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Luthi-Carter R, Cappelli S, Le Roux-Bourdieu M, Tentillier N, Quinn JP, Petrozziello T, Gopalakrishnan L, Sethi P, Choudhary H, Bartolini G, Gebara E, Stuani C, Font L, An J, Ortega V, Sage J, Kosa E, Trombetta BA, Simeone R, Seredenina T, Afroz T, Berry JD, Arnold SE, Carlyle BC, Adolfsson O, Sadri-Vakili G, Buratti E, Bowser R, Agbas A. Location and function of TDP-43 in platelets, alterations in neurodegenerative diseases and arising considerations for current plasma biobank protocols. Sci Rep 2024; 14:21837. [PMID: 39294194 PMCID: PMC11410945 DOI: 10.1038/s41598-024-70822-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
The TAR DNA Binding Protein 43 (TDP-43) has been implicated in the pathogenesis of human neurodegenerative diseases and exhibits hallmark neuropathology in amyotrophic lateral sclerosis (ALS). Here, we explore its tractability as a plasma biomarker of disease and describe its localization and possible functions in the cytosol of platelets. Novel TDP-43 immunoassays were developed on three different technical platforms and qualified for specificity, signal-to-noise ratio, detection range, variation, spike recovery and dilution linearity in human plasma samples. Surprisingly, implementation of these assays demonstrated that biobank-archived plasma samples yielded considerable heterogeneity in TDP-43 levels. Importantly, subsequent investigation attributed these differences to variable platelet recovery. Fractionations of fresh blood revealed that ≥ 95% of the TDP-43 in platelet-containing plasma was compartmentalized within the platelet cytosol. We reasoned that this highly concentrated source of TDP-43 comprised an interesting substrate for biochemical analyses. Additional characterization of platelets revealed the presence of the disease-associated phosphoserine 409/410 TDP-43 proteoform and many neuron- and astrocyte-expressed TDP-43 mRNA targets. Considering these striking similarities, we propose that TDP-43 may serve analogous functional roles in platelets and synapses, and that the study of platelet TDP-43 might provide a window into disease-related TDP-43 dyshomeostasis in the central nervous system.
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Affiliation(s)
- Ruth Luthi-Carter
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland.
| | - Sara Cappelli
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | | | - Noemie Tentillier
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - James P Quinn
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
- MassGeneral Institute for Neurodegenerative Disease, 114 16th Street, Charlestown, MA, 02129, USA
- Eisai US, 35 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Tiziana Petrozziello
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Lathika Gopalakrishnan
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Purva Sethi
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
| | - Himanshi Choudhary
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | - Giorgia Bartolini
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Elias Gebara
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | - Laure Font
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Jiyan An
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Vanessa Ortega
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Jessica Sage
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
- Boehringer Ingelheim Vetmedica, St Joseph, MO, 64503, USA
| | - Edina Kosa
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
| | - Bianca A Trombetta
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
| | - Roberto Simeone
- Dipartimento di Medicina Trasfusionale Giuliano-Isontina, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), Trieste, Italy
| | - Tamara Seredenina
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Tariq Afroz
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - James D Berry
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
- Neurological Clinical Research Institute, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Steven E Arnold
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
- MassGeneral Institute for Neurodegenerative Disease, 114 16th Street, Charlestown, MA, 02129, USA
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Becky C Carlyle
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
- Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX13QU, UK
| | - Oskar Adolfsson
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Ghazaleh Sadri-Vakili
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- MassGeneral Institute for Neurodegenerative Disease, 114 16th Street, Charlestown, MA, 02129, USA
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | - Robert Bowser
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Abdulbaki Agbas
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
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2
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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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3
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Busselez J, Uzbekov RE, Franco B, Pancione M. New insights into the centrosome-associated spliceosome components as regulators of ciliogenesis and tissue identity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1776. [PMID: 36717357 DOI: 10.1002/wrna.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 02/01/2023]
Abstract
Biomolecular condensates are membrane-less assemblies of proteins and nucleic acids. Centrosomes are biomolecular condensates that play a crucial role in nuclear division, cytoskeletal remodeling, and cilia formation in animal cells. Spatial omics technology is providing new insights into the dynamic exchange of spliceosome components between the nucleus and the centrosome/cilium. Intriguingly, centrosomes are emerging as cytoplasmic sites for information storage, enriched with RNA molecules and RNA-processing proteins. Furthermore, growing evidence supports the view that nuclear spliceosome components assembled at the centrosome function as potential coordinators of splicing subprograms, pluripotency, and cell differentiation. In this article, we first discuss the current understanding of the centrosome/cilium complex, which controls both stem cell differentiation and pluripotency. We next explore the molecular mechanisms that govern splicing factor assembly and disassembly around the centrosome and examine how RNA processing pathways contribute to ciliogenesis. Finally, we discuss numerous unresolved compelling questions regarding the centrosome-associated spliceosome components and transcript variants within the cytoplasm as sources of RNA-based secondary messages in the regulation of cell identity and cell fate determination. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > RNA Processing.
