301
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Vučićević D, Schrewe H, Orom UA. Molecular mechanisms of long ncRNAs in neurological disorders. Front Genet 2014; 5:48. [PMID: 24624135 PMCID: PMC3941653 DOI: 10.3389/fgene.2014.00048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/15/2014] [Indexed: 01/02/2023] Open
Abstract
Long non-coding RNAs (ncRNAs) have added an unexpected layer of complexity in the regulation of gene expression. Mounting evidence now links long ncRNAs to fundamental biological processes such as development and differentiation, and recent research shows important involvement of long ncRNAs in a variety of diseases including neurodegenerative disorders, such as Parkinson’s, Alzheimer’s, spinocerebellar ataxia, and Huntington’s diseases. Furthermore, long ncRNAs are speculated to be implicated in development of psychiatric disorders such as schizophrenia and bipolar disorders. Long ncRNAs contribute to these disorders in diverse ways, from regulation of transcription to modulation of RNA processing and translation. In this review, we describe the diverse mechanisms reported for long ncRNAs, and discuss how they could mechanistically be involved in the development of neurological disorders.
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Affiliation(s)
- Dubravka Vučićević
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Heinrich Schrewe
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Ulf A Orom
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics Berlin, Germany
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302
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Johnsson P, Lipovich L, Grandér D, Morris KV. Evolutionary conservation of long non-coding RNAs; sequence, structure, function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1840:1063-71. [PMID: 24184936 PMCID: PMC3909678 DOI: 10.1016/j.bbagen.2013.10.035] [Citation(s) in RCA: 504] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/15/2013] [Accepted: 10/21/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND Recent advances in genomewide studies have revealed the abundance of long non-coding RNAs (lncRNAs) in mammalian transcriptomes. The ENCODE Consortium has elucidated the prevalence of human lncRNA genes, which are as numerous as protein-coding genes. Surprisingly, many lncRNAs do not show the same pattern of high interspecies conservation as protein-coding genes. The absence of functional studies and the frequent lack of sequence conservation therefore make functional interpretation of these newly discovered transcripts challenging. Many investigators have suggested the presence and importance of secondary structural elements within lncRNAs, but mammalian lncRNA secondary structure remains poorly understood. It is intriguing to speculate that in this group of genes, RNA secondary structures might be preserved throughout evolution and that this might explain the lack of sequence conservation among many lncRNAs. SCOPE OF REVIEW Here, we review the extent of interspecies conservation among different lncRNAs, with a focus on a subset of lncRNAs that have been functionally investigated. The function of lncRNAs is widespread and we investigate whether different forms of functionalities may be conserved. MAJOR CONCLUSIONS Lack of conservation does not imbue a lack of function. We highlight several examples of lncRNAs where RNA structure appears to be the main functional unit and evolutionary constraint. We survey existing genomewide studies of mammalian lncRNA conservation and summarize their limitations. We further review specific human lncRNAs which lack evolutionary conservation beyond primates but have proven to be both functional and therapeutically relevant. GENERAL SIGNIFICANCE Pioneering studies highlight a role in lncRNAs for secondary structures, and possibly the presence of functional "modules", which are interspersed with longer and less conserved stretches of nucleotide sequences. Taken together, high-throughput analysis of conservation and functional composition of the still-mysterious lncRNA genes is only now becoming feasible.
