesis. In this review, we describe how box C/D and H/ACA snoRNAs are processed and assembled with core proteins to form functional RNP particles. Their biogenesis involve several transport factors that first direct pre-snoRNPs to Cajal bodies, where some processing steps are believed to take place, and then to nucleoli. Assembly of core proteins involves the HSP90/R2TP chaperone-cochaperone system for both box C/D and H/ACA RNAs, but also several factors specific for each family. These assembly factors chaperone unassembled core proteins, regulate the formation and disassembly of pre-snoRNP intermediates, and control the activity of immature particles. The AAA+ ATPase RUVBL1 and RUVBL2 belong to the R2TP co-chaperones and play essential roles in snoRNP biogenesis, as well as in the formation of other macro-molecular complexes. Despite intensive research, their mechanisms of action are still incompletely understood.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS, 9 Avenue de la forêt de Haye, 54505 Vandoeuvre-les-Nancy Cedex, France, Université de Lorraine, Campus Biologie –Santé, CS 50184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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21
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Di Giorgio ML, Esposito A, Maccallini P, Micheli E, Bavasso F, Gallotta I, Vernì F, Feiguin F, Cacchione S, McCabe BD, Di Schiavi E, Raffa GD. WDR79/TCAB1 plays a conserved role in the control of locomotion and ameliorates phenotypic defects in SMA models. Neurobiol Dis 2017; 105:42-50. [PMID: 28502804 DOI: 10.1016/j.nbd.2017.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/19/2017] [Accepted: 05/10/2017] [Indexed: 12/22/2022] Open
Abstract
SMN (Survival Motor Neuron) deficiency is the predominant cause of spinal muscular atrophy (SMA), a severe neurodegenerative disorder that can lead to progressive paralysis and death. Although SMN is required in every cell for proper RNA metabolism, the reason why its loss is especially critical in the motor system is still unclear. SMA genetic models have been employed to identify several modifiers that can ameliorate the deficits induced by SMN depletion. Here we focus on WDR79/TCAB1, a protein important for the biogenesis of several RNA species that has been shown to physically interact with SMN in human cells. We show that WDR79 depletion results in locomotion defects in both Drosophila and Caenorhabditis elegans similar to those elicited by SMN depletion. Consistent with this observation, we find that SMN overexpression rescues the WDR79 loss-of-function phenotype in flies. Most importantly, we also found that WDR79 overexpression ameliorates the locomotion defects induced by SMN depletion in both flies and worms. Our results collectively suggest that WDR79 and SMN play evolutionarily conserved cooperative functions in the nervous system and suggest that WDR79/TCAB1 may have the potential to modify SMA pathogenesis.
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Affiliation(s)
- Maria Laura Di Giorgio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | | | - Paolo Maccallini
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Emanuela Micheli
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Francesca Bavasso
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Ivan Gallotta
- Institute of Genetics and Biophysics - ABT, CNR, Naples, Italy
| | - Fiammetta Vernì
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Stefano Cacchione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
| | | | - Elia Di Schiavi
- Institute of Genetics and Biophysics - ABT, CNR, Naples, Italy; Institute of Bioscience and Bioresources, CNR, Naples, Italy
| | - Grazia Daniela Raffa
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy.
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22
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Chen ZX, Oliver B, Zhang YE, Gao G, Long M. Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biol Evol 2017; 9:981-992. [PMID: 28338961 PMCID: PMC5398296 DOI: 10.1093/gbe/evx054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2017] [Indexed: 12/24/2022] Open
Abstract
Inverted duplicates are a type of repetitive DNA motifs consist of two copies of reverse complementary sequences separated by a spacer sequence. They can lead to genome instability and many may have no function, but some functional small RNAs are processed from hairpins transcribed from these elements. It is not clear whether the pervasive numbers of such elements in genomes, especially those of mammals, is the result of high generation rates of neutral or slightly deleterious duplication events or positive selection for functionality. To test the functionality of intergenic inverted duplicates without known functions, we used mirror duplicates, a type of repetitive DNA motifs with few reported functions and little potential to form hairpins when transcribed, as a nonfunctional control. We identified large numbers of inverted duplicates within intergenic regions of human and mouse genomes, as well as 19 other vertebrate genomes. Structure characterization of these inverted duplicates revealed higher proportion to form stable hairpins compared with converted mirror duplicates, suggesting that inverted duplicates may produce hairpin RNAs. Expression profiling across tissues demonstrated that 7.8% of human and 5.7% of mouse inverted duplicates were expressed even under strict criteria. We found that expressed inverted duplicates were more likely to be structurally stable than both unexpressed inverted duplicates and expressed converted mirror duplicates. By dating inverted duplicates in the vertebrate phylogenetic tree, we observed higher conservation of inverted duplicates than mirror duplicates. These observations support the notion that expressed inverted duplicates may be functional through forming hairpin RNAs.
