201
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Auboeuf D. Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210; Laboratory of Biology and Modelling of the Cell; Site Jacques Monod; Lyon France
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202
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The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol 2017; 19:45-58. [PMID: 28875994 DOI: 10.1038/nrm.2017.77] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The discovery of the genetic code and tRNAs as decoders of the code transformed life science. However, after establishing the role of tRNAs in protein synthesis, the field moved to other parts of the RNA world. Now, tRNA research is blooming again, with demonstration of the involvement of tRNAs in various other pathways beyond translation and in adapting translation to environmental cues. These roles are linked to the presence of tRNA sequence variants known as isoacceptors and isodecoders, various tRNA base modifications, the versatility of protein binding partners and tRNA fragmentation events, all of which collectively create an incalculable complexity. This complexity provides a vast repertoire of tRNA species that can serve various functions in cellular homeostasis and in adaptation of cellular functions to changing environments, and it likely arose from the fundamental role of RNAs in early evolution.
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203
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Cognat V, Morelle G, Megel C, Lalande S, Molinier J, Vincent T, Small I, Duchêne AM, Maréchal-Drouard L. The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. Nucleic Acids Res 2017; 45:3460-3472. [PMID: 27899576 PMCID: PMC5389709 DOI: 10.1093/nar/gkw1122] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/27/2016] [Indexed: 11/16/2022] Open
Abstract
In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19–26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.
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Affiliation(s)
- Valérie Cognat
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Geoffrey Morelle
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.,Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia
| | - Cyrille Megel
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Stéphanie Lalande
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Jean Molinier
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Timothée Vincent
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia
| | - Anne-Marie Duchêne
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Laurence Maréchal-Drouard
- Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
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204
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Fay MM, Lyons SM, Ivanov P. RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms. J Mol Biol 2017; 429:2127-2147. [PMID: 28554731 PMCID: PMC5603239 DOI: 10.1016/j.jmb.2017.05.017] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 11/26/2022]
Abstract
G-quadruplexes (G4s) are extremely stable DNA or RNA secondary structures formed by sequences rich in guanine. These structures are implicated in many essential cellular processes, and the number of biological functions attributed to them continues to grow. While DNA G4s are well understood on structural and, to some extent, functional levels, RNA G4s and their functions have received less attention. The presence of bona fide RNA G4s in cells has long been a matter of debate. The development of G4-specific antibodies and ligands hinted on their presence in vivo, but recent advances in RNA sequencing coupled with chemical footprinting suggested the opposite. In this review, we will critically discuss the biology of RNA G4s focusing on the molecular mechanisms underlying their proposed functions.
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Affiliation(s)
- Marta M Fay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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205
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Soares AR, Santos M. Discovery and function of transfer RNA-derived fragments and their role in disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28608481 DOI: 10.1002/wrna.1423] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/16/2017] [Accepted: 03/23/2017] [Indexed: 01/02/2023]
Abstract
Until recently, transfer RNAs (tRNAs) were thought to function in protein translation only. However, recent findings demonstrate that both pre- and mature tRNAs can undergo endonucleolytic cleavage by different ribonucleases originating different types of small non-coding RNAs, known as tRNA-derived fragments (tRFs). tRFs are classified according to their origin and are implicated in various cellular processes, namely apoptosis, protein synthesis control, and RNA interference. Although their functions are still poorly understood, their mechanisms of action vary according to the tRF sub-type. Several tRFs have been associated with cancer, neurodegenerative disorders, and viral infections and growing evidence shows that they may constitute novel molecular targets for modulating pathological processes. Here, we recapitulate the current knowledge of tRF biology, highlight the known functions and mechanisms of action of the different sub-classes of tRFs and discuss their implications in human disease. WIREs RNA 2017, 8:e1423. doi: 10.1002/wrna.1423 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ana Raquel Soares
- Institute of Biomedicine iBiMED, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Institute of Biomedicine iBiMED, University of Aveiro, Aveiro, Portugal
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206
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Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses. Sci Rep 2017; 7:2018. [PMID: 28515481 PMCID: PMC5435695 DOI: 10.1038/s41598-017-02291-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/03/2017] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5′-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NFκB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5′-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place.
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207
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Chronically stressed or stress-preconditioned neurons fail to maintain stress granule assembly. Cell Death Dis 2017; 8:e2788. [PMID: 28492545 PMCID: PMC5520719 DOI: 10.1038/cddis.2017.199] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/31/2017] [Accepted: 05/04/2017] [Indexed: 12/18/2022]
Abstract
Dysregulation of stress granules (SGs) and their resident proteins contributes to pathogenesis of a number of (neuro)degenerative diseases. Phosphorylation of eIF2α is an event integrating different types of cellular stress and it is required for SG assembly. Phosphorylated eIF2α (p-eIF2α) is upregulated in the nervous system in some neurodegenerative conditions. We found that increasing p-eIF2α level by proteasomal inhibition in cultured cells, including mouse and human neurons, before a SG-inducing stress ('stress preconditioning'), limits their ability to maintain SG assembly. This is due to upregulation of PP1 phosphatase regulatory subunits GADD34 and/or CReP in preconditioned cells and early decline of p-eIF2α levels during subsequent acute stress. In two model systems with constitutively upregulated p-eIF2α, mouse embryonic fibroblasts lacking CReP and brain neurons of tau transgenic mice, SG formation was also impaired. Thus, neurons enduring chronic stress or primed by a transient mild stress fail to maintain p-eIF2α levels following subsequent acute stress, which would compromise protective function of SGs. Our findings provide experimental evidence on possible loss of function for SGs in certain neurodegenerative diseases.
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208
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Bates PJ, Reyes-Reyes EM, Malik MT, Murphy EM, O'Toole MG, Trent JO. G-quadruplex oligonucleotide AS1411 as a cancer-targeting agent: Uses and mechanisms. Biochim Biophys Acta Gen Subj 2017; 1861:1414-1428. [PMID: 28007579 DOI: 10.1016/j.bbagen.2016.12.015] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/16/2016] [Accepted: 12/17/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND AS1411 is a 26-mer G-rich DNA oligonucleotide that forms a variety of G-quadruplex structures. It was identified based on its cancer-selective antiproliferative activity and subsequently determined to be an aptamer to nucleolin, a multifunctional protein that preferentially binds quadruplex nucleic acids and which is present at high levels on the surface of cancer cells. AS1411 has exceptionally efficient cellular internalization compared to non-quadruplex DNA sequences. SCOPE OF REVIEW Recent developments related to AS1411 will be examined, with a focus on its use for targeted delivery of therapeutic and imaging agents. MAJOR CONCLUSIONS Numerous research groups have used AS1411 as a targeting agent to deliver nanoparticles, oligonucleotides, and small molecules into cancer cells. Studies in animal models have demonstrated that AS1411-linked materials can accumulate selectively in tumors following systemic administration. The mechanism underlying the cancer-targeting ability of AS1411 is not completely understood, but recent studies suggest a model that involves: (1) initial uptake by macropinocytosis, a form of endocytosis prevalent in cancer cells; (2) stimulation of macropinocytosis by a nucleolin-dependent mechanism resulting in further uptake; and (3) disruption of nucleolin-mediated trafficking and efflux leading to cargoes becoming trapped inside cancer cells. SIGNIFICANCE Human trials have indicated that AS1411 is safe and can induce durable remissions in a few patients, but new strategies are needed to maximize its clinical impact. A better understanding of the mechanisms by which AS1411 targets and kills cancer cells may hasten the development of promising technologies using AS1411-linked nanoparticles or conjugates for cancer-targeted therapy and imaging. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Paula J Bates
- Department of Medicine, University of Louisville, USA; James Graham Brown Cancer Center, University of Louisville, USA.