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Affiliation(s)
- Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Rustem E Uzbekov
- Faculté de Médecine, Université de Tours, Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medicine, Medical Genetics, University of Naples "Federico II", Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine program, University of Naples Federico II, Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, Madrid, Spain
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
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David JK, Maden SK, Wood MA, Thompson RF, Nellore A. Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biol 2022; 23:240. [PMID: 36369064 PMCID: PMC9652823 DOI: 10.1186/s13059-022-02789-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. RESULTS We compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss' [Formula: see text]) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection. CONCLUSIONS Short-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods.
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Affiliation(s)
- Julianne K. David
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,Present Address: Base5 Genomics, Inc., Mountain View, CA USA
| | - Sean K. Maden
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.21107.350000 0001 2171 9311Present Address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Mary A. Wood
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.429936.30000 0004 5914 210XPortland VA Research Foundation, Portland, OR USA ,Present Address: Phase Genomics, Inc., Seattle, WA USA
| | - Reid F. Thompson
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.484322.bDivision of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Radiation Medicine, Oregon Health & Science University, Portland, OR USA
| | - Abhinav Nellore
- grid.5288.70000 0000 9758 5690Computational Biology Program, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Surgery, Oregon Health & Science University, Portland, OR USA
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6
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Nagel M, Noss M, Xu J, Horn N, Ueffing M, Boldt K, Schuele R. The kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells. RNA (NEW YORK, N.Y.) 2022; 29:rna.079426.122. [PMID: 36316088 PMCID: PMC9808568 DOI: 10.1261/rna.079426.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Neurons critically depend on regulated RNA localization and tight control of spatio-temporal gene expression to maintain their morphological and functional integrity. Mutations in the kinesin motor protein gene KIF1C cause Hereditary Spastic Paraplegia, an autosomal recessive disease leading to predominant degeneration of the long axons of central motoneurons. In this study we aimed to gain insight into the molecular function of KIF1C and understand how KIF1C dysfunction contributes to motoneuron degeneration. We used affinity proteomics in neuronally differentiated neuroblastoma cells (SH-SY5Y) to identify the protein complex associated with KIF1C in neuronal cells; candidate interactions were then validated by immunoprecipitation and mislocalization of putative KIF1C cargoes was studied by immunostainings. We found KIF1C to interact with all core components of the exon junction complex (EJC); expression of mutant KIF1C in neuronal cells leads to loss of the typical localization distally in neurites. Instead, EJC core components accumulate in the pericentrosomal region, here co-localizing with mutant KIF1C. These findings suggest KIF1C as a neuronal transporter of the EJC. Interestingly, the binding of KIF1C to the EJC is RNA-mediated, as treatment with RNAse prior to immunoprecipitation almost completely abolishes the interaction. Silica-based solid-phase extraction of UV-crosslinked RNA-protein complexes furthermore supports direct interaction of KIF1C with RNA, as recently also demonstrated for kinesin heavy chain. Taken together, our findings are consistent with a model where KIF1C transports mRNA in an EJC-bound and therefore transcriptionally silenced state along neurites, thus providing the missing link between the EJC and mRNA localization in neurons.
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Affiliation(s)
- Maike Nagel
- German Center for Neurodegenerative Diseases, Tuebingen; Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen; Graduate School of Cellular and Molecular Neuroscience
| | - Marvin Noss
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen
| | - Jishu Xu
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen; Institute of Medical Genetics and Applied Genomics, University of Tuebingen; Graduate School
| | - Nicola Horn
- Institute for Ophthalmic Research, University of Tuebingen
| | - Marius Ueffing
- Institute of Ophthalmic Research, University of Tuebingen
| | - Karsten Boldt
- Institute of Ophthalmic Research, University of Tuebingen
| | - Rebecca Schuele
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tuebingen; German Center for Neurodegenerative Diseases, Tuebingen
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7
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Mishra P, Sankar SHH, Gosavi N, Bharathavikru RS. RNA nucleoprotein complexes in biological systems. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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8
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Gao Y, Pang AP, Ma L, Wang H, Durrani S, Li B, Wu FG, Lin F. Intron retention coupled with nonsense-mediated decay is involved in cellulase biosynthesis in cellulolytic fungi. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:53. [PMID: 35590374 PMCID: PMC9118705 DOI: 10.1186/s13068-022-02141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Knowledge on regulatory networks associated with cellulase biosynthesis is prerequisite for exploitation of such regulatory systems in enhancing cellulase production with low cost. The biological functions of intron retention (IR) and nonsense-mediated mRNA decay (NMD) in filamentous fungi is lack of study, let alone their roles in cellulase biosynthesis. RESULTS We found that major cellulase genes (cel7a, cel7b, and cel3a) exhibited concomitant decrease in IR rates and increase in their gene expression in T. reesei under cellulase-producing condition (cellulose and lactose) that was accompanied with a more active NMD pathway, as compared to cellulase non-producing condition (glucose). In the presence of the NMD pathway inhibitor that successfully repressed the NMD pathway, the mRNA levels of cellulase genes were sharply down-regulated, but the rates of IR in these genes were significantly up-regulated. Consistently, the cellulase activities were severely inhibited. In addition, the NMD pathway inhibitor caused the downregulated mRNA levels of two important genes of the target of rapamycin (TOR) pathway, trfkbp12 and trTOR1. The absence of gene trfkbp12 made the cellulase production in T. reesei more sensitive to the NMD pathway inhibitor. CONCLUSIONS All these findings suggest that the IR of cellulase genes regulates their own gene expression by coupling with the NMD pathway, which might involve the TOR pathway. Our results provide better understanding on intron retention, the NMD pathway, and cellulase production mechanism in filamentous fungi.