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Affiliation(s)
- Zhen-Xia Chen
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, P.R. China.,National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.,Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, P.R. China
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Ge Gao
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, P.R. China
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago
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23
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Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, Zavolan M. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res 2017; 45:2341-2353. [PMID: 28031372 PMCID: PMC5389715 DOI: 10.1093/nar/gkw1321] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2΄-O-ribose methylation sites. We thereby assigned the snoRNA guide to a known methylation site in the 18S rRNA, we uncovered a novel partially methylated site in the 28S ribosomal RNA, and we captured a site in the 28S rRNA in interaction with multiple snoRNAs. Although we also captured mRNAs in interaction with snoRNAs, we did not detect 2΄-O-methylation of these targets. Our study provides an integrated approach to the comprehensive characterization of 2΄-O-methylation targets of snoRNAs in species beyond those in which these interactions have been traditionally studied and contributes to the rapidly developing field of 'epitranscriptomics'.
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MESH Headings
- Algorithms
- Base Sequence
- Cross-Linking Reagents/chemistry
- Databases, Genetic
- High-Throughput Nucleotide Sequencing/methods
- Immunoprecipitation
- Methylation
- Protein Binding
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribose/metabolism
- Software
- Transcriptome
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | | | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Switzerland
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Arnau Vina-Vilaseca
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
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24
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Abstract
Aside from nucleoli, Cajal bodies (CBs) are the best-characterized organelles of mammalian cell nuclei. Like nucleoli, CBs concentrate ribonucleoproteins (RNPs), in particular, spliceosomal small nuclear RNPs (snRNPs) and small nucleolar RNPs (snoRNPs). In one of the best-defined functions of CBs, most of the snoRNPs are involved in site-specific modification of snRNAs. The two major modifications are pseudouridylation and 2'-O-methylation that are guided by the box H/ACA and C/D snoRNPs, respectively. This review details the modifications, their function, the mechanism of modification, and the machineries involved. We dissect the different classes of noncoding RNAs that meet in CBs, guides and substrates. Open questions and conundrums, often raised and appearing due to experimental limitations, are pointed out and discussed. The emphasis of the review is on mammalian CBs and their function in modification of noncoding RNAs.
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Affiliation(s)
- U Thomas Meier
- a Albert Einstein College of Medicine , Department of Anatomy and Structural Biology , Bronx , NY , USA
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25
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Ketele A, Kiss T, Jády BE. Human intron-encoded AluACA RNAs and telomerase RNA share a common element promoting RNA accumulation. RNA Biol 2016; 13:1274-1285. [PMID: 27726486 PMCID: PMC5207380 DOI: 10.1080/15476286.2016.1239689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Mammalian cells express hundreds of intron-encoded box H/ACA RNAs which fold into a common hairpin-hinge-hairpin-tail structure, interact with 4 evolutionarily conserved proteins, dyskerin, Nop10, Nhp2 and Gar1, and function mainly in RNA pseudouridylation. The human telomerase H/ACA RNA (hTR) directs telomeric DNA synthesis and it carries a 5'-terminal domain encompassing the telomeric template sequence. The primary hTR transcript is synthesized from an independent gene by RNA polymerase II and undergoes 3' end processing controlled by the 3'-terminal H/ACA domain. The apical stem-loop of the 3' hairpin of hTR carries a unique biogenesis-promoting element, the BIO motif that promotes hTR processing and RNP assembly. AluACA RNAs represent a distinct class of human H/ACA RNAs; they are processed from intronic Alu repetitive sequences. As compared to canonical H/ACA RNAs, the AluACA RNAs carry unusually short or long 5' hairpins and generally, they accumulate at low levels. Here, we demonstrate that the suboptimal 5' hairpins are responsible for the weak expression of AluACA RNAs. We also show that AluACA RNAs frequently carry a processing/stabilization element that is structurally and functionally indistinguishable from the hTR BIO motif. Both hTR and AluACA biogenesis-promoting elements are located in the terminal stem-loop of the 3'-terminal H/ACA hairpin, they show perfect structural conservation and are functionally interchangeable in in vivo RNA processing reactions. Our results demonstrate that the BIO motif, instead of being confined to hTR, is a more general H/ACA RNP biogenesis-facilitating element that can also promote processing/assembly of intron-encoded AluACA RNPs.