| | | | - Mohammad T Malik
- Department of Medicine, University of Louisville, USA; James Graham Brown Cancer Center, University of Louisville, USA
| | - Emily M Murphy
- Department of Biomedical Engineering, University of Louisville, USA
| | - Martin G O'Toole
- Department of Biomedical Engineering, University of Louisville, USA
| | - John O Trent
- Department of Medicine, University of Louisville, USA; James Graham Brown Cancer Center, University of Louisville, USA
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209
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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210
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Li S, Chen Y, Sun D, Bai R, Gao X, Yang Y, Sheng J, Xu Z. Angiogenin Prevents Progranulin A9D Mutation-Induced Neuronal-Like Cell Apoptosis Through Cleaving tRNAs into tiRNAs. Mol Neurobiol 2017; 55:1338-1351. [DOI: 10.1007/s12035-017-0396-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/10/2017] [Indexed: 12/20/2022]
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211
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Hoang TT, Raines RT. Molecular basis for the autonomous promotion of cell proliferation by angiogenin. Nucleic Acids Res 2017; 45:818-831. [PMID: 27915233 PMCID: PMC5314776 DOI: 10.1093/nar/gkw1192] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/13/2016] [Accepted: 11/20/2016] [Indexed: 12/13/2022] Open
Abstract
Canonical growth factors act indirectly via receptor-mediated signal transduction pathways. Here, we report on an autonomous pathway in which a growth factor is internalized, has its localization regulated by phosphorylation, and ultimately uses intrinsic catalytic activity to effect epigenetic change. Angiogenin (ANG), a secreted vertebrate ribonuclease, is known to promote cell proliferation, leading to neovascularization as well as neuroprotection in mammals. Upon entering cells, ANG encounters the cytosolic ribonuclease inhibitor protein, which binds with femtomolar affinity. We find that protein kinase C and cyclin-dependent kinase phosphorylate ANG, enabling ANG to evade its inhibitor and enter the nucleus. After migrating to the nucleolus, ANG cleaves promoter-associated RNA, which prevents the recruitment of the nucleolar remodeling complex to the ribosomal DNA promoter. The ensuing derepression of rDNA transcription promotes cell proliferation. The biochemical basis for this unprecedented mechanism of signal transduction suggests new modalities for the treatment of cancers and neurological disorders.
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Affiliation(s)
- Trish T Hoang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ronald T Raines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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212
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Mahboubi H, Stochaj U. Cytoplasmic stress granules: Dynamic modulators of cell signaling and disease. Biochim Biophys Acta Mol Basis Dis 2017; 1863:884-895. [PMID: 28095315 DOI: 10.1016/j.bbadis.2016.12.022] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/15/2016] [Accepted: 12/26/2016] [Indexed: 12/14/2022]
Abstract
Stress granule (SG) assembly is a conserved cellular strategy to minimize stress-related damage and promote cell survival. Beyond their fundamental role in the stress response, SGs have emerged as key players for human health. As such, SG assembly is associated with cancer, neurodegenerative disorders, ischemia, and virus infections. SGs and granule-related signaling circuits are therefore promising targets to improve therapeutic intervention for several diseases. This is clinically relevant, because pharmacological drugs can affect treatment outcome by modulating SG formation. As membraneless and highly dynamic compartments, SGs regulate translation, ribostasis and proteostasis. Moreover, they serve as signaling hubs that determine cell viability and stress recovery. Various compounds can modulate SG formation and dynamics. Rewiring cell signaling through SG manipulation thus represents a new strategy to control cell fate under various physiological and pathological conditions.
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Affiliation(s)
- Hicham Mahboubi
- Department of Physiology, McGill University, Montreal, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, Canada.
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213
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Guo Y, Strickland SA, Mohan S, Li S, Bosompem A, Vickers KC, Zhao S, Sheng Q, Kim AS. MicroRNAs and tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute myeloid leukemia. Leuk Lymphoma 2017; 58:1-15. [PMID: 28084850 DOI: 10.1080/10428194.2016.1272680] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders of the elderly that carry an increased risk of progression to acute myeloid leukemia (AML). Since small non-coding RNAs (sRNAs), including microRNA (miRNAs), act as regulators of cellular differentiation, we hypothesized that changes to sRNAs might be implicated in the progression of MDS to AML. We conducted sRNA sequencing on three sets of patients: Group A (MDS patients who never progressed to AML); Group B (MDS patients who later progressed to an AML); and Group C (AML patients with myelodysplasia-related changes, including patients with a known preceding diagnosis of MDS). We identified five miRNAs that differentiated Groups A and B, independent of bone marrow blast percentage, including three members of the miR-181 family, as well as differential patterns of miRNA isoforms (isomiRs) and tDRs. Thus, we have identified sRNA biomarkers that predict MDS cases that are likely to progress to AML.
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Affiliation(s)
- Yan Guo
- a Center for Quantitative Sciences , Vanderbilt University , Nashville , TN , USA
| | - Stephen A Strickland
- b Department of Medicine, Division of Hematology/Oncology , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Sanjay Mohan
- b Department of Medicine, Division of Hematology/Oncology , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Shaoying Li
- c Hematopathology Department , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Amma Bosompem
- d Department of Pathology , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Kasey C Vickers
- e Department of Medicine , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Shilin Zhao
- f Department of Cancer Biology , Vanderbilt University , Nashville , TN , USA
| | - Quanhu Sheng
- f Department of Cancer Biology , Vanderbilt University , Nashville , TN , USA
| | - Annette S Kim
- g Department of Pathology, Brigham and Women's Hospital , Boston , MA , USA
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214
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Rouleau S, Jodoin R, Garant JM, Perreault JP. RNA G-Quadruplexes as Key Motifs of the Transcriptome. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:1-20. [PMID: 28382477 DOI: 10.1007/10_2017_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G-Quadruplexes are non-canonical secondary structures that can be adopted under physiological conditions by guanine-rich DNA and RNA molecules. They have been reported to occur, and to perform multiple biological functions, in the genomes and transcriptomes of many species, including humans. This chapter focuses specifically on RNA G-quadruplexes and reviews the most recent discoveries in the field, as well as addresses the upcoming challenges researchers studying these structures face.
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Affiliation(s)
- Samuel Rouleau
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Rachel Jodoin
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Jean-Michel Garant
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8.
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215
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Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disorder that is characterized by a progressive degeneration of the upper and lower motor neurons. Most cases appear to be sporadic, but 5-10 % of cases have a family history of the disease. High-throughput DNA sequencing and related genomic capture tools are methodological advances which have rapidly contributed to an acceleration in the discovery of genetic risk factors for both familial and sporadic ALS. It is interesting to note that as the number of ALS genes grows, many of the proteins they encode are in shared intracellular processes. This review will summarize some of the recent advances and gene discovery made in ALS.
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216
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Chen Q, Yan W, Duan E. Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications. Nat Rev Genet 2016; 17:733-743. [PMID: 27694809 PMCID: PMC5441558 DOI: 10.1038/nrg.2016.106] [Citation(s) in RCA: 306] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Once deemed heretical, emerging evidence now supports the notion that the inheritance of acquired characteristics can occur through ancestral exposures or experiences and that certain paternally acquired traits can be 'memorized' in the sperm as epigenetic information. The search for epigenetic factors in mammalian sperm that transmit acquired phenotypes has recently focused on RNAs and, more recently, RNA modifications. Here, we review insights that have been gained from studying sperm RNAs and RNA modifications, and their roles in influencing offspring phenotypes. We discuss the possible mechanisms by which sperm become acquisitive following environmental-somatic-germline interactions, and how they transmit paternally acquired phenotypes by shaping early embryonic development.