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Affiliation(s)
- Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Leyao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bingzhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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9
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Díaz M, Mesa-Herrera F, Marín R. DHA and Its Elaborated Modulation of Antioxidant Defenses of the Brain: Implications in Aging and AD Neurodegeneration. Antioxidants (Basel) 2021; 10:antiox10060907. [PMID: 34205196 PMCID: PMC8228037 DOI: 10.3390/antiox10060907] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
DHA (docosahexaenoic acid) is perhaps the most pleiotropic molecule in nerve cell biology. This long-chain highly unsaturated fatty acid has evolved to accomplish essential functions ranging from structural components allowing fast events in nerve cell membrane physiology to regulation of neurogenesis and synaptic function. Strikingly, the plethora of DHA effects has to take place within the hostile pro-oxidant environment of the brain parenchyma, which might suggest a molecular suicide. In order to circumvent this paradox, different molecular strategies have evolved during the evolution of brain cells to preserve DHA and to minimize the deleterious effects of its oxidation. In this context, DHA has emerged as a member of the “indirect antioxidants” family, the redox effects of which are not due to direct redox interactions with reactive species, but to modulation of gene expression within thioredoxin and glutathione antioxidant systems and related pathways. Weakening or deregulation of these self-protecting defenses orchestrated by DHA is associated with normal aging but also, more worryingly, with the development of neurodegenerative diseases. In the present review, we elaborate on the essential functions of DHA in the brain, including its role as indirect antioxidant, the selenium connection for proper antioxidant function and their changes during normal aging and in Alzheimer’s disease.
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Affiliation(s)
- Mario Díaz
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, School of Biology, Universidad de La Laguna, 38206 Tenerife, Spain;
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSP), Universidad de La Laguna, 38206 Tenerife, Spain
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38206 Tenerife, Spain;
- Correspondence:
| | - Fátima Mesa-Herrera
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, School of Biology, Universidad de La Laguna, 38206 Tenerife, Spain;
| | - Raquel Marín
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38206 Tenerife, Spain;
- Laboratory of Cellular Neurobiology, Department of Basic Medical Sciences, School of Medicine, Universidad de La Laguna, 38206 Tenerife, Spain
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10
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Ziff OJ, Taha DM, Crerar H, Clarke BE, Chakrabarti AM, Kelly G, Neeves J, Tyzack GE, Luscombe NM, Patani R. Reactive astrocytes in ALS display diminished intron retention. Nucleic Acids Res 2021; 49:3168-3184. [PMID: 33684213 PMCID: PMC8034657 DOI: 10.1093/nar/gkab115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Reactive astrocytes are implicated in amyotrophic lateral sclerosis (ALS), although the mechanisms controlling reactive transformation are unknown. We show that decreased intron retention (IR) is common to human-induced pluripotent stem cell (hiPSC)-derived astrocytes carrying ALS-causing mutations in VCP, SOD1 and C9orf72. Notably, transcripts with decreased IR and increased expression are overrepresented in reactivity processes including cell adhesion, stress response and immune activation. This was recapitulated in public-datasets for (i) hiPSC-derived astrocytes stimulated with cytokines to undergo reactive transformation and (ii) in vivo astrocytes following selective deletion of TDP-43. We also re-examined public translatome sequencing (TRAP-seq) of astrocytes from a SOD1 mouse model, which revealed that transcripts upregulated in translation significantly overlap with transcripts exhibiting decreased IR. Using nucleocytoplasmic fractionation of VCP mutant astrocytes coupled with mRNA sequencing and proteomics, we identify that decreased IR in nuclear transcripts is associated with enhanced nonsense mediated decay and increased cytoplasmic expression of transcripts and proteins regulating reactive transformation. These findings are consistent with a molecular model for reactive transformation in astrocytes whereby poised nuclear reactivity-related IR transcripts are spliced, undergo nuclear-to-cytoplasmic translocation and translation. Our study therefore provides new insights into the molecular regulation of reactive transformation in astrocytes.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
| | - Doaa M Taha
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Hamish Crerar
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Benjamin E Clarke
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia E Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
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11
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Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TYT, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XHF, Westbrook TF. Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell 2021; 184:384-403.e21. [PMID: 33450205 PMCID: PMC8635244 DOI: 10.1016/j.cell.2020.12.031] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Many oncogenic insults deregulate RNA splicing, often leading to hypersensitivity of tumors to spliceosome-targeted therapies (STTs). However, the mechanisms by which STTs selectively kill cancers remain largely unknown. Herein, we discover that mis-spliced RNA itself is a molecular trigger for tumor killing through viral mimicry. In MYC-driven triple-negative breast cancer, STTs cause widespread cytoplasmic accumulation of mis-spliced mRNAs, many of which form double-stranded structures. Double-stranded RNA (dsRNA)-binding proteins recognize these endogenous dsRNAs, triggering antiviral signaling and extrinsic apoptosis. In immune-competent models of breast cancer, STTs cause tumor cell-intrinsic antiviral signaling, downstream adaptive immune signaling, and tumor cell death. Furthermore, RNA mis-splicing in human breast cancers correlates with innate and adaptive immune signatures, especially in MYC-amplified tumors that are typically immune cold. These findings indicate that dsRNA-sensing pathways respond to global aberrations of RNA splicing in cancer and provoke the hypothesis that STTs may provide unexplored strategies to activate anti-tumor immune pathways.