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Affiliation(s)
- Amandine Ketele
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Center de Biologie Intégrative, Université Paul Sabatier , Toulouse Cedex 9, France
| | - Tamás Kiss
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Center de Biologie Intégrative, Université Paul Sabatier , Toulouse Cedex 9, France.,b Biological Research Center, Hungarian Academy of Sciences , Szeged , Hungary
| | - Beáta E Jády
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Center de Biologie Intégrative, Université Paul Sabatier , Toulouse Cedex 9, France
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Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, Zavolan M, Gruber AR. An updated human snoRNAome. Nucleic Acids Res 2016; 44:5068-82. [PMID: 27174936 PMCID: PMC4914119 DOI: 10.1093/nar/gkw386] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/23/2016] [Indexed: 12/18/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the post-transcriptional processing of other non-coding RNAs (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing. In order to construct an up-to-date catalog of human snoRNAs we have combined data from various databases, de novo prediction and extensive literature review. In total, we list more than 750 curated genomic loci that give rise to snoRNA and snoRNA-like genes. Utilizing small RNA-seq data from the ENCODE project, our study characterizes the plasticity of snoRNA expression identifying both constitutively as well as cell type specific expressed snoRNAs. Especially, the comparison of malignant to non-malignant tissues and cell types shows a dramatic perturbation of the snoRNA expression profile. Finally, we developed a high-throughput variant of the reverse-transcriptase-based method for identifying 2'-O-methyl modifications in RNAs termed RimSeq. Using the data from this and other high-throughput protocols together with previously reported modification sites and state-of-the-art target prediction methods we re-estimate the snoRNA target RNA interaction network. Our current results assign a reliable modification site to 83% of the canonical snoRNAs, leaving only 76 snoRNA sequences as orphan.
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Affiliation(s)
- Hadi Jorjani
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany
| | - Dominik J Jedlinski
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, D-04103 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria Santa Fe Institute, NM-87501Santa Fe, USA
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
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Abstract
Our current view of the nucleolus has been shaped by the concept that the organization of this prominent compartment within the nucleus is primarily dictated by its function, the making of ribosome subunits. Whether ribosome biogenesis is framed by a dedicated nucleolar scaffold has remained unclear. In this issue of The EMBO Journal, Caudron‐Herger and colleagues present evidence for a nucleolar skeleton composed of non‐coding RNA enriched in Alu repeat elements.
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Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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Lin P, Mobasher ME, Hakakian Y, Kakarla V, Naseem AF, Ziai H, Alawi F. Differential requirements for H/ACA ribonucleoprotein components in cell proliferation and response to DNA damage. Histochem Cell Biol 2015; 144:543-58. [PMID: 26265134 DOI: 10.1007/s00418-015-1359-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2015] [Indexed: 02/07/2023]
Abstract
H/ACA ribonucleoproteins (RNPs) are comprised of four conserved proteins, dyskerin, NHP2, NOP10, and GAR1, and a function-specifying, noncoding H/ACA RNA. H/ACA RNPs contribute to telomerase assembly and stabilization, and posttranscriptional processing of nascent ribosomal RNA and spliceosomal RNA. However, very little is known about the coordinated action of the four proteins in other biologic processes. As described herein, we observed a differential requirement for the proteins in cell proliferation and identified a possible reliance for these factors in regulation of specific DNA damage biomarkers. In particular, GAR1 expression was upregulated following exposure to all forms of genotoxic stress tested. In contrast, levels of the other proteins were either reduced or unaffected. Only GAR1 showed an altered subcellular localization with a shift from the nucleolus to the nucleoplasm after ultraviolet-C irradiation and doxorubicin treatments. Transient siRNA-mediated depletion of GAR1 and dyskerin arrested cell proliferation, whereas loss of either NHP2 or NOP10 had no effect. Finally, loss of dyskerin, GAR1, NHP2, and NOP10, respectively, limited the accumulation of DNA damage biomarkers. However, the individual responses were dependent upon the specific type of damage incurred. In general, loss of GAR1 had the most suppressive effect on the biomarkers tested. Since the specific responses to genotoxic stress, the contribution of each protein to cell proliferation, and the activation of DNA damage biomarkers were not equivalent, this suggests the possibility that at least some of the proteins, most notably GAR1, may potentially function independently of their respective roles within H/ACA RNP complexes.