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Affiliation(s)
- Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89512, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89512, USA
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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217
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Emerging Roles of tRNA-derived Fragments in Viral Infections: The Case of Respiratory Syncytial Virus. Mol Ther 2016; 23:1557-8. [PMID: 26442802 DOI: 10.1038/mt.2015.161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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218
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Lyons SM, Achorn C, Kedersha NL, Anderson PJ, Ivanov P. YB-1 regulates tiRNA-induced Stress Granule formation but not translational repression. Nucleic Acids Res 2016; 44:6949-60. [PMID: 27174937 PMCID: PMC5001593 DOI: 10.1093/nar/gkw418] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/30/2016] [Indexed: 12/16/2022] Open
Abstract
Stress-induced angiogenin (ANG)-mediated tRNA cleavage promotes a cascade of cellular events that starts with production of tRNA-derived stress-induced RNAs (tiRNAs) and culminates with enhanced cell survival. This stress response program relies on a subset tiRNAs that inhibit translation initiation and induce the assembly of stress granules (SGs), cytoplasmic ribonucleoprotein complexes with cytoprotective and pro-survival properties. SG-promoting tiRNAs bear oligoguanine motifs at their 5'-ends, assemble G-quadruplex-like structures and interact with the translational silencer YB-1. We used CRISPR/Cas9-based genetic manipulations and biochemical approaches to examine the role of YB-1 in tiRNA-mediated translational repression and SG assembly. We found that YB-1 directly binds to tiRNAs via its cold shock domain. This interaction is required for packaging of tiRNA-repressed mRNAs into SGs but is dispensable for tiRNA-mediated translational repression. Our studies reveal the functional role of YB-1 in the ANG-mediated stress response program.
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Affiliation(s)
- Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Chris Achorn
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nancy L Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA The Broad Institute of Harvard and M.I.T., Cambridge, MA 02142, USA
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219
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De Nicola B, Lech CJ, Heddi B, Regmi S, Frasson I, Perrone R, Richter SN, Phan AT. Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome. Nucleic Acids Res 2016; 44:6442-51. [PMID: 27298260 PMCID: PMC5291261 DOI: 10.1093/nar/gkw432] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
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Affiliation(s)
- Beatrice De Nicola
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore Department of Molecular Medicine, University of Padua, Italy
| | - Christopher J Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Sagar Regmi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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220
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Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem 2016; 291:18041-57. [PMID: 27369081 DOI: 10.1074/jbc.m116.718478] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 12/13/2022] Open
Abstract
Cells engage numerous signaling pathways in response to oxidative stress that together repair macromolecular damage or direct the cell toward apoptosis. As a result of DNA damage, mitochondrial DNA or nuclear DNA has been shown to enter the cytoplasm where it binds to "DNA sensors," which in turn initiate signaling cascades. Here we report data that support a novel signaling pathway in response to oxidative stress mediated by specific guanine-rich sequences that can fold into G-quadruplex DNA (G4DNA). In response to oxidative stress, we demonstrate that sequences capable of forming G4DNA appear at increasing levels in the cytoplasm and participate in assembly of stress granules. Identified proteins that bind to endogenous G4DNA in the cytoplasm are known to modulate mRNA translation and participate in stress granule formation. Consistent with these findings, stress granule formation is known to regulate mRNA translation during oxidative stress. We propose a signaling pathway whereby cells can rapidly respond to DNA damage caused by oxidative stress. Guanine-rich sequences that are excised from damaged genomic DNA are proposed to enter the cytoplasm where they can regulate translation through stress granule formation. This newly proposed role for G4DNA provides an additional molecular explanation for why such sequences are prevalent in the human genome.
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Affiliation(s)
- Alicia K Byrd
- From the Departments of Biochemistry and Molecular Biology and
| | - Boris L Zybailov
- From the Departments of Biochemistry and Molecular Biology and the University of Arkansas at Little Rock/University of Arkansas for Medical Sciences (UALR/UAMS) Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Leena Maddukuri
- From the Departments of Biochemistry and Molecular Biology and
| | - Jun Gao
- From the Departments of Biochemistry and Molecular Biology and
| | - John C Marecki
- From the Departments of Biochemistry and Molecular Biology and
| | - Mihir Jaiswal
- the University of Arkansas at Little Rock/University of Arkansas for Medical Sciences (UALR/UAMS) Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Matthew R Bell
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Megan R Reed
- From the Departments of Biochemistry and Molecular Biology and
| | - Shubeena Chib
- From the Departments of Biochemistry and Molecular Biology and
| | - Samuel G Mackintosh
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Angus M MacNicol
- the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and Neurobiology and Developmental Sciences and
| | - Giulia Baldini
- From the Departments of Biochemistry and Molecular Biology and
| | - Robert L Eoff
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Kevin D Raney
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
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221
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Bowden HA, Dormann D. Altered mRNP granule dynamics in FTLD pathogenesis. J Neurochem 2016; 138 Suppl 1:112-33. [PMID: 26938019 DOI: 10.1111/jnc.13601] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/13/2022]
Abstract
In neurons, RNA-binding proteins (RBPs) play a key role in post-transcriptional gene regulation, for example alternative splicing, mRNA localization in neurites and local translation upon synaptic stimulation. There is increasing evidence that defective or mislocalized RBPs - and consequently altered mRNA processing - lead to neuronal dysfunction and cause neurodegeneration, including frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Cytosolic RBP aggregates containing TAR DNA-binding protein of 43 kDa (TDP-43) or fused in sarcoma (FUS) are a common hallmark of both disorders. There is mounting evidence that translationally silent mRNP granules, such as stress granules or transport granules, play an important role in the formation of these RBP aggregates. These granules are thought to be 'catalytic convertors' of RBP aggregation by providing a high local concentration of RBPs. As recently shown in vitro, RBPs that contain a so-called low-complexity domain start to 'solidify' and eventually aggregate at high protein concentrations. The same may happen in mRNP granules in vivo, leading to 'solidified' granules that lose their dynamic properties and ability to fulfill their physiological functions. This may result in a disturbed stress response, altered mRNA transport and local translation, and formation of pathological TDP-43 or FUS aggregates, all of which may contribute to neuronal dysfunction and neurodegeneration. Here, we discuss the general functional properties of these mRNP granules, how their dynamics may be disrupted in frontotemporal lobar degeneration/amyotrophic lateral sclerosis, for example by loss or gain of function of TDP-43 and FUS, and how this may contribute to the development of RBP aggregates and neurotoxicity. In this review, we discuss how dynamic mRNP granules, such as stress granules or neuronal transport granules, may be converted into pathological aggregates containing misfolded RNA-binding proteins (RBPs), such as TDP-43 and FUS. Abnormal interactions between low-complexity domains in RBPs may cause dynamic mRNP granules to solidify and become dysfunctional. This may result in a disturbed stress response, altered mRNA transport and local translation, as well as RBP aggregation, all of which may contribute to neuronal dysfunction and neurodegeneration.
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Affiliation(s)
- Hilary A Bowden
- Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany
| | - Dorothee Dormann
- BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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222
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Szaflarski W, Fay MM, Kedersha N, Zabel M, Anderson P, Ivanov P. Vinca alkaloid drugs promote stress-induced translational repression and stress granule formation. Oncotarget 2016; 7:30307-22. [PMID: 27083003 PMCID: PMC5058682 DOI: 10.18632/oncotarget.8728] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/31/2016] [Indexed: 12/03/2022] Open
Abstract
Resistance to chemotherapy drugs is a serious therapeutic problem and its underlying molecular mechanisms are complex. Stress granules (SGs), cytoplasmic ribonucleoprotein complexes assembled in cells exposed to stress, are implicated in various aspects of cancer cell metabolism and survival. SGs promote the survival of stressed cells by reprogramming gene expression and inhibiting pro-apoptotic signaling cascades. We show that the vinca alkaloid (VA) class of anti-neoplastic agents potently activates a SG-mediated stress response program. VAs inhibit translation initiation by simultaneous activation of eIF4E-BP1 and phosphorylation of eIF2α, causing polysome disassembly and SG assembly. VA-induced SGs contain canonical SG components but lack specific signaling molecules. Blocking VA-induced SG assembly by inactivating eIF4EBP1 or inhibiting eIF2α phosphorylation decreases cancer cell viability and promotes apoptosis. Our data describe previously unappreciated effects of VAs on cellular RNA metabolism and illuminate the roles of SGs in cancer cell survival.