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Affiliation(s)
- Per Johnsson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detriot, MI, USA
| | - Dan Grandér
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kevin V Morris
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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303
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Long non-coding RNA in health and disease. J Mol Med (Berl) 2014; 92:337-46. [PMID: 24531795 DOI: 10.1007/s00109-014-1131-8] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) interact with the nuclear architecture and are involved in fundamental biological mechanisms, such as imprinting, histone-code regulation, gene activation, gene repression, lineage determination, and cell proliferation, all by regulating gene expression. Understanding the lncRNA regulation of transcriptional or post-transcriptional gene regulation expands our knowledge of disease. Several associations between altered lncRNA function and gene expression have been linked to clinical disease phenotypes. Early advances have been made in developing lncRNAs as biomarkers. Several mouse models reveal that human lncRNAs have very diverse functions. Their involvement in gene and genome regulation as well as disease underscores the importance of lncRNA-mediated regulatory networks. Because of their tissue-specific expression potential, their function as activators or repressors, and their selective targeting of genes, lncRNAs are of potential therapeutic interest. We review the regulatory mechanisms of lncRNAs, their major functional principles, and discuss their role in Mendelian disorders, cancer, cardiovascular disease, and neurological disorders.
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304
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Farris SP, Mayfield RD. RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:275-300. [PMID: 25172479 DOI: 10.1016/b978-0-12-801105-8.00011-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA microarrays have been used for over a decade to profile gene expression on a genomic scale. While this technology has advanced our understanding of complex cellular function, the reliance of microarrays on hybridization kinetics results in several technical limitations. For example, knowledge of the sequences being probed is required, distinguishing similar sequences is difficult because of cross-hybridization, and the relatively narrow dynamic range of the signal limits sensitivity. Recently, new technologies have been introduced that are based on novel sequencing methodologies. These next-generation sequencing methods do not have the limitations inherent to microarrays. Next-generation sequencing is unique since it allows the detection of all known and novel RNAs present in biological samples without bias toward known transcripts. In addition, the expression of coding and noncoding RNAs, alternative splicing events, and expressed single nucleotide polymorphisms (SNPs) can be identified in a single experiment. Furthermore, this technology allows for remarkably higher throughput while lowering sequencing costs. This significant shift in throughput and pricing makes low-cost access to whole genomes possible and more importantly expands sequencing applications far beyond traditional uses (Morozova & Marra, 2008) to include sequencing the transcriptome (RNA-Seq), providing detail on gene structure, alternative splicing events, expressed SNPs, and transcript size (Mane et al., 2009; Tang et al., 2009; Walter et al., 2009), in a single experiment, while also quantifying the absolute abundance of genes, all with greater sensitivity and dynamic range than the competing cDNA microarray technology (Mortazavi, Williams, McCue, Schaeffer, & Wold, 2008).
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Affiliation(s)
- Sean P Farris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712.
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305
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Guennewig B, Cooper AA. The Central Role of Noncoding RNA in the Brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:153-94. [DOI: 10.1016/b978-0-12-801105-8.00007-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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306
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Genomics of alternative splicing: evolution, development and pathophysiology. Hum Genet 2014; 133:679-87. [PMID: 24378600 DOI: 10.1007/s00439-013-1411-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/15/2013] [Indexed: 12/11/2022]
Abstract
Alternative splicing is a major cellular mechanism in metazoans for generating proteomic diversity. A large proportion of protein-coding genes in multicellular organisms undergo alternative splicing, and in humans, it has been estimated that nearly 90 % of protein-coding genes-much larger than expected-are subject to alternative splicing. Genomic analyses of alternative splicing have illuminated its universal role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. Disruption of the splicing machinery has been found to drive pathophysiology, and indeed reprogramming of aberrant splicing can provide novel approaches to the development of molecular therapy. This review focuses on the recent progress in our understanding of alternative splicing brought about by the unprecedented explosive growth of genomic data and highlights the relevance of human splicing variation on disease and therapy.