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Affiliation(s)
- Ping Lin
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA
| | - Maral E Mobasher
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA
| | - Yasaman Hakakian
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA
| | - Veena Kakarla
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA
| | - Anum F Naseem
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA
| | - Heliya Ziai
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA
| | - Faizan Alawi
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, Levy Building - Room 328B, Philadelphia, PA, 19104, USA.
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Henriksson S, Farnebo M. On the road with WRAP53β: guardian of Cajal bodies and genome integrity. Front Genet 2015; 6:91. [PMID: 25852739 PMCID: PMC4371746 DOI: 10.3389/fgene.2015.00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/19/2015] [Indexed: 12/16/2022] Open
Abstract
The WRAP53 gene encodes both an antisense transcript (WRAP53α) that stabilizes the tumor suppressor p53 and a protein (WRAP53β) involved in maintenance of Cajal bodies, telomere elongation and DNA repair. WRAP53β is one of many proteins containing WD40 domains, known to mediate a variety of cellular processes. These proteins lack enzymatic activity, acting instead as platforms for the assembly of large complexes of proteins and RNAs thus facilitating their interactions. WRAP53β mediates site-specific interactions between Cajal body factors and DNA repair proteins. Moreover, dysfunction of this protein has been linked to premature aging, cancer and neurodegeneration. Here we summarize the current state of knowledge concerning the multifaceted roles of WRAP53β in intracellular trafficking, formation of the Cajal body, DNA repair and maintenance of genomic integrity and discuss potential crosstalk between these processes.
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Affiliation(s)
- Sofia Henriksson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm, Sweden
| | - Marianne Farnebo
- Department of Oncology-Pathology, Cancer Centrum Karolinska, Karolinska Institutet Stockholm, Sweden
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Fong YW, Ho JJ, Inouye C, Tjian R. The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells. eLife 2014; 3. [PMID: 25407680 PMCID: PMC4270071 DOI: 10.7554/elife.03573] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/19/2014] [Indexed: 01/06/2023] Open
Abstract
Acquisition of pluripotency is driven largely at the transcriptional level by activators OCT4, SOX2, and NANOG that must in turn cooperate with diverse coactivators to execute stem cell-specific gene expression programs. Using a biochemically defined in vitro transcription system that mediates OCT4/SOX2 and coactivator-dependent transcription of the Nanog gene, we report the purification and identification of the dyskerin (DKC1) ribonucleoprotein complex as an OCT4/SOX2 coactivator whose activity appears to be modulated by a subset of associated small nucleolar RNAs (snoRNAs). The DKC1 complex occupies enhancers and regulates the expression of key pluripotency genes critical for self-renewal in embryonic stem (ES) cells. Depletion of DKC1 in fibroblasts significantly decreased the efficiency of induced pluripotent stem (iPS) cell generation. This study thus reveals an unanticipated transcriptional role of the DKC1 complex in stem cell maintenance and somatic cell reprogramming. DOI:http://dx.doi.org/10.7554/eLife.03573.001 The stem cells found in an embryo are able to develop into any of the cell types found in the body of the animal: an ability called pluripotency. When a cell becomes a specialized cell type, such as a nerve cell or a muscle cell, it loses this ability. However, mature cells can be reprogrammed back to a pluripotent state by artificially introducing certain proteins (known as ‘reprogramming factors’) into the mature cells. A core group of reprogramming factors are known to activate networks of genes that are normally only expressed in stem cells, and by doing so trigger and maintain a pluripotent state. Other proteins help these core factors to regulate these networks of genes. In 2011, researchers discovered that a protein complex called XPC—which is normally involved in DNA repair—also helps two core reprogramming factors to activate an important gene related to pluripotency. Now, Fong et al., including several of the researchers involved in the 2011 work, have identified another unexpected partner for the same two core reprogramming factors. The protein complex, called DKC1, has a number of known functions related to the processing of RNA molecules. This complex has also been linked to a fatal, rare human disorder called dyskeratosis congenita—a condition that affects many parts of the body, including the skin and bone marrow. Fong et al. found that when embryonic stems cells from mice are depleted of the DKC1 complex, the activation of important pluripotency-related genes by two of the core reprogramming factors is markedly reduced. The XPC and DKC1 protein complexes were found to interact in pluripotent cells, and together they can activate a pluripotency-related gene to a greater extent than either can individually. Fong et al. propose that DKC1 binds to XPC, which in turn binds to two of the core reprogramming factors. The DKC1 complex also binds to RNA molecules, and Fong et al. found that when the DKC1 complex binds to certain RNAs it is more able to help reprogramming factors activate pluripotency-related genes. On the other hand, other RNA molecules seem to inhibit the complex's ability to activate these genes. Mutations identified in people with dyskeratosis congenita can prevent the DKC1 complex from binding to a subset of human RNA molecules. Moreover, the activity of stem cells is impaired in people with this developmental condition. As such, one of the next challenges will be to investigate if these mutations and RNA binding could be linked to problems with the activation of genes related to pluripotency in stem cells. DOI:http://dx.doi.org/10.7554/eLife.03573.002
