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Spreafico M, Grillo B, Rusconi F, Battaglioli E, Venturin M. Multiple Layers of CDK5R1 Regulation in Alzheimer's Disease Implicate Long Non-Coding RNAs. Int J Mol Sci 2018; 19:ijms19072022. [PMID: 29997370 PMCID: PMC6073344 DOI: 10.3390/ijms19072022] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 11/16/2022] Open
Abstract
Cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1) gene encodes for p35, the main activator of Cyclin-dependent kinase 5 (CDK5). The active p35/CDK5 complex is involved in numerous aspects of brain development and function, and its deregulation is closely associated to Alzheimer's disease (AD) onset and progression. We recently showed that miR-15/107 family can negatively regulate CDK5R1 expression modifying mRNA stability. Interestingly, miRNAs belonging to miR-15/107 family are downregulated in AD brain while CDK5R1 is upregulated. Long non-coding RNAs (lncRNAs) are emerging as master regulators of gene expression, including miRNAs, and their dysregulation has been implicated in the pathogenesis of AD. Here, we evaluated the existence of an additional layer of CDK5R1 expression regulation provided by lncRNAs. In particular, we focused on three lncRNAs potentially regulating CDK5R1 expression levels, based on existing data: NEAT1, HOTAIR, and MALAT1. We demonstrated that NEAT1 and HOTAIR negatively regulate CDK5R1 mRNA levels, while MALAT1 has a positive effect. We also showed that all three lncRNAs positively control miR-15/107 family of miRNAs. Moreover, we evaluated the expression of NEAT1, HOTAIR, and MALAT1 in AD and control brain tissues. Interestingly, NEAT1 displayed increased expression levels in temporal cortex and hippocampus of AD patients. Interestingly, we observed a strong positive correlation between CDK5R1 and NEAT1 expression levels in brain tissues, suggesting a possible neuroprotective role of NEAT1 in AD to compensate for increased CDK5R1 levels. Overall, our work provides evidence of another level of CDK5R1 expression regulation mediated by lncRNAs and points to NEAT1 as a biomarker, as well as a potential pharmacological target for AD therapy.
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Affiliation(s)
- Marco Spreafico
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
| | - Barbara Grillo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
| | - Francesco Rusconi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
| | - Elena Battaglioli
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
- Istituto di Neuroscienze, CNR, Via Vanvitelli 32, 20129 Milano, Italy.
| | - Marco Venturin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Italy.
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152
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Shelkovnikova TA, Kukharsky MS, An H, Dimasi P, Alexeeva S, Shabir O, Heath PR, Buchman VL. Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis. Mol Neurodegener 2018; 13:30. [PMID: 29859124 PMCID: PMC5984788 DOI: 10.1186/s13024-018-0263-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/25/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Paraspeckles are subnuclear bodies assembled on a long non-coding RNA (lncRNA) NEAT1. Their enhanced formation in spinal neurons of sporadic amyotrophic lateral sclerosis (ALS) patients has been reported but underlying mechanisms are unknown. The majority of ALS cases are characterized by TDP-43 proteinopathy. In current study we aimed to establish whether and how TDP-43 pathology may augment paraspeckle assembly. METHODS Paraspeckle formation in human samples was analysed by RNA-FISH and laser capture microdissection followed by qRT-PCR. Mechanistic studies were performed in stable cell lines, mouse primary neurons and human embryonic stem cell-derived neurons. Loss and gain of function for TDP-43 and other microRNA pathway factors were modelled by siRNA-mediated knockdown and protein overexpression. RESULTS We show that de novo paraspeckle assembly in spinal neurons and glial cells is a hallmark of both sporadic and familial ALS with TDP-43 pathology. Mechanistically, loss of TDP-43 but not its cytoplasmic accumulation or aggregation augments paraspeckle assembly in cultured cells. TDP-43 is a component of the microRNA machinery, and recently, paraspeckles have been shown to regulate pri-miRNA processing. Consistently, downregulation of core protein components of the miRNA pathway also promotes paraspeckle assembly. In addition, depletion of these proteins or TDP-43 results in accumulation of endogenous dsRNA and activation of type I interferon response which also stimulates paraspeckle formation. We demonstrate that human or mouse neurons in vitro lack paraspeckles, but a synthetic dsRNA is able to trigger their de novo formation. Finally, paraspeckles are protective in cells with compromised microRNA/dsRNA metabolism, and their assembly can be promoted by a small-molecule microRNA enhancer. CONCLUSIONS Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.