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Affiliation(s)
- Witold Szaflarski
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań, Poland
| | - Marta M Fay
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nancy Kedersha
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Maciej Zabel
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań, Poland
| | - Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
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223
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Alsultan AA, Waller R, Heath PR, Kirby J. The genetics of amyotrophic lateral sclerosis: current insights. Degener Neurol Neuromuscul Dis 2016; 6:49-64. [PMID: 30050368 PMCID: PMC6053097 DOI: 10.2147/dnnd.s84956] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder that results in loss of the upper and lower motor neurons from motor cortex, brainstem, and spinal cord. While the majority of cases are sporadic, approximately 10% show familial inheritance. ALS is usually inherited in an autosomal dominant manner, although autosomal recessive and X-linked inheritance do occur. To date, 24 of the genes at 26 loci have been identified; these include loci linked to ALS and to frontotemporal dementia-ALS, where family pedigrees contain individuals with frontotemporal dementia with/without ALS. The most commonly established genetic causes of familial ALS (FALS) to date are the presence of a hexanucleotide repeat expansion in the C9ORF72 gene (39.3% FALS) and mutation of SOD1, TARDBP, and FUS, with frequencies of 12%-23.5%, 5%, and 4.1%, respectively. However, with the increasing use of next-generation sequencing of small family pedigrees, this has led to an increasing number of genes being associated with ALS. This review provides a comprehensive review on the genetics of ALS and an update of the pathogenic mechanisms associated with these genes. Commonly implicated pathways have been established, including RNA processing, the protein degradation pathways of autophagy and ubiquitin-proteasome system, as well as protein trafficking and cytoskeletal function. Elucidating the role genetics plays in both FALS and sporadic ALS is essential for understanding the subsequent cellular dysregulation that leads to motor neuron loss, in order to develop future effective therapeutic strategies.
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Affiliation(s)
- Afnan A Alsultan
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK,
| | - Rachel Waller
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK,
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK,
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK,
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224
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Sheng J, Xu Z. Three decades of research on angiogenin: a review and perspective. Acta Biochim Biophys Sin (Shanghai) 2016; 48:399-410. [PMID: 26705141 DOI: 10.1093/abbs/gmv131] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023] Open
Abstract
As a member of the vertebrate-specific secreted ribonucleases, angiogenin (ANG) was first isolated and identified solely by its ability to induce new blood vessel formation, and now, it has been recognized to play important roles in various physiological and pathological processes through regulating cell proliferation, survival, migration, invasion, and/or differentiation. ANG exhibits very weak ribonucleolytic activity that is critical for its biological functions, and exerts its functions through activating different signaling transduction pathways in different target cells. A series of recent studies have indicated that ANG contributes to cellular nucleic acid metabolism. Here, we comprehensively review the results of studies regarding the structure, mechanism, and function of ANG over the past three decades. Moreover, current problems and future research directions of ANG are discussed. The understanding of the function and mechanism of ANG in a wide context will help to better delineate its roles in diseases, especially in cancer and neurodegenerative diseases.
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Affiliation(s)
- Jinghao Sheng
- Institute of Environmental Health, Zhejiang University School of Public Health, Hangzhou 310058, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhengping Xu
- Institute of Environmental Health, Zhejiang University School of Public Health, Hangzhou 310058, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
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225
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Chi S, Jiang T, Tan L, Yu JT. Distinct neurological disorders with C9orf72 mutations: genetics, pathogenesis, and therapy. Neurosci Biobehav Rev 2016; 66:127-42. [PMID: 27139021 DOI: 10.1016/j.neubiorev.2016.03.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 12/12/2022]
Abstract
The G4C2 repeat expansion within C9orf72 has been recently identified as the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis. This mutation has also been detected in a variety of other neurological diseases with distinct clinical manifestations. The exact mechanisms of how this mutation leads to the wide spectrum of clinical syndromes remain unknown. A series of molecular changes together with some potential modifiers may play a key role. Nucleolar stress, nucleocytoplasmic transport defect, oxidative damage, inhibited stress granules assembly, activated endoplasmic reticulum stress, and inhibited proteasome activity are mechanisms that contribute to the pathogenesis of these diseases. Additional mutations, epigenetic modifiers, and repeat size are potential modifiers that modulate specific phenotypes on the basis of the molecular changes. Here, we summarize distinct C9orf72-related neurological disorders and their corresponding neuropathological changes. Then, we elucidate the existing molecular knowledge and the potential modifiers. Finally, we detail the main target of treatment aiming at controlling expanded RNA transcripts.
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Affiliation(s)
- Song Chi
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, Shandong, China
| | - Teng Jiang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, Shandong, China.
| | - Jin-Tai Yu
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, Shandong, China.
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226
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Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Thioflavin T as an efficient fluorescence sensor for selective recognition of RNA G-quadruplexes. Sci Rep 2016; 6:24793. [PMID: 27098781 PMCID: PMC4838840 DOI: 10.1038/srep24793] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/05/2016] [Indexed: 12/29/2022] Open
Abstract
RNA G-quadruplexes (G4s) play important roles in translational regulation, mRNA processing events and gene expression. Therefore, a fluorescent probe that is capable of efficiently recognizing RNA G-quadruplex structures among other RNA forms is highly desirable. In this study, a water-soluble fluorogenic dye (i.e., Thioflavin T (ThT)) was employed to recognize RNA G-quadruplex structures using UV-Vis absorption spectra, fluorescence spectra and emission lifetime experiments. By stacking on the G-tetrad, the ThT probe exhibited highly specific recognition of RNA G-quadruplex structures with striking fluorescence enhancement compared with other RNA forms. The specific binding demonstrates that ThT is an efficient fluorescence sensor that can distinguish G4 and non-G4 RNA structures.
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Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
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227
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Huang HY, Hopper AK. Multiple Layers of Stress-Induced Regulation in tRNA Biology. Life (Basel) 2016; 6:life6020016. [PMID: 27023616 PMCID: PMC4931453 DOI: 10.3390/life6020016] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 01/28/2023] Open
Abstract
tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple layers of regulatory mechanisms in each step of tRNA biogenesis. For example, tRNA 3′ trailer processing is altered upon nutrient stress; tRNA modification is reprogrammed under various stresses; nuclear accumulation of tRNAs occurs upon nutrient deprivation; tRNA halves accumulate upon oxidative stress. Here we address how environmental stresses can affect nearly every step of tRNA biology and we describe the possible regulatory mechanisms that influence the function or expression of tRNAs under stress conditions.
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Affiliation(s)
- Hsiao-Yun Huang
- Department of Biology, Indiana University, 915 E third St., Myers 300, Bloomington, IN 47405, USA.