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Affiliation(s)
- Yick W Fong
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jaclyn J Ho
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Carla Inouye
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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McMahon M, Contreras A, Ruggero D. Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:173-89. [PMID: 25363811 DOI: 10.1002/wrna.1266] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/25/2014] [Accepted: 08/07/2014] [Indexed: 12/26/2022]
Abstract
A myriad of structurally and functionally diverse noncoding RNAs (ncRNAs) have recently been implicated in numerous human diseases including cancer. Small nucleolar RNAs (snoRNAs), the most abundant group of intron-encoded ncRNAs, are classified into two families (box C/D snoRNAs and box H/ACA snoRNAs) and are required for post-transcriptional modifications on ribosomal RNA (rRNA). There is now a growing appreciation that nucleotide modifications on rRNA may impart regulatory potential to the ribosome; however, the functional consequence of site-specific snoRNA-guided modifications remains poorly defined. Discovered almost 20 years ago, H/ACA snoRNAs are required for the conversion of specific uridine residues to pseudouridine on rRNA. Interestingly, recent reports indicate that the levels of subsets of H/ACA snoRNAs required for pseudouridine modifications at specific sites on rRNA are altered in several diseases, particularly cancer. In this review, we describe recent advances in understanding the downstream consequences of H/ACA snoRNA-guided modifications on ribosome function, discuss the possible mechanism by which H/ACA snoRNAs may be regulated, and explore prospective expanding functions of H/ACA snoRNAs. Furthermore, we discuss the potential biological implications of alterations in H/ACA snoRNA expression in several human diseases.
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Affiliation(s)
- Mary McMahon
- School of Medicine and Department of Urology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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Brosius J. The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function. Cold Spring Harb Perspect Biol 2014; 6:a016089. [PMID: 25081515 DOI: 10.1101/cshperspect.a016089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary principles valid today become apparent in such models already. Furthermore, many features of eukaryotic genome architecture might have their origins in an RNA or RNA/protein (RNP) world, including the onset of a further transition, when DNA replaced RNA as the genetic bookkeeper of the cell. Chromosome maintenance, splicing, and regulatory function via RNA may be deeply rooted in the RNA/RNP worlds. Mostly in eukaryotes, conversion from RNA to DNA is still ongoing, which greatly impacts the plasticity of extant genomes. Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery.
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Affiliation(s)
- Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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Marnef A, Richard P, Pinzón N, Kiss T. Targeting vertebrate intron-encoded box C/D 2'-O-methylation guide RNAs into the Cajal body. Nucleic Acids Res 2014; 42:6616-29. [PMID: 24753405 PMCID: PMC4041459 DOI: 10.1093/nar/gku287] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 03/26/2014] [Accepted: 03/26/2014] [Indexed: 02/03/2023] Open
Abstract
Post-transcriptional pseudouridylation and 2'-O-methylation of splicesomal small nuclear ribonucleic acids (snRNAs) is mediated by box H/ACA and box C/D small Cajal body (CB)-specific ribonucleoproteins (scaRNPs), respectively. The WD-repeat protein 79 (WDR79) has been proposed to interact with both classes of modification scaRNPs and target them into the CB. The box H/ACA scaRNAs carry the common CAB box motif (consensus, ugAG) that is required for both WDR79 binding and CB-specific accumulation. Thus far, no cis-acting CB-localization element has been reported for vertebrate box C/D scaRNAs. In this study, systematic mutational analysis of the human U90 and another newly identified box C/D scaRNA, mgU2-47, demonstrated that the CB-specific accumulation of vertebrate intron-encoded box C/D scaRNAs relies on GU- or UG-dominated dinucleotide repeat sequences which are predicted to form the terminal stem-loop of the RNA apical hairpin. While the loop nucleotides are unimportant, the adjacent terminal helix that is composed mostly of consecutive G.U and U.G wobble base-pairs is essential for CB-specific localization of box C/D scaRNAs. Co-immunoprecipitation experiments confirmed that the newly identified CB localization element, called the G.U/U.G wobble stem, is crucial for in vivo association of box C/D scaRNPs with WDR79.