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307
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Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol 2013; 88:1604-16. [PMID: 24257595 DOI: 10.1128/jvi.02989-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) reactivation involves the ordered induction of approximately 90 viral genes that participate in the generation of infectious virions. Using strand-specific RNA-seq to assess the EBV transcriptome during reactivation, we found extensive bidirectional transcription extending across nearly the entire genome. In contrast, only 4% of the EBV genome is currently bidirectionally annotated. Most of the newly identified transcribed regions show little evidence of coding potential, supporting noncoding roles for most of these RNAs. Based on previous cellular long noncoding RNA size calculations, we estimate that there are likely hundreds more EBV genes expressed during reactivation than was previously known. Limited 5' and 3' rapid amplification of cDNA ends (RACE) experiments and findings of novel splicing events by RNA-seq suggest that the complexity of the viral genome during reactivation may be even greater. Further analysis of antisense transcripts at some of the EBV latency gene loci showed that they are "late" genes, they are nuclear, and they tend to localize in areas of the nucleus where others find newly synthesized viral genomes. This raises the possibility that these transcripts perform functions such as new genome processing, stabilization, organization, etc. The finding of a significantly more complex EBV transcriptome during reactivation changes our view of the viral production process from one that is facilitated and regulated almost entirely by previously identified viral proteins to a process that also involves the contribution of a wide array of virus encoded noncoding RNAs. Epstein-Barr virus (EBV) is a herpesvirus that infects the majority of the world's population, in rare cases causing serious disease such as lymphoma and gastric carcinoma. Using strand-specific RNA-seq, we have studied viral gene expression during EBV reactivation and have discovered hundreds more viral transcripts than were previously known. The finding of alternative splicing and the prevalence of overlapping transcripts indicate additional complexity. Most newly identified transcribed regions do not encode proteins but instead likely function as noncoding RNA molecules which could participate in regulating gene expression, gene splicing or even activities such as viral genome processing. These findings broaden the scope of what we need to consider to understand the viral manufacturing process. As more detailed studies are undertaken they will likely change the way we view this process as a whole.
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308
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Aprea J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M, Dahl A, Groszer M, Hiller M, Calegari F. Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment. EMBO J 2013; 32:3145-60. [PMID: 24240175 DOI: 10.1038/emboj.2013.245] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/23/2013] [Indexed: 12/17/2022] Open
Abstract
Transcriptome analysis of somatic stem cells and their progeny is fundamental to identify new factors controlling proliferation versus differentiation during tissue formation. Here, we generated a combinatorial, fluorescent reporter mouse line to isolate proliferating neural stem cells, differentiating progenitors and newborn neurons that coexist as intermingled cell populations during brain development. Transcriptome sequencing revealed numerous novel long non-coding (lnc)RNAs and uncharacterized protein-coding transcripts identifying the signature of neurogenic commitment. Importantly, most lncRNAs overlapped neurogenic genes and shared with them a nearly identical expression pattern suggesting that lncRNAs control corticogenesis by tuning the expression of nearby cell fate determinants. We assessed the power of our approach by manipulating lncRNAs and protein-coding transcripts with no function in corticogenesis reported to date. This led to several evident phenotypes in neurogenic commitment and neuronal survival, indicating that our study provides a remarkably high number of uncharacterized transcripts with hitherto unsuspected roles in brain development. Finally, we focussed on one lncRNA, Miat, whose manipulation was found to trigger pleiotropic effects on brain development and aberrant splicing of Wnt7b. Hence, our study suggests that lncRNA-mediated alternative splicing of cell fate determinants controls stem-cell commitment during neurogenesis.
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Affiliation(s)
- Julieta Aprea
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, Dresden, Germany
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309
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Fenoglio C, Ridolfi E, Galimberti D, Scarpini E. An emerging role for long non-coding RNA dysregulation in neurological disorders. Int J Mol Sci 2013; 14:20427-42. [PMID: 24129177 PMCID: PMC3821623 DOI: 10.3390/ijms141020427] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/18/2013] [Accepted: 09/25/2013] [Indexed: 12/16/2022] Open
Abstract
A novel class of transcripts, long non coding RNAs (lncRNAs), has recently emerged as key players in several biological processes, including dosage compensation, genomic imprinting, chromatin regulation, embryonic development and segmentation, stem cell pluripotency, cell fate determination and potentially many other biological processes, which still are to be elucidated. LncRNAs are pervasively transcribed in the genome and several lines of evidence correlate dysregulation of different lncRNAs to human diseases including neurological disorders. Although their mechanisms of action are yet to be fully elucidated, evidence suggests lncRNA contributions to the pathogenesis of a number of diseases. In this review, the current state of knowledge linking lncRNAs to different neurological disorders is discussed and potential future directions are considered.