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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228
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Wang Y, Li H, Sun Q, Yao Y. Characterization of Small RNAs Derived from tRNAs, rRNAs and snoRNAs and Their Response to Heat Stress in Wheat Seedlings. PLoS One 2016; 11:e0150933. [PMID: 26963812 PMCID: PMC4786338 DOI: 10.1371/journal.pone.0150933] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 02/22/2016] [Indexed: 12/21/2022] Open
Abstract
Small RNAs (sRNAs) derived from non-coding RNAs (ncRNAs), such as tRNAs, rRNAs and snoRNAs, have been identified in various organisms. Several observations have indicated that cleavage of tRNAs and rRNAs is induced by various stresses. To clarify whether sRNAs in wheat derived from tRNAs (stRNAs), rRNAs (srRNAs) and snoRNAs (sdRNAs) are produced specifically in association with heat stress responses, we carried out a bioinformatic analysis of sRNA libraries from wheat seedlings and performed comparisons between control and high-temperature-treated samples to measure the differential abundance of stRNAs, srRNAs and sdRNAs. We found that the production of sRNAs from tRNAs, 5.8S rRNAs, and 28S rRNAs was more specific than that from 5S rRNAs and 18S rRNAs, and more than 95% of the stRNAs were processed asymmetrically from the 3’ or 5’ ends of mature tRNAs. We identified 333 stRNAs and 8,822 srRNAs that were responsive to heat stress. Moreover, the expression of stRNAs derived from tRNA-Val-CAC, tRNA-Thr-UGU, tRNA-Tyr-GUA and tRNA-Ser-UGA was not only up-regulated under heat stress but also induced by osmotic stress, suggesting that the increased cleavage of tRNAs might be a mechanism that developed in wheat seedlings to help them cope with adverse environmental conditions.
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Affiliation(s)
- Yu Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongxia Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qixin Sun
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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229
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Kleene KC. Position-dependent interactions of Y-box protein 2 (YBX2) with mRNA enable mRNA storage in round spermatids by repressing mRNA translation and blocking translation-dependent mRNA decay. Mol Reprod Dev 2016; 83:190-207. [PMID: 26773323 DOI: 10.1002/mrd.22616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/08/2016] [Indexed: 12/18/2022]
Abstract
Many mRNAs encoding proteins needed for the construction of the specialized organelles of spermatozoa are stored as translationally repressed, free messenger ribonucleoproteins in round spermatids, to be actively translated in elongating and elongated spermatids. The factors that repress translation in round spermatids, however, have been elusive. Two lines of evidence implicate the highly abundant and well-known translational repressor, Y-box protein 2 (YBX2), as a critical factor: First, protamine 1 (Prm1) and sperm-mitochondria cysteine-rich protein (Smcp) mRNAs are prematurely recruited onto polysomes in Ybx2-knockout mouse round spermatids. Second, mutations in 3' untranslated region (3'UTR) cis-elements that abrogate YBX2 binding activate translation of Prm1 and Smcp mRNAs in round spermatids of transgenic mice. The abundance of YBX2 and its affinity for variable sequences, however, raise questions of how YBX2 targets specific mRNAs for repression. Mutations to the Prm1 and Smcp mRNAs in transgenic mice reveal that strong repression in round spermatids requires YBX2 binding sites located near the 3' ends of their 3'UTRs as locating the same sites in upstream positions produce negligible repression. This location-dependence implies that the assembly of repressive complexes is nucleated by adjacent cis-elements that enable cooperative interactions of YBX2 with co-factors. The available data suggest that, in vertebrates, YBX2 has the important role of coordinating the storage of translationally repressed mRNAs in round spermatids by inhibiting translational activity and the degradation of transcripts via translation-dependent deadenylation. These insights should facilitiate future experiments designed to unravel how YBX2 targets mRNAs for repression in round spermatids and how mutations in the YBX2 gene cause infertility in humans. Mol. Reprod. Dev. 83: 190-207, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kenneth C Kleene
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts
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230
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Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. Nat Protoc 2016; 11:476-89. [PMID: 26866791 DOI: 10.1038/nprot.2016.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RNA digestions catalyzed by many ribonucleases generate RNA fragments that contain a 2',3'-cyclic phosphate (cP) at their 3' termini. However, standard RNA-seq methods are unable to accurately capture cP-containing RNAs because the cP inhibits the adapter ligation reaction. We recently developed a method named cP-RNA-seq that is able to selectively amplify and sequence cP-containing RNAs. Here we describe the cP-RNA-seq protocol in which the 3' termini of all RNAs, except those containing a cP, are cleaved through a periodate treatment after phosphatase treatment; hence, subsequent adapter ligation and cDNA amplification steps are exclusively applied to cP-containing RNAs. cP-RNA-seq takes ∼6 d, excluding the time required for sequencing and bioinformatics analyses, which are not covered in detail in this protocol. Biochemical validation of the existence of cP in the identified RNAs takes ∼3 d. Even though the cP-RNA-seq method was developed to identify angiogenin-generating 5'-tRNA halves as a proof of principle, the method should be applicable to global identification of cP-containing RNA repertoires in various transcriptomes.
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231
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Mami I, Tavernier Q, Bouvier N, Aboukamis R, Desbuissons G, Rabant M, Poindessous V, Laurent-Puig P, Beaune P, Tharaux PL, Thervet E, Chevet E, Anglicheau D, Pallet N. A Novel Extrinsic Pathway for the Unfolded Protein Response in the Kidney. J Am Soc Nephrol 2016; 27:2670-83. [PMID: 26823555 DOI: 10.1681/asn.2015060703] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/30/2015] [Indexed: 12/11/2022] Open
Abstract
The ribonuclease angiogenin is a component of the mammalian stress response, and functions in both cell-autonomous and non-cell-autonomous ways to promote tissue adaptation to injury. We recently showed that angiogenin regulates tissue homeostasis during AKI associated with endoplasmic reticulum (ER) stress through the production of transfer RNA fragments that interfere with translation initiation and thereby alleviate ER stress. However, whether the paracrine signaling mediated by angiogenin secretion is a genuine component of the ER stress response to kidney injury is unknown. Here, we explored the molecular mechanisms by which angiogenin is secreted upon ER stress, and determined how it modulates the inflammatory microenvironment. In cultured renal epithelial cells, ER stress specifically induced angiogenin secretion under the selective control of inositol-requiring enzyme 1α, a key activator of the unfolded protein response. The transcription factors spliced X-box-binding protein 1 and p65, which are activated by inositol-requiring enzyme 1α upon ER stress, each bound the angiogenin promoter and controlled the amount of angiogenin secreted. Furthermore, p65 promoted angiogenin transcription in an ER stress-dependent manner. Similar to secretion of the ER stress-induced proinflammatory cytokine IL-6, secretion of angiogenin required the ER-Golgi pathway. Notably, incubation of human macrophages with angiogenin promoted macrophage reprogramming toward an activated and proinflammatory phenotype. In patients, angiogenin expression increased upon renal inflammation, and the urinary concentration of angiogenin correlated with the extent of immune-mediated kidney injury. Collectively, our data identify angiogenin as a mediator of the ER stress-dependent inflammatory response and as a potential noninvasive biomarker of AKI.