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Affiliation(s)
- Aline Marnef
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Patrica Richard
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Natalia Pinzón
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 9, France Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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Acute dyskerin depletion triggers cellular senescence and renders osteosarcoma cells resistant to genotoxic stress-induced apoptosis. Biochem Biophys Res Commun 2014; 446:1268-75. [PMID: 24690175 DOI: 10.1016/j.bbrc.2014.03.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 03/22/2014] [Indexed: 01/02/2023]
Abstract
Dyskerin is a conserved, nucleolar RNA-binding protein implicated in an increasing array of fundamental cellular processes. Germline mutation in the dyskerin gene (DKC1) is the cause of X-linked dyskeratosis congenita (DC). Conversely, wild-type dyskerin is overexpressed in sporadic cancers, and high-levels may be associated with poor prognosis. It was previously reported that acute loss of dyskerin function via siRNA-mediated depletion slowed the proliferation of transformed cell lines. However, the mechanisms remained unclear. Using human U2OS osteosarcoma cells, we show that siRNA-mediated dyskerin depletion induced cellular senescence as evidenced by proliferative arrest, senescence-associated heterochromatinization and a senescence-associated molecular profile. Senescence can render cells resistant to apoptosis. Conversely, chromatin relaxation can reverse the repressive effects of senescence-associated heterochromatinization on apoptosis. To this end, genotoxic stress-induced apoptosis was suppressed in dyskerin-depleted cells. In contrast, agents that induce chromatin relaxation, including histone deacetylase inhibitors and the DNA intercalator chloroquine, sensitized dyskerin-depleted cells to apoptosis. Dyskerin is a core component of the telomerase complex and plays an important role in telomere homeostasis. Defective telomere maintenance resulting in premature senescence is thought to primarily underlie the pathogenesis of X-linked DC. Since U2OS cells are telomerase-negative, this leads us to conclude that loss of dyskerin function can also induce cellular senescence via mechanisms independent of telomere shortening.
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Yu YT, Meier UT. RNA-guided isomerization of uridine to pseudouridine--pseudouridylation. RNA Biol 2014; 11:1483-94. [PMID: 25590339 PMCID: PMC4615163 DOI: 10.4161/15476286.2014.972855] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 09/12/2014] [Indexed: 01/13/2023] Open
Abstract
Box H/ACA ribonucleoproteins (RNPs), each consisting of one unique guide RNA and 4 common core proteins, constitute a family of complex enzymes that catalyze, in an RNA-guided manner, the isomerization of uridines to pseudouridines (Ψs) in RNAs, a reaction known as pseudouridylation. Over the years, box H/ACA RNPs have been extensively studied revealing many important aspects of these RNA modifying machines. In this review, we focus on the composition, structure, and biogenesis of H/ACA RNPs. We explain the mechanism of how this enzyme family recognizes and specifies its target uridine in a substrate RNA. We discuss the substrates of box H/ACA RNPs, focusing on rRNA (rRNA) and spliceosomal small nuclear RNA (snRNA). We describe the modification product Ψ and its contribution to RNA function. Finally, we consider possible mechanisms of the bone marrow failure syndrome dyskeratosis congenita and of prostate and other cancers linked to mutations in H/ACA RNPs.