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Affiliation(s)
- Elizabeth A Bowling
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jarey H Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fade Gong
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - William Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ik Sun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Siddhartha Tyagi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mayra Orellana
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah J Kurley
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rocio Dominguez-Vidaña
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hsiang-Ching Chung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tiffany Y-T Hsu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander B Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heyuan Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jitendra K Meena
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gino M Canlas
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swarnima Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Calla M Olson
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Miles
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lihua Yu
- H3Biomedicine, Cambridge, MA 02139, USA
| | | | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristen L Karlin
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
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12
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Identification of Genomewide Alternative Splicing Events in Sequential, Isogenic Clinical Isolates of Candida albicans Reveals a Novel Mechanism of Drug Resistance and Tolerance to Cellular Stresses. mSphere 2020; 5:5/4/e00608-20. [PMID: 32817456 PMCID: PMC7426172 DOI: 10.1128/msphere.00608-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of resistance in Candida albicans, an opportunistic pathogen, against the commonly used antifungals is becoming a major obstacle in its treatment. The necessity to identify new drug targets demands fundamental insights into the mechanisms used by this organism to develop drug resistance. C. albicans has introns in 4 to 6% of its genes, the functions of which remain largely unknown. Using the RNA-sequencing data from isogenic pairs of azole-sensitive and -resistant isolates of C. albicans, here, we show how C. albicans uses modulations in mRNA splicing to overcome antifungal drug stress. Alternative splicing (AS)—a process by which a single gene gives rise to different protein isoforms in eukaryotes—has been implicated in many basic cellular processes, but little is known about its role in drug resistance and fungal pathogenesis. The most common human fungal pathogen, Candida albicans, has introns in 4 to 6% of its genes, the functions of which remain largely unknown. Here, we report AS regulating drug resistance in C. albicans. Comparative RNA-sequencing of two different sets of sequential, isogenic azole-sensitive and -resistant isolates of C. albicans revealed differential expression of splice isoforms of 14 genes. One of these was the superoxide dismutase gene SOD3, which contains a single intron. The sod3Δ/Δ mutant was susceptible to the antifungals amphotericin B (AMB) and menadione (MND). While AMB susceptibility was rescued by overexpression of both the spliced and unspliced SOD3 isoforms, only the spliced isoform could overcome MND susceptibility, demonstrating the functional relevance of this splicing in developing drug resistance. Furthermore, unlike AMB, MND inhibits SOD3 splicing and acts as a splicing inhibitor. Consistent with these observations, MND exposure resulted in increased levels of unspliced SOD3 isoform that are unable to scavenge reactive oxygen species (ROS), resulting in increased drug susceptibility. Collectively, these observations suggest that AS is a novel mechanism for stress adaptation and overcoming drug susceptibility in C. albicans. IMPORTANCE The emergence of resistance in Candida albicans, an opportunistic pathogen, against the commonly used antifungals is becoming a major obstacle in its treatment. The necessity to identify new drug targets demands fundamental insights into the mechanisms used by this organism to develop drug resistance. C. albicans has introns in 4 to 6% of its genes, the functions of which remain largely unknown. Using the RNA-sequencing data from isogenic pairs of azole-sensitive and -resistant isolates of C. albicans, here, we show how C. albicans uses modulations in mRNA splicing to overcome antifungal drug stress.
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13
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Dardente H, English WR, Valluru MK, Kanthou C, Simpson D. Debunking the Myth of the Endogenous Antiangiogenic Vegfaxxxb Transcripts. Trends Endocrinol Metab 2020; 31:398-409. [PMID: 32396842 DOI: 10.1016/j.tem.2020.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/28/2019] [Accepted: 01/14/2020] [Indexed: 12/19/2022]
Abstract
In this opinion article we critically assess evidence for the existence of a family of antiangiogenic vascular endothelial growth factor (Vegfaxxxb) transcripts, arising from the use of a phylogenetically conserved alternative distal splice site within exon 8 of the VEGFA gene. We explain that prior evidence for Vegfaxxxb transcripts in tissues rests heavily upon flawed RT-PCR methodologies, with the extensive use of 5'-tailing in primer design being the main issue. Furthermore, our analysis of large RNA-seq data sets (human and ovine) fails to identify a single Vegfaxxxb transcript. Therefore, we challenge the very existence of Vegfaxxxb transcripts, which further questions the physiological relevance of studies based on the use of 'anti-VEGFAxxxb' antibodies. Our analysis has implications for the proposed therapeutic use of isoform-specific anti-VEGFA strategies for treating cancer and retinopathies.