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Affiliation(s)
- Iadh Mami
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France
| | - Quentin Tavernier
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France
| | - Nicolas Bouvier
- Service de Néphrologie, Centre Hospitalier Unversitaire de Caen, Caen, France
| | - Rim Aboukamis
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France
| | - Geoffroy Desbuissons
- Université Paris Descartes, Paris, France; Service de Néphrologie, INSERM U1151, Institut Necker Enfants Malades, Paris, France
| | - Marion Rabant
- Université Paris Descartes, Paris, France; Service d'Anatomopathologie, Hôpital Necker, Paris, France
| | - Virginie Poindessous
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France
| | - Pierre Laurent-Puig
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France; Service de Biochimie, Service de Néphrologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Philippe Beaune
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France; Service de Biochimie, Service de Néphrologie, Hôpital Européen Georges Pompidou, Paris, France
| | | | - Eric Thervet
- Université Paris Descartes, Paris, France; Service de Néphrologie, Centre Hospitalier Unversitaire de Caen, Caen, France; Service de Néphrologie, Centre Hospitalier Unversitaire de Caen, Caen, France
| | - Eric Chevet
- Oncogenesis Stress Signaling Laboratory, ER440 INSERM, Université de Rennes 1, Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Dany Anglicheau
- Université Paris Descartes, Paris, France; Service de Néphrologie, INSERM U1151, Institut Necker Enfants Malades, Paris, France
| | - Nicolas Pallet
- Institut National de la Santé et de le Recherche Médicale (INSERM) U1147, Centre Universitaire des Saints Pères, Paris, France; Université Paris Descartes, Paris, France; Service de Biochimie, Service de Néphrologie, Hôpital Européen Georges Pompidou, Paris, France;
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232
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Diebel KW, Zhou K, Clarke AB, Bemis LT. Beyond the Ribosome: Extra-translational Functions of tRNA Fragments. Biomark Insights 2016; 11:1-8. [PMID: 26843810 PMCID: PMC4734663 DOI: 10.4137/bmi.s35904] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 01/05/2023] Open
Abstract
High-throughput sequencing studies of small RNAs reveal a complex milieu of noncoding RNAs in biological samples. Early data analysis was often limited to microRNAs due to their regulatory nature and potential as biomarkers; however, many more classes of noncoding RNAs are now being recognized. A class of fragments initially excluded from analysis were those derived from transfer RNAs (tRNAs) because they were thought to be degradation products. More recently, critical cellular function has been attributed to tRNA fragments (tRFs), and their conservation across all domains of life has propelled them into an emerging area of scientific study. The biogenesis of tRFs is currently being elucidated, and initial studies show that a diverse array of tRFs are generated from all parts of a tRNA molecule. The goal of this review was to present what is currently known about tRFs and their potential as biomarkers for the earlier detection of disease.
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Affiliation(s)
- Kevin W Diebel
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
| | - Kun Zhou
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
| | - Aaron B Clarke
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
| | - Lynne T Bemis
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
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233
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Zhao Q, Zhou Y, Li Y, Gu W, Zhang Q, Liu J. Luminescent Iridium(III) Complex Labeled DNA for Graphene Oxide-Based Biosensors. Anal Chem 2016; 88:1892-9. [DOI: 10.1021/acs.analchem.5b04324] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Qingcheng Zhao
- Jiangsu
Key Laboratory for Carbon-Based Functional Materials and Devices,
Institute of Functional Nano and Soft Materials (FUNSOM), Collaborative
Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yuyang Zhou
- Jiangsu
Key Laboratory of Environmental Functional Materials, School of Chemistry,
Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yingying Li
- Jiangsu
Key Laboratory for Carbon-Based Functional Materials and Devices,
Institute of Functional Nano and Soft Materials (FUNSOM), Collaborative
Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wei Gu
- Jiangsu
Key Laboratory for Carbon-Based Functional Materials and Devices,
Institute of Functional Nano and Soft Materials (FUNSOM), Collaborative
Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qi Zhang
- Jiangsu
Key Laboratory for Carbon-Based Functional Materials and Devices,
Institute of Functional Nano and Soft Materials (FUNSOM), Collaborative
Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jian Liu
- Jiangsu
Key Laboratory for Carbon-Based Functional Materials and Devices,
Institute of Functional Nano and Soft Materials (FUNSOM), Collaborative
Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China
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234
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Abstract
tRFs and tiRNAs are two new classes of regulatory non-coding small RNAs that are derived from the cleavage of pre-existing tRNAs. tRFs are 18-22 nt long and are classified into the tRF-5, tRF-3, and tRF-1 series. Here, we discuss in detail the regulatory roles of tRFs in translation, viral infections, and carcinogenesis. Moreover, we have reviewed the association of tRFs with Argonaute proteins, including their potential to function as miRNAs. Interestingly, few miRNAs are generated from pre-existing tRNAs. Hence, tRNAs generate similar-sized tRFs and miRNAs, leading to misannotations due to cross mapping of tRFs and tRNA-derived miRNAs during deep sequencing data analysis. Therefore, it is important to catalogue the overlapping sequences between tRNA-derived miRNAs and tRFs. We have catalogued the miRNAs that overlap with tRFs sequences in humans using miRBase. We identified 20 tRNA-derived miRNAs that share sequences with tRFs. Of the 20 miRNAs, 5 miRNAs (miR-3182, miR-4521, miR-1260a, miR-1260b, and miR-7977) showed significant prediction scores. Furthermore, we have identified a lysine degradation pathway as a common regulatory pathway for miR-1260a, miR-1260b, and miR-3182 by using DIANA-mirPath.
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235
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Perrone R, Doria F, Butovskaya E, Frasson I, Botti S, Scalabrin M, Lago S, Grande V, Nadai M, Freccero M, Richter SN. Synthesis, Binding and Antiviral Properties of Potent Core-Extended Naphthalene Diimides Targeting the HIV-1 Long Terminal Repeat Promoter G-Quadruplexes. J Med Chem 2015; 58:9639-52. [PMID: 26599611 PMCID: PMC4690987 DOI: 10.1021/acs.jmedchem.5b01283] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
We have previously reported that
stabilization of the G-quadruplex
structures in the HIV-1 long terminal repeat (LTR) promoter suppresses
viral transcription. Here we sought to develop new G-quadruplex ligands
to be exploited as antiviral compounds by enhancing binding toward
the viral G-quadruplex structures. We synthesized naphthalene diimide
derivatives with a lateral expansion of the aromatic core. The new
compounds were able to bind/stabilize the G-quadruplex to a high extent,
and some of them displayed clear-cut selectivity toward the viral
G-quadruplexes with respect to the human telomeric G-quadruplexes.
This feature translated into low nanomolar anti-HIV-1 activity toward
two viral strains and encouraging selectivity indexes. The selectivity
depended on specific recognition of LTR loop residues; the mechanism
of action was ascribed to inhibition of LTR promoter activity in cells.
This is the first example of G-quadruplex ligands that show increased
selectivity toward the viral G-quadruplexes and display remarkable
antiviral activity.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Silvia Botti
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Sara Lago
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Vincenzo Grande
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
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236
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Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Directly lighting up RNA G-quadruplexes from test tubes to living human cells. Nucleic Acids Res 2015; 43:9575-86. [PMID: 26476445 PMCID: PMC4787783 DOI: 10.1093/nar/gkv1040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022] Open
Abstract
RNA G-quadruplexes (G4s) are one of the key components of the transcriptome that act as efficient post-transcriptional regulatory elements in living cells. To conduct further studies of the unique biological functions of RNA G4s, techniques need to be developed that can efficiently recognize RNA G4 structures under various conditions, in fixed cells and living cells, as well as in vitro. This paper presents the development of such a method, a new technique using a cyanine dye called CyT, which can detect both canonical and non-canonical RNA G4 structures from test tubes to living human cells. The ability of CyT to distinguish between G4 and nonG4 RNA offers a promising tool for future RNA G4-based biomarker discovery and potential diagnostic applications.
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Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
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237
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Tosoni E, Frasson I, Scalabrin M, Perrone R, Butovskaya E, Nadai M, Palù G, Fabris D, Richter SN. Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription. Nucleic Acids Res 2015; 43:8884-97. [PMID: 26354862 PMCID: PMC4605322 DOI: 10.1093/nar/gkv897] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 01/26/2023] Open
Abstract
Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy.
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Affiliation(s)
- Elena Tosoni
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Dan Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
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238
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Saikia M, Hatzoglou M. The Many Virtues of tRNA-derived Stress-induced RNAs (tiRNAs): Discovering Novel Mechanisms of Stress Response and Effect on Human Health. J Biol Chem 2015; 290:29761-8. [PMID: 26463210 DOI: 10.1074/jbc.r115.694661] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In mammalian cells, mature tRNAs are cleaved by stress-activated ribonuclease angiogenin to generate 5'- and 3'-tRNA halves: a novel class of small non-coding RNAs of 30-40 nucleotides in length. The biogenesis and biological functions of tRNA halves are emerging areas of research. This review will discuss the most recent findings on: (i) the mechanism and regulation of their biogenesis, (ii) their mechanism of action (we will specifically discuss their role in the protein synthesis inhibition and the intrinsic pathway of apoptosis), and (iii) their effects on the human physiology and disease conditions.