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Key Words
- DC, dyskeratosis congenita
- H/ACA
- HH, hoyeraal-hreidarsson syndrome
- PIKK, phosphatidylinositol 3-kinase-related kinase
- PUA, pseudouridylase and archaeosine transglycosylase
- RNA modification
- RNA-guided
- RNP, ribonucleoprotein
- SMN, survival of motor neuron protein
- SSD, SHQ1 specific domain
- U, uridine
- X-DC, X-linked dyskeratosis congenita
- dyskeratosis congenita
- prostate cancer
- pseudouridine
- rRNA
- rRNA, ribosomal RNA
- ribonucleoproteins
- sca, small Cajal body
- snRNA, small nuclear RNA
- sno, small nucleolar
- snoRNA
- snoRNA, small nucleolar RNA
- spliceosomal small nuclear RNA
- tRNA, transfer RNA
- ψ, pseudouridine, 5-ribosyluracil
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MESH Headings
- Dyskeratosis Congenita/genetics
- Dyskeratosis Congenita/metabolism
- Dyskeratosis Congenita/pathology
- Humans
- Isomerism
- Male
- Mutation
- Nucleic Acid Conformation
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Pseudouridine/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Yi-Tao Yu
- University of Rochester Medical Center; Department of Biochemistry and Biophysics; Center for RNA Biology; Rochester, NY USA
| | - U Thomas Meier
- Albert Einstein College of Medicine; Department of Anatomy and Structural Biology; Bronx, NY USA
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Deryusheva S, Gall JG. Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function. RNA (NEW YORK, N.Y.) 2013; 19:1802-14. [PMID: 24149844 PMCID: PMC3884663 DOI: 10.1261/rna.042028.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/23/2013] [Indexed: 05/05/2023]
Abstract
The spliceosomal small nuclear RNAs (snRNAs) are modified post-transcriptionally by introduction of pseudouridines and 2'-O-methyl modifications, which are mediated by box H/ACA and box C/D guide RNAs, respectively. Because of their concentration in the nuclear Cajal body (CB), these guide RNAs are known as small CB-specific (sca) RNAs. In the cell, scaRNAs are associated with the WD-repeat protein WDR79. We used coimmunoprecipitation with WDR79 to recover seven new scaRNAs from Drosophila cell lysates. We demonstrated concentration of these new scaRNAs in the CB by in situ hybridization, and we verified experimentally that they can modify their putative target RNAs. Surprisingly, one of the new scaRNAs targets U6 snRNA, whose modification is generally assumed to occur in the nucleolus, not in the CB. Two other scaRNAs have dual guide functions, one for an snRNA and one for 28S rRNA. Again, the modification of 28S rRNA is assumed to take place in the nucleolus. These findings suggest that canonical scaRNAs may have functions in addition to their established role in modifying U1, U2, U4, and U5 snRNAs. We discuss the likelihood that processing by scaRNAs is not limited to the CB.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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Alawi F, Lin P. Dyskerin localizes to the mitotic apparatus and is required for orderly mitosis in human cells. PLoS One 2013; 8:e80805. [PMID: 24303026 PMCID: PMC3841160 DOI: 10.1371/journal.pone.0080805] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
Dyskerin is a highly conserved, nucleolar RNA-binding protein with established roles in small nuclear ribonucleoprotein biogenesis, telomerase and telomere maintenance and precursor rRNA processing. Telomerase is functional during S phase and the bulk of rRNA maturation occurs during G1 and S phases; both processes are inactivated during mitosis. Yet, we show that during the course of cell cycle progression, human dyskerin expression peaks during G2/M in parallel with the upregulation of pro-mitotic factors. Dyskerin redistributed from the nucleolus in interphase cells to the perichromosomal region during prometaphase, metaphase and anaphase. With continued anaphase progression, dyskerin also localized to the cytoplasm within the mid-pole region. Loss of dyskerin function via siRNA-mediated depletion promoted G2/M accumulation and this was accompanied by an increased mitotic index and activation of the spindle assembly checkpoint. Live cell imaging further revealed an array of mitotic defects including delayed prometaphase progression, a significantly increased incidence of multi-polar spindles, and anaphase bridges culminating in micronucleus formation. Together, these findings suggest that dyskerin is a highly dynamic protein throughout the cell cycle and increases the repertoire of fundamental cellular processes that are disrupted by absence of its normal function.
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Affiliation(s)
- Faizan Alawi
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Ping Lin
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Thumati NR, Zeng XL, Au HHT, Jang CJ, Jan E, Wong JMY. Severity of X-linked dyskeratosis congenita (DKCX) cellular defects is not directly related to dyskerin (DKC1) activity in ribosomal RNA biogenesis or mRNA translation. Hum Mutat 2013; 34:1698-707. [PMID: 24115260 DOI: 10.1002/humu.22447] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/13/2013] [Indexed: 01/14/2023]
Abstract
Dyskerin (encoded by the DKC1 locus) is the pseudouridine synthase responsible for the modification of noncoding RNA. Dyskerin is also an obligate member of the telomerase enzyme, and participates in the biogenesis of telomerase. Genetic lesions at the DKC1 locus are associated with X-linked dyskeratosis congenita (X-DC) and the Hoyeraal-Hreidarsson Syndrome (HHS). Both syndromes have been linked to deficient telomere maintenance, but little is known about the RNA modification activities of dyskerin in X-DC and HHS cells. To evaluate whether X-DC-associated dyskerin mutations affect the modification or function of ribosomal RNA, we studied five telomerase-rescued X-DC cells (X-DC(T) ). Our data revealed a small reproducible loss of pseudouridines in mature rRNA in two X-DC variants. However, we found no difference in protein synthesis between telomerized wild-type (WT(T) ) and X-DC(T) cells, with an internal ribosomal entry site translation assay, or by measuring total protein synthesis in live cells. X-DC(T) cells and WT(T) cells also exhibited similar tolerances to ionizing radiation and endoplasmic reticulum stress. Despite the loss in rRNA pseudouridine modification, functional perturbations from these changes are secondary to the telomere maintenance defects of X-DC. Our data show that telomere dysfunction is the primary and unifying etiology of X-DC.