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Affiliation(s)
- Hugues Dardente
- PRC, INRA, CNRS, IFCE, Université de Tours, 37380 Nouzilly, France.
| | - William R English
- Department of Oncology and Metabolism, Tumour Microcirculation Group, University of Sheffield, School of Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Manoj K Valluru
- Department of Oncology and Metabolism, Tumour Microcirculation Group, University of Sheffield, School of Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Chryso Kanthou
- Department of Oncology and Metabolism, Tumour Microcirculation Group, University of Sheffield, School of Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
| | - David Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT7 1NN, UK
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14
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Monteuuis G, Wong JJL, Bailey CG, Schmitz U, Rasko JEJ. The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Res 2020; 47:11497-11513. [PMID: 31724706 PMCID: PMC7145568 DOI: 10.1093/nar/gkz1068] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Justin J L Wong
- Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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15
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Sherpa C, Grice SFJL. Structural Fluidity of the Human Immunodeficiency Virus Rev Response Element. Viruses 2020; 12:v12010086. [PMID: 31940828 PMCID: PMC7019801 DOI: 10.3390/v12010086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 01/22/2023] Open
Abstract
Nucleocytoplasmic transport of unspliced and partially spliced human immunodeficiency virus (HIV) RNA is mediated in part by the Rev response element (RRE), a ~350 nt cis-acting element located in the envelope coding region of the viral genome. Understanding the interaction of the RRE with the viral Rev protein, cellular co-factors, and its therapeutic potential has been the subject of almost three decades of structural studies, throughout which a recurring discussion theme has been RRE topology, i.e., whether it comprises 4 or 5 stem-loops (SLs) and whether this has biological significance. Moreover, while in vitro mutagenesis allows the construction of 4 SL and 5 SL RRE conformers and testing of their roles in cell culture, it has not been immediately clear if such findings can be translated to a clinical setting. Herein, we review several articles demonstrating remarkable flexibility of the HIV-1 and HIV-2 RREs following initial observations that HIV-1 resistance to trans-dominant Rev therapy was founded in structural rearrangement of its RRE. These observations can be extended not only to cell culture studies demonstrating a growth advantage for the 5 SL RRE conformer but also to evolution in RRE topology in patient isolates. Finally, RRE conformational flexibility provides a target for therapeutic intervention, and we describe high throughput screening approaches to exploit this property.
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16
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Pal S, Medatwal N, Kumar S, Kar A, Komalla V, Yavvari PS, Mishra D, Rizvi ZA, Nandan S, Malakar D, Pillai M, Awasthi A, Das P, Sharma RD, Srivastava A, Sengupta S, Dasgupta U, Bajaj A. A Localized Chimeric Hydrogel Therapy Combats Tumor Progression through Alteration of Sphingolipid Metabolism. ACS CENTRAL SCIENCE 2019; 5:1648-1662. [PMID: 31660434 PMCID: PMC6813554 DOI: 10.1021/acscentsci.9b00551] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Indexed: 05/14/2023]
Abstract
Rapid proliferation of cancer cells assisted by endothelial cell-mediated angiogenesis and acquired inflammation at the tumor microenvironment (TME) lowers the success rate of chemotherapeutic regimens. Therefore, targeting these processes using localized delivery of a minimally toxic drug combination may be a promising strategy. Here, we present engineering of a biocompatible self-assembled lithocholic acid-dipeptide derived hydrogel (TRI-Gel) that can maintain sustained delivery of antiproliferating doxorubicin, antiangiogenic combretastatin-A4 and anti-inflammatory dexamethasone. Application of TRI-Gel therapy to a murine tumor model promotes enhanced apoptosis with a concurrent reduction in angiogenesis and inflammation, leading to effective abrogation of tumor proliferation and increased median survival with reduced drug resistance. In-depth RNA-sequencing analysis showed that TRI-Gel therapy induced transcriptome-wide alternative splicing of many genes responsible for oncogenic transformation including sphingolipid genes. We demonstrate that TRI-Gel therapy targets the reversal of a unique intron retention event in β-glucocerebrosidase 1 (Gba1), thereby increasing the availability of functional Gba1 protein. An enhanced Gba1 activity elevates ceramide levels responsible for apoptosis and decreases glucosylceramides to overcome drug resistance. Therefore, TRI-Gel therapy provides a unique system that affects the TME via post-transcriptional modulations of sphingolipid metabolic genes, thereby opening a new and rational approach to cancer therapy.
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Affiliation(s)
- Sanjay Pal
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
- Kalinga
Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India
| | - Nihal Medatwal
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
- Manipal
Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sandeep Kumar
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
- Manipal
Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Animesh Kar
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Varsha Komalla
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Prabhu Srinivas Yavvari
- Department
of Chemistry, Indian Institute of Science
Education and Research, Bhopal 462066, Madhya Pradesh, India
| | - Deepakkumar Mishra
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Zaigham Abbas Rizvi
- Translational
Health Science and Technology
Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Shiv Nandan
- Amity Institute
of Integrative Sciences and Health, Amity
University Haryana, Panchgaon, Manesar, Gurgaon 122413, Haryana, India
| | - Dipankar Malakar
- SCIEX, 121 Udyog Vihar,
Phase IV, Gurgaon 122015, Haryana, India
| | - Manoj Pillai
- SCIEX, 121 Udyog Vihar,
Phase IV, Gurgaon 122015, Haryana, India
| | - Amit Awasthi
- Translational
Health Science and Technology
Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Prasenjit Das
- Department
of Pathology, All India Institute of Medical
Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ravi Datta Sharma
- Amity Institute
of Integrative Sciences and Health, Amity
University Haryana, Panchgaon, Manesar, Gurgaon 122413, Haryana, India
| | - Aasheesh Srivastava
- Department
of Chemistry, Indian Institute of Science
Education and Research, Bhopal 462066, Madhya Pradesh, India
| | - Sagar Sengupta
- National
Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ujjaini Dasgupta
- Amity Institute
of Integrative Sciences and Health, Amity
University Haryana, Panchgaon, Manesar, Gurgaon 122413, Haryana, India
- E-mail: . (U.D.)
| | - Avinash Bajaj
- Laboratory
of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon
Expressway, Faridabad 121001, Haryana, India
- E-mail: . (A.B.)