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Affiliation(s)
| | - Michail S Kukharsky
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
| | - Haiyan An
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Pasquale Dimasi
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Svetlana Alexeeva
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Osman Shabir
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
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153
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Creugny A, Fender A, Pfeffer S. Regulation of primary microRNA processing. FEBS Lett 2018; 592:1980-1996. [PMID: 29683487 DOI: 10.1002/1873-3468.13067] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the adjustment of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated.
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Affiliation(s)
- Antoine Creugny
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Aurélie Fender
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Sébastien Pfeffer
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
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154
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Paraspeckles: Where Long Noncoding RNA Meets Phase Separation. Trends Biochem Sci 2018; 43:124-135. [DOI: 10.1016/j.tibs.2017.12.001] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/26/2022]
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155
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Sun Q, Hao Q, Prasanth KV. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet 2018; 34:142-157. [PMID: 29249332 PMCID: PMC6002860 DOI: 10.1016/j.tig.2017.11.005] [Citation(s) in RCA: 388] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
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156
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Latgé G, Poulet C, Bours V, Josse C, Jerusalem G. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers. Int J Mol Sci 2018; 19:ijms19010123. [PMID: 29301303 PMCID: PMC5796072 DOI: 10.3390/ijms19010123] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.
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Affiliation(s)
- Guillaume Latgé
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Christophe Poulet
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Center of Genetics, University Hospital (CHU), 4500 Liège, Belgium.
| | - Claire Josse
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Guy Jerusalem
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
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157
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Fallik N, Bar-Lavan Y, Greenshpan Y, Goldstein O, Grosch M, Drukker M, Gazit R. Neat1 in hematopoietic stem cells. Oncotarget 2017; 8:109575-109586. [PMID: 29312630 PMCID: PMC5752543 DOI: 10.18632/oncotarget.22729] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/10/2017] [Indexed: 12/26/2022] Open
Abstract
Hematopoietic Stem Cells (HSCs) generate blood and immune cells through a hierarchical process of differentiation. Genes that regulate this process are of great interest for understanding normal and also malignant hematopoiesis. Surprisingly, however, very little is known about long-non-coding RNAs (lncRNA) in HSCs. Neat1 is a lncRNA that plays a major role in the formation of sub-nuclear structures called paraspeckles, and was reported to regulate proliferation and differentiation in other cells types. We detected Neat1 expression using RNA-seq data and RT-qPCR in HSCs, progenitors and effector immune cells, by specific detection of its isoforms. Neat1 is highly expressed in stem and progenitor cells, yet it shows significant reduction in granulocytes. Microscopically, Neat1 is detected as sharp nuclear foci. Paraspeckle proteins NONO and PSPC1 are detected as aggregated nuclear foci in fresh primary hematopoietic cells, and in cultured cells. Induction of differentiation in vitro was found to enhance Neat1 expression. Taken together, our data demonstrate for the first time the expression of Neat1 and paraspeckles formation in HSCs and along hematopoiesis.
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Affiliation(s)
- Noam Fallik
- The Shraga Segal Department for Microbiology Immunology and Genetics, Faculty of Health Sciences, The Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Yael Bar-Lavan
- The Shraga Segal Department for Microbiology Immunology and Genetics, Faculty of Health Sciences, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Center for Regenerative Medicine and Stem Cells, The Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Yariv Greenshpan
- The Shraga Segal Department for Microbiology Immunology and Genetics, Faculty of Health Sciences, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, The Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Oron Goldstein
- The Shraga Segal Department for Microbiology Immunology and Genetics, Faculty of Health Sciences, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Center for Regenerative Medicine and Stem Cells, The Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Markus Grosch
- Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Roi Gazit
- The Shraga Segal Department for Microbiology Immunology and Genetics, Faculty of Health Sciences, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, The Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Center for Regenerative Medicine and Stem Cells, The Ben-Gurion University of the Negev, Be'er Sheva, Israel
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