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Affiliation(s)
- Naresh R Thumati
- Molecular and Cellular Pharmacology Group, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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Nizami ZF, Gall JG. Pearls are novel Cajal body-like structures in the Xenopus germinal vesicle that are dependent on RNA pol III transcription. Chromosome Res 2013; 20:953-69. [PMID: 23135638 DOI: 10.1007/s10577-012-9320-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have identified novel nuclear bodies, which we call pearls, in the giant oocyte nuclei of Xenopus laevis and Xenopus tropicalis. Pearls are attached to the lampbrush chromosomes at specific loci that are transcribed by RNA polymerase III, and they disappear after inhibition of polymerase III activity. Pearls are enriched for small Cajal body-specific RNAs (scaRNAs), which are guide RNAs that modify specific nucleotides on splicing snRNAs. Surprisingly, snRNAs themselves are not present in pearls, suggesting that pearls are not functionally equivalent to Cajal bodies in other systems, which contain both snRNAs and scaRNAs. We suggest that pearls may function in the processing of RNA polymerase III transcripts, such as tRNA, 5S rRNA, and other short non-coding RNAs.
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Affiliation(s)
- Zehra F Nizami
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
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Makarova JA, Ivanova SM, Tonevitsky AG, Grigoriev AI. New functions of small nucleolar RNAs. BIOCHEMISTRY (MOSCOW) 2013; 78:638-50. [DOI: 10.1134/s0006297913060096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Ge J, Yu YT. RNA pseudouridylation: new insights into an old modification. Trends Biochem Sci 2013; 38:210-8. [PMID: 23391857 PMCID: PMC3608706 DOI: 10.1016/j.tibs.2013.01.002] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/22/2012] [Accepted: 01/07/2013] [Indexed: 12/18/2022]
Abstract
Pseudouridine is the most abundant post-transcriptionally modified nucleotide in various stable RNAs of all organisms. Pseudouridine is derived from uridine via base-specific isomerization, resulting in an extra hydrogen-bond donor that distinguishes it from other nucleotides. In eukaryotes, uridine-to-pseudouridine isomerization is catalyzed primarily by box H/ACA RNPs, ribonucleoproteins that act as pseudouridylases. When introduced into RNA, pseudouridine contributes significantly to RNA-mediated cellular processes. It was recently discovered that pseudouridylation can be induced by stress, suggesting a regulatory role for pseudouridine. It has also been reported that pseudouridine can be artificially introduced into mRNA by box H/ACA RNPs and that such introduction can mediate nonsense-to-sense codon conversion, thus demonstrating a new means of generating coding or protein diversity.
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Affiliation(s)
- Junhui Ge
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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Martens-Uzunova ES, Olvedy M, Jenster G. Beyond microRNA--novel RNAs derived from small non-coding RNA and their implication in cancer. Cancer Lett 2013; 340:201-11. [PMID: 23376637 DOI: 10.1016/j.canlet.2012.11.058] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 12/13/2022]
Abstract
Over the recent years, Next Generation Sequencing (NGS) technologies targeting the microRNA transcriptome revealed the existence of many different RNA fragments derived from small RNA species other than microRNA. Although initially discarded as RNA turnover artifacts, accumulating evidence suggests that RNA fragments derived from small nucleolar RNA (snoRNA) and transfer RNA (tRNA) are not just random degradation products but rather stable entities, which may have functional activity in the normal and malignant cell. This review summarizes new findings describing the detection and alterations in expression of snoRNA-derived (sdRNA) and tRNA-derived (tRF) RNAs. We focus on the possible interactions of sdRNAs and tRFs with the canonical microRNA pathways in the cell and present current hypotheses on the function of these RNAs.
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