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17
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Splicing regulatory factors in breast cancer hallmarks and disease progression. Oncotarget 2019; 10:6021-6037. [PMID: 31666932 PMCID: PMC6800274 DOI: 10.18632/oncotarget.27215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. Moreover, we could relate expression of representative genes of four other hallmarks (enabling replicative mortality, genomic instability, avoiding immune destruction and evading growth suppression) to splice factor levels in human breast cancer tumors, suggesting that also these hallmarks could be regulated by splice factors. Since many splice factors are involved in multiple hallmarks of cancer, inhibiting splice factors might provide a new layer of oncogenic control and a powerful method to combat breast cancer progression.
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18
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Boudreault S, Roy P, Lemay G, Bisaillon M. Viral modulation of cellular RNA alternative splicing: A new key player in virus-host interactions? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1543. [PMID: 31034770 PMCID: PMC6767064 DOI: 10.1002/wrna.1543] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
Abstract
Upon viral infection, a tug of war is triggered between host cells and viruses to maintain/gain control of vital cellular functions, the result of which will ultimately dictate the fate of the host cell. Among these essential cellular functions, alternative splicing (AS) is an important RNA maturation step that allows exons, or parts of exons, and introns to be retained in mature transcripts, thereby expanding proteome diversity and function. AS is widespread in higher eukaryotes, as it is estimated that nearly all genes in humans are alternatively spliced. Recent evidence has shown that upon infection by numerous viruses, the AS landscape of host‐cells is affected. In this review, we summarize recent advances in our understanding of how virus infection impacts the AS of cellular transcripts. We also present various molecular mechanisms allowing viruses to modulate cellular AS. Finally, the functional consequences of these changes in the RNA splicing signatures during virus–host interactions are discussed. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing
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Affiliation(s)
- Simon Boudreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Patricia Roy
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Guy Lemay
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Martin Bisaillon
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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19
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Zhao L, Yi S. Transcriptional landscape of alternative splicing during peripheral nerve injury. J Cell Physiol 2018; 234:6876-6885. [PMID: 30362529 DOI: 10.1002/jcp.27446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Abstract
Alternative splicing (AS) regulates a variety of biological activities in numerous tissues and organs, including the nervous system. However, the existence and specific roles of AS events during peripheral nerve repair and regeneration remain largely undetermined. In the current study, by mapping splice-crossing sequence reads, we identified AS events and relevant spliced genes in rat sciatic nerve stumps following sciatic nerve crush. AS-related genes at 1, 4, 7, and 14 days post nerve crush were compared with those at 0 day to discover alternatively spliced genes induced by sciatic nerve crush. These injury-induced alternatively spliced genes were then categorized to diseases and biological functions, genetic networks, and canonical signaling pathways. Bioinformatic analysis indicated that these alternatively spliced genes were mainly correlated to immune response, cellular growth, and cellular function maintenance. Our study elucidated AS events following peripheral nerve injury and might help deepen our understanding of the molecular mechanisms underlying peripheral nerve regeneration.
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Affiliation(s)
- Lili Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Sheng Yi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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20
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Jackson DP, Ting JH, Pozniak PD, Meurice C, Schleidt SS, Dao A, Lee AH, Klinman E, Jordan-Sciutto KL. Identification and characterization of two novel alternatively spliced E2F1 transcripts in the rat CNS. Mol Cell Neurosci 2018; 92:1-11. [PMID: 29936143 DOI: 10.1016/j.mcn.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 06/05/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022] Open
Abstract
E2F1 is a transcription factor classically known to regulate G0/G1 to S phase progression in the cell cycle. In addition, E2F1 also regulates a wide range of apoptotic genes and thus has been well studied in the context of neuronal death and neurodegenerative diseases. However, its function and regulation in the mature central nervous system are not well understood. Alternative splicing is a well-conserved post-transcriptional mechanism common in cells of the CNS and is necessary to generate diverse functional modifications to RNA or protein products from genes. Heretofore, physiologically significant alternatively spliced E2F1 transcripts have not been reported. In the present study, we report the identification of two novel alternatively spliced E2F1 transcripts: E2F1b, an E2F1 transcript retaining intron 5, and E2F1c, an E2F1 transcript excluding exon 6. These alternatively spliced transcripts are observed in the brain and neural cell types including neurons, astrocytes, and undifferentiated oligodendrocytes. The expression of these E2F1 transcripts is distinct during maturation of primary hippocampal neuroglial cells. Pharmacologically-induced global translation inhibition with cycloheximide, anisomycin or thapsigargin lead to significantly reduced expression of E2F1a, E2F1b and E2F1c. Conversely, increasing neuronal activity by elevating the concentration of potassium chloride selectively increased the expression of E2F1b. Furthermore, experiments expressing these variants in vitro show the transcripts can be translated to generate a protein product. Taken together, our data suggest that the alternatively spliced E2F1 transcript behave differently than the E2F1a transcript, and our results provide a foundation for future investigation of the function of E2F1 splice variants in the CNS.