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Affiliation(s)
- Chiara Fenoglio
- Department of Pathophysiology and Transplantation, University of Milan, "Dino Ferrari" Center, IRCCS Cà Granda Foundation Ospedale Maggiore Policlinico, Via F.Sforza 35, Milan 20122, Italy.
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310
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Abstract
Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs. Recent studies of lncRNAs across different species have revealed a diverse population of RNA molecules of differing size and function. RNA sequencing studies suggest transcription throughout the genome, so there is a need to understand how sequence relates to functional and structural relationships amongst RNA molecules. Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function. Rather, relative genomic position in relation to a target is fundamentally important. In this review, we describe issues of key importance in functional assessment of lncRNA and how this might apply to lncRNAs important in neurodevelopment.
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Affiliation(s)
- Carl Ernst
- Douglas Hospital Research Institute Montreal, QC, Canada ; Department of Psychiatry, McGill University Montreal, QC, Canada
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311
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Ernst C, Morton CC. Identification and function of long non-coding RNA. Front Cell Neurosci 2013; 7:168. [PMID: 24106460 PMCID: PMC3788346 DOI: 10.3389/fncel.2013.00168] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/09/2013] [Indexed: 12/25/2022] Open
Abstract
Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs. Recent studies of lncRNAs across different species have revealed a diverse population of RNA molecules of differing size and function. RNA sequencing studies suggest transcription throughout the genome, so there is a need to understand how sequence relates to functional and structural relationships amongst RNA molecules. Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function. Rather, relative genomic position in relation to a target is fundamentally important. In this review, we describe issues of key importance in functional assessment of lncRNA and how this might apply to lncRNAs important in neurodevelopment.
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Affiliation(s)
- Carl Ernst
- Douglas Hospital Research Institute Montreal, QC, Canada ; Department of Psychiatry, McGill University Montreal, QC, Canada
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312
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Abstract
Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs. Recent studies of lncRNAs across different species have revealed a diverse population of RNA molecules of differing size and function. RNA sequencing studies suggest transcription throughout the genome, so there is a need to understand how sequence relates to functional and structural relationships amongst RNA molecules. Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function. Rather, relative genomic position in relation to a target is fundamentally important. In this review, we describe issues of key importance in functional assessment of lncRNA and how this might apply to lncRNAs important in neurodevelopment.
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Affiliation(s)
- Carl Ernst
- Douglas Hospital Research Institute Montreal, QC, Canada ; Department of Psychiatry, McGill University Montreal, QC, Canada
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313
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Bergmann JH, Spector DL. Long non-coding RNAs: modulators of nuclear structure and function. Curr Opin Cell Biol 2013; 26:10-8. [PMID: 24529241 DOI: 10.1016/j.ceb.2013.08.005] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 02/06/2023]
Abstract
Long non-coding (lnc)RNAs are emerging key factors in the regulation of various cellular processes. In the nucleus, these include the organization of nuclear sub-structures, the alteration of chromatin state, and the regulation of gene expression through the interaction with effector proteins and modulation of their activity. Collectively, lncRNAs form the core of attractive models explaining aspects of structural and dynamic regulation in the nucleus across time and space. Here we review recent studies that characterize the molecular function of a subset of these molecules in the regulation and fine-tuning of nuclear state.
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Affiliation(s)
- Jan H Bergmann
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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314
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Contribution of Long Noncoding RNAs to Autism Spectrum Disorder Risk. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2013; 113:35-59. [DOI: 10.1016/b978-0-12-418700-9.00002-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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