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Affiliation(s)
- Mridusmita Saikia
- From the Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, New York 14853 and
| | - Maria Hatzoglou
- the Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
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239
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Synaptic vesicles contain small ribonucleic acids (sRNAs) including transfer RNA fragments (trfRNA) and microRNAs (miRNA). Sci Rep 2015; 5:14918. [PMID: 26446566 PMCID: PMC4597359 DOI: 10.1038/srep14918] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/08/2015] [Indexed: 12/29/2022] Open
Abstract
Synaptic vesicles (SVs) are neuronal presynaptic organelles that load and release neurotransmitter at chemical synapses. In addition to classic neurotransmitters, we have found that synaptic vesicles isolated from the electric organ of Torpedo californica, a model cholinergic synapse, contain small ribonucleic acids (sRNAs), primarily the 5' ends of transfer RNAs (tRNAs) termed tRNA fragments (trfRNAs). To test the evolutionary conservation of SV sRNAs we examined isolated SVs from the mouse central nervous system (CNS). We found abundant levels of sRNAs in mouse SVs, including trfRNAs and micro RNAs (miRNAs) known to be involved in transcriptional and translational regulation. This discovery suggests that, in addition to inducing changes in local dendritic excitability through the release of neurotransmitters, SVs may, through the release of specific trfRNAs and miRNAs, directly regulate local protein synthesis. We believe these findings have broad implications for the study of chemical synaptic transmission.
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240
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Shigematsu M, Kirino Y. tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins. GENE REGULATION AND SYSTEMS BIOLOGY 2015; 9:27-33. [PMID: 26401098 PMCID: PMC4567038 DOI: 10.4137/grsb.s29411] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/28/2015] [Accepted: 07/09/2015] [Indexed: 12/21/2022]
Abstract
The advent of next-generation sequencing technologies has not only accelerated findings on various novel non-coding RNA (ncRNA) species but also led to the revision of the biological significance and versatility of fundamental RNA species with canonical function, such as transfer RNAs (tRNAs). Although tRNAs are best known as adapter components of translational machinery, recent studies suggest that tRNAs are not always end products but can further serve as a source for short ncRNAs. In many organisms, various tRNA-derived ncRNA species are produced from mature tRNAs or their precursor transcripts as functional molecules involved in various biological processes beyond translation. In this review, we focus on the tRNA-derived ncRNAs associated with Argonaute proteins and summarize recent studies on their conceivable biogenesis factors and on their emerging roles in gene expression regulation as regulatory RNAs.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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241
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Tuorto F, Herbst F, Alerasool N, Bender S, Popp O, Federico G, Reitter S, Liebers R, Stoecklin G, Gröne HJ, Dittmar G, Glimm H, Lyko F. The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis. EMBO J 2015; 34:2350-62. [PMID: 26271101 PMCID: PMC4570521 DOI: 10.15252/embj.201591382] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/16/2015] [Indexed: 12/17/2022] Open
Abstract
The Dnmt2 enzyme utilizes the catalytic mechanism of eukaryotic DNA methyltransferases to methylate several tRNAs at cytosine 38. Dnmt2 mutant mice, flies, and plants were reported to be viable and fertile, and the biological function of Dnmt2 has remained elusive. Here, we show that endochondral ossification is delayed in newborn Dnmt2-deficient mice, which is accompanied by a reduction of the haematopoietic stem and progenitor cell population and a cell-autonomous defect in their differentiation. RNA bisulfite sequencing revealed that Dnmt2 methylates C38 of tRNA AspGTC, GlyGCC, and ValAAC, thus preventing tRNA fragmentation. Proteomic analyses from primary bone marrow cells uncovered systematic differences in protein expression that are due to specific codon mistranslation by tRNAs lacking Dnmt2-dependent methylation. Our observations demonstrate that Dnmt2 plays an important role in haematopoiesis and define a novel function of C38 tRNA methylation in the discrimination of near-cognate codons, thereby ensuring accurate polypeptide synthesis.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Friederike Herbst
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nader Alerasool
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Popp
- Mass Spectrometry Core Unit, MDC, Berlin, Germany
| | - Giuseppina Federico
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | - Sonja Reitter
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center (DKFZ) and Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Reinhard Liebers
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Georg Stoecklin
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center (DKFZ) and Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hermann-Josef Gröne
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | | | - Hanno Glimm
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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242
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Mami I, Bouvier N, El Karoui K, Gallazzini M, Rabant M, Laurent-Puig P, Li S, Tharaux PL, Beaune P, Thervet E, Chevet E, Hu GF, Pallet N. Angiogenin Mediates Cell-Autonomous Translational Control under Endoplasmic Reticulum Stress and Attenuates Kidney Injury. J Am Soc Nephrol 2015. [PMID: 26195817 DOI: 10.1681/asn.2015020196] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Endoplasmic reticulum (ER) stress is involved in the pathophysiology of kidney disease and aging, but the molecular bases underlying the biologic outcomes on the evolution of renal disease remain mostly unknown. Angiogenin (ANG) is a ribonuclease that promotes cellular adaptation under stress but its contribution to ER stress signaling remains elusive. In this study, we investigated the ANG-mediated contribution to the signaling and biologic outcomes of ER stress in kidney injury. ANG expression was significantly higher in samples from injured human kidneys than in samples from normal human kidneys, and in mouse and rat kidneys, ANG expression was specifically induced under ER stress. In human renal epithelial cells, ER stress induced ANG expression in a manner dependent on the activity of transcription factor XBP1, and ANG promoted cellular adaptation to ER stress through induction of stress granules and inhibition of translation. Moreover, the severity of renal lesions induced by ER stress was dramatically greater in ANG knockout mice (Ang(-/-)) mice than in wild-type mice. These results indicate that ANG is a critical mediator of tissue adaptation to kidney injury and reveal a physiologically relevant ER stress-mediated adaptive translational control mechanism.
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Affiliation(s)
- Iadh Mami
- Institut National de la Sante et de la Recherche Médicale (INSERM) U1147, Saints-Pères Research Center Paris, France; Paris Descartes University Paris, France
| | | | - Khalil El Karoui
- Paris Descartes University Paris, France; INSERM U1151, Sick Childrens Necker Institute Paris, France
| | - Morgan Gallazzini
- Paris Descartes University Paris, France; INSERM U1151, Sick Childrens Necker Institute Paris, France
| | - Marion Rabant
- Paris Descartes University Paris, France; Pathology Department, Necker Hospital Paris, France
| | - Pierre Laurent-Puig
- Institut National de la Sante et de la Recherche Médicale (INSERM) U1147, Saints-Pères Research Center Paris, France; Paris Descartes University Paris, France; Clinical Chemistry and
| | - Shuping Li
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts
| | | | - Philippe Beaune
- Institut National de la Sante et de la Recherche Médicale (INSERM) U1147, Saints-Pères Research Center Paris, France; Paris Descartes University Paris, France; Clinical Chemistry and
| | - Eric Thervet
- Paris Descartes University Paris, France; Nephrology Departments, Georges Pompidou European Hospital Paris, France
| | - Eric Chevet
- INSERM, UMR-U1053, Team Endoplasmic Reticulum Stress and Cancer, Bordeaux, France
| | - Guo-Fu Hu
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts
| | - Nicolas Pallet
- Institut National de la Sante et de la Recherche Médicale (INSERM) U1147, Saints-Pères Research Center Paris, France; Paris Descartes University Paris, France; Clinical Chemistry and Nephrology Departments, Georges Pompidou European Hospital Paris, France;
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243
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Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci U S A 2015; 112:E3816-25. [PMID: 26124144 DOI: 10.1073/pnas.1510077112] [Citation(s) in RCA: 258] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sex hormones and their receptors play critical roles in the development and progression of the breast and prostate cancers. Here we report that a novel type of transfer RNA (tRNA)-derived small RNA, termed Sex HOrmone-dependent TRNA-derived RNAs (SHOT-RNAs), are specifically and abundantly expressed in estrogen receptor (ER)-positive breast cancer and androgen receptor (AR)-positive prostate cancer cell lines. SHOT-RNAs are not abundantly present in ER(-) breast cancer, AR(-) prostate cancer, or other examined cancer cell lines from other tissues. ER-dependent accumulation of SHOT-RNAs is not limited to a cell culture system, but it also occurs in luminal-type breast cancer patient tissues. SHOT-RNAs are produced from aminoacylated mature tRNAs by angiogenin-mediated anticodon cleavage, which is promoted by sex hormones and their receptors. Resultant 5'- and 3'-SHOT-RNAs, corresponding to 5'- and 3'-tRNA halves, bear a cyclic phosphate (cP) and an amino acid at the 3'-end, respectively. By devising a "cP-RNA-seq" method that is able to exclusively amplify and sequence cP-containing RNAs, we identified the complete repertoire of 5'-SHOT-RNAs. Furthermore, 5'-SHOT-RNA, but not 3'-SHOT-RNA, has significant functional involvement in cell proliferation. These results have unveiled a novel tRNA-engaged pathway in tumorigenesis of hormone-dependent cancers and implicate SHOT-RNAs as potential candidates for biomarkers and therapeutic targets.