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Affiliation(s)
- Dan P Jackson
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Jenhao H Ting
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Paul D Pozniak
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Claire Meurice
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie S Schleidt
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Anh Dao
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Amy H Lee
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Eva Klinman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelly L Jordan-Sciutto
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA.
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21
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Ortiz R, Georgieva MV, Gutiérrez S, Pedraza N, Fernández-Moya SM, Gallego C. Recruitment of Staufen2 Enhances Dendritic Localization of an Intron-Containing CaMKIIα mRNA. Cell Rep 2018; 20:13-20. [PMID: 28683307 DOI: 10.1016/j.celrep.2017.06.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/30/2017] [Accepted: 06/08/2017] [Indexed: 02/07/2023] Open
Abstract
Regulation of mRNA localization is a conserved cellular process observed in many types of cells and organisms. Asymmetrical mRNA distribution plays a particularly important role in the nervous system, where local translation of localized mRNA represents a key mechanism in synaptic plasticity. CaMKIIα is a very abundant mRNA detected in neurites, consistent with its crucial role at glutamatergic synapses. Here, we report the presence of CaMKIIα mRNA isoforms that contain intron i16 in dendrites, RNA granules, and synaptoneurosomes from primary neurons and brain. This subpopulation of unspliced mRNA preferentially localizes to distal dendrites in a synaptic-activity-dependent manner. Staufen2, a well-established marker of RNA transport in dendrites, interacts with intron i16 sequences and enhances its distal dendritic localization, pointing to the existence of intron-mediated mechanisms in the molecular pathways that modulate dendritic transport and localization of synaptic mRNAs.
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Affiliation(s)
- Raúl Ortiz
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Maya V Georgieva
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Sara Gutiérrez
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Neus Pedraza
- Institut de Recerca Biomèdica de Lleida (IRBLleida), Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, 25198 Lleida, Catalonia, Spain
| | - Sandra M Fernández-Moya
- Biomedical Center, Division of Anatomy and Cell Biology, Ludwig Maximilians University, 82152 Planegg-Martinsried, Germany
| | - Carme Gallego
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain.
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22
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Rekosh D, Hammarskjold ML. Intron retention in viruses and cellular genes: Detention, border controls and passports. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1470. [PMID: 29508942 DOI: 10.1002/wrna.1470] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/04/2018] [Accepted: 01/24/2018] [Indexed: 02/06/2023]
Abstract
Intron retention (IR), where one or more introns remain in the RNA after splicing, was long thought to be rare in mammalian cells, albeit common in plants and some viruses. Largely due to the development of better methods for RNA analysis, it has now been recognized that IR is much more common than previously thought and that this mechanism is likely to play an important role in mammalian gene regulation. To date, most publications and reviews about IR have described the resulting mRNAs as "dead end" products, with no direct consequence for the proteome. However, there are also many reports of mRNAs with retained introns giving rise to alternative protein isoforms. Although this was originally revealed in viral systems, there are now numerous examples of bona fide cellular proteins that are translated from mRNAs with retained introns. These new isoforms have sometimes been shown to have important regulatory functions. In this review, we highlight recent developments in this area and the research on viruses that led the way to the realization of the many ways in which mRNAs with retained introns can be regulated. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing RNA Export and Localization > Nuclear Export/Import RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- David Rekosh
- The Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia.,Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - Marie-Louise Hammarskjold
- The Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia.,Department of Microbiology, University of Venda, Thohoyandou, South Africa
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23
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Auboeuf D. Alternative mRNA processing sites decrease genetic variability while increasing functional diversity. Transcription 2017; 9:75-87. [PMID: 29099315 PMCID: PMC5834221 DOI: 10.1080/21541264.2017.1373891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions. However, this concept raises two main questions. First, do alternative mRNA processing pathways have a role other than generating mRNA and protein diversity? Second, is the cellular function of mRNA variants restricted to the biogenesis of functional protein isoforms? Here, I propose that the co-transcriptional use of alternative mRNA processing sites allows first, the resolution of co-transcriptional biophysical constraints that may otherwise result in DNA instability, and second, increases the diversity of cellular functions of mRNAs in a manner that is not restricted to protein synthesis.