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244
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O'Day E, Le MTN, Imai S, Tan SM, Kirchner R, Arthanari H, Hofmann O, Wagner G, Lieberman J. An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates. J Biol Chem 2015; 290:17909-17922. [PMID: 26045559 DOI: 10.1074/jbc.m115.665521] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 01/01/2023] Open
Abstract
Lin28 is an evolutionarily conserved RNA-binding protein that inhibits processing of pre-let-7 microRNAs (miRNAs) and regulates translation of mRNAs that control developmental timing, pluripotency, metabolism, and tumorigenesis. The RNA features that mediate Lin28 binding to the terminal loops of let-7 pre-miRNAs and to Lin28-responsive elements (LREs) in mRNAs are not well defined. Here we show that Lin28 target datasets are enriched for RNA sequences predicted to contain stable planar structures of 4 guanines known as G-quartets (G4s). The imino NMR spectra of pre-let-7 loops and LREs contain resonances characteristic of G4 hydrogen bonds. These sequences bind to a G4-binding fluorescent dye, N-methyl-mesoporphyrin IX (NMM). Mutations and truncations in the RNA sequence that prevent G4 formation also prevent Lin28 binding. The addition of Lin28 to a pre-let-7 loop or an LRE reduces G4 resonance intensity and NMM binding, suggesting that Lin28 may function to remodel G4s. Further, we show that NMM inhibits Lin28 binding. Incubation of a human embryonal carcinoma cell line with NMM reduces its stem cell traits. In particular it increases mature let-7 levels, decreases OCT4, HMGA1, CCNB1, CDK4, and Lin28A protein, decreases sphere formation, and inhibits colony formation. Our results suggest a previously unknown structural feature of Lin28 targets and a new strategy for manipulating Lin28 function.
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Affiliation(s)
- Elizabeth O'Day
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Minh T N Le
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Shunsuke Imai
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Shen Mynn Tan
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Rory Kirchner
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Haribabu Arthanari
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Oliver Hofmann
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Gerhard Wagner
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
| | - Judy Lieberman
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115.
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245
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Simone R, Fratta P, Neidle S, Parkinson GN, Isaacs AM. G-quadruplexes: Emerging roles in neurodegenerative diseases and the non-coding transcriptome. FEBS Lett 2015; 589:1653-68. [PMID: 25979174 DOI: 10.1016/j.febslet.2015.05.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/29/2015] [Accepted: 05/02/2015] [Indexed: 12/14/2022]
Abstract
G-rich sequences in DNA and RNA have a propensity to fold into stable secondary structures termed G-quadruplexes. G-quadruplex forming sequences are widespread throughout the human genome, within both, protein coding and non-coding genes, and regulatory regions. G-quadruplexes have been implicated in multiple cellular functions including chromatin epigenetic regulation, DNA recombination, transcriptional regulation of gene promoters and enhancers, and translation. Here we will review the evidence for the occurrence of G-quadruplexes both in vitro and in vivo; their role in neurological diseases including G-quadruplex-forming repeat expansions in the C9orf72 gene in frontotemporal dementia and amyotrophic lateral sclerosis and loss of the G-quadruplex binding protein FMRP in the intellectual disability fragile X syndrome. We also review mounting evidence that supports a role for G-quadruplexes in regulating the processing or function of a range of non-coding RNAs. Finally we will highlight current perspectives for therapeutic interventions that target G-quadruplexes.
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Affiliation(s)
- Roberto Simone
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Pietro Fratta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Sobell Department of Motor Neuroscience and Movement, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Gary N Parkinson
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
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246
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Wilusz JE. Controlling translation via modulation of tRNA levels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:453-70. [PMID: 25919480 DOI: 10.1002/wrna.1287] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/13/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are critical adaptor molecules that carry amino acids to a messenger RNA (mRNA) template during protein synthesis. Although tRNAs have commonly been viewed as abundant 'house-keeping' RNAs, it is becoming increasingly clear that tRNA expression is tightly regulated. Depending on a cell's proliferative status, the pool of active tRNAs is rapidly changed, enabling distinct translational programs to be expressed in differentiated versus proliferating cells. Here, I highlight several post-transcriptional regulatory mechanisms that allow the expression or functions of tRNAs to be altered. Modulating the modification status or structural stability of individual tRNAs can cause those specific tRNA transcripts to selectively accumulate or be degraded. Decay generally occurs via the rapid tRNA decay pathway or by the nuclear RNA surveillance machinery. In addition, the CCA-adding enzyme plays a critical role in determining the fate of a tRNA. The post-transcriptional addition of CCA to the 3' ends of stable tRNAs generates the amino acid attachment site, whereas addition of CCACCA to unstable tRNAs prevents aminoacylation and marks the tRNA for degradation. In response to various stresses, tRNAs can accumulate in the nucleus or be further cleaved into small RNAs, some of which inhibit translation. By implementing these various post-transcriptional control mechanisms, cells are able to fine-tune tRNA levels to regulate subsets of mRNAs as well as overall translation rates.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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247
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Surveillance and cleavage of eukaryotic tRNAs. Int J Mol Sci 2015; 16:1873-93. [PMID: 25599528 PMCID: PMC4307339 DOI: 10.3390/ijms16011873] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/09/2015] [Indexed: 12/27/2022] Open
Abstract
Beyond their central role in protein synthesis, transfer RNAs (tRNAs) have many other crucial functions. This includes various roles in the regulation of gene expression, stress responses, metabolic processes and priming reverse transcription. In the RNA world, tRNAs are, with ribosomal RNAs, among the most stable molecules. Nevertheless, they are not eternal. As key elements of cell function, tRNAs need to be continuously quality-controlled. Two tRNA surveillance pathways have been identified. They act on hypo-modified or mis-processed pre-tRNAs and on mature tRNAs lacking modifications. A short overview of these two pathways will be presented here. Furthermore, while the exoribonucleases acting in these pathways ultimately lead to complete tRNA degradation, numerous tRNA-derived fragments (tRFs) are present within a cell. These cleavage products of tRNAs now potentially emerge as a new class of small non-coding RNAs (sncRNAs) and are suspected to have important regulatory functions. The tRFs are evolutionarily widespread and created by cleavage at different positions by various endonucleases. Here, we review our present knowledge on the biogenesis and function of tRFs in various organisms.
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248
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