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Affiliation(s)
- Didier Auboeuf
- a Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell , 46 Allée d'Italie Site Jacques Monod, Lyon , France
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24
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Tronik‐Le Roux D, Renard J, Vérine J, Renault V, Tubacher E, LeMaoult J, Rouas‐Freiss N, Deleuze J, Desgrandschamps F, Carosella ED. Novel landscape of HLA-G isoforms expressed in clear cell renal cell carcinoma patients. Mol Oncol 2017; 11:1561-1578. [PMID: 28815885 PMCID: PMC5664004 DOI: 10.1002/1878-0261.12119] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/21/2017] [Accepted: 07/29/2017] [Indexed: 12/14/2022] Open
Abstract
Immune checkpoints are powerful inhibitory molecules that promote tumor survival. Their blockade is now recognized as providing effective therapeutic benefit against cancer. Human leukocyte antigen G (HLA-G), a recently identified immune checkpoint, has been detected in many types of primary tumors and metastases, in malignant effusions as well as on tumor-infiltrating cells, particularly in patients with clear cell renal cell carcinoma (ccRCC). Here, in order to define a possible anticancer therapy, we used a molecular approach based on an unbiased strategy that combines transcriptome determination and immunohistochemical labeling, to analyze in-depth the HLA-G isoforms expressed in these tumors. We found that the expression of HLA-G is highly variable among tumors and distinct areas of the same tumor, testifying a marked inter- and intratumor heterogeneity. Moreover, our results generate an inventory of novel HLA-G isoforms which includes spliced forms that have an extended 5'-region and lack the transmembrane and alpha-1 domains. So far, these isoforms could not be detected by any method available and their assessment may improve the procedure by which tumors are analyzed. Collectively, our approach provides the first extensive portrait of HLA-G in ccRCC and reveals data that should prove suitable for the tailoring of future clinical applications.
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Affiliation(s)
- Diana Tronik‐Le Roux
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Julie Renard
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Jérôme Vérine
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- Service d'Anatomo‐PathologieAP‐HP, Hôpital Saint‐LouisParisFrance
| | - Victor Renault
- Centre d'Etudes du Polymorphisme HumainFondation Jean DaussetParisFrance
| | - Emmanuel Tubacher
- Centre d'Etudes du Polymorphisme HumainFondation Jean DaussetParisFrance
| | - Joel LeMaoult
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Nathalie Rouas‐Freiss
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Jean‐François Deleuze
- Centre d'Etudes du Polymorphisme HumainFondation Jean DaussetParisFrance
- Centre National de GénotypageInstitut de GénomiqueCEAEvryFrance
| | - François Desgrandschamps
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- Service d'UrologieAP‐HP, Hôpital Saint‐LouisParisFrance
| | - Edgardo D. Carosella
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
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25
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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26
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Urbanek MO, Krzyzosiak WJ. Discriminating RNA variants with single-molecule allele-specific FISH. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:230-241. [DOI: 10.1016/j.mrrev.2016.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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27
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Jacob AG, Smith CWJ. Intron retention as a component of regulated gene expression programs. Hum Genet 2017; 136:1043-1057. [PMID: 28391524 PMCID: PMC5602073 DOI: 10.1007/s00439-017-1791-x] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/29/2017] [Indexed: 12/16/2022]
Abstract
Intron retention has long been an exemplar of regulated splicing with case studies of individual events serving as models that provided key mechanistic insights into the process of splicing control. In organisms such as plants and budding yeast, intron retention is well understood as a major mechanism of gene expression regulation. In contrast, in mammalian systems, the extent and functional significance of intron retention have, until recently, remained greatly underappreciated. Technical challenges to the global detection and quantitation of transcripts with retained introns have often led to intron retention being overlooked or dismissed as “noise”. Now, however, with the wealth of information available from high-throughput deep sequencing, combined with focused computational and statistical analyses, we are able to distinguish clear intron retention patterns in various physiological and pathological contexts. Several recent studies have demonstrated intron retention as a central component of gene expression programs during normal development as well as in response to stress and disease. Furthermore, these studies revealed various ways in which intron retention regulates protein isoform production, RNA stability and translation efficiency, and rapid induction of expression via post-transcriptional splicing of retained introns. In this review, we highlight critical findings from these transcriptomic studies and discuss commonalties in the patterns prevalent in intron retention networks at the functional and regulatory levels.
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Affiliation(s)
- Aishwarya G Jacob
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK.
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28
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
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Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
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29
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Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. G3-GENES GENOMES GENETICS 2017; 7:203-219. [PMID: 27852012 PMCID: PMC5217110 DOI: 10.1534/g3.116.036020] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
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30
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Catalá A, Díaz M. Editorial: Impact of Lipid Peroxidation on the Physiology and Pathophysiology of Cell Membranes. Front Physiol 2016; 7:423. [PMID: 27713704 PMCID: PMC5031777 DOI: 10.3389/fphys.2016.00423] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/07/2016] [Indexed: 11/29/2022] Open
Affiliation(s)
- Angel Catalá
- Facultad de Ciencias Exactas, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA-CCT La Plata-CONICET), Universidad Nacional de La Plata La Plata, Argentina
| | - Mario Díaz
- Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias, Sección Biología, Universidad de La LagunaTenerife, Spain; Unidad Asociada de Investigación CSIC-ULL "Fisiología y Biofísica de la Membrana Celular en Patologías Neurodegenerativas y Tumorales"Tenerife, Spain
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31
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Sequence analysis of the Hsp70 family in moss and evaluation of their functions in abiotic stress responses. Sci Rep 2016; 6:33650. [PMID: 27644410 PMCID: PMC5028893 DOI: 10.1038/srep33650] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/31/2016] [Indexed: 11/30/2022] Open
Abstract
The 70-kD heat shock proteins (Hsp70s) are highly conserved molecular chaperones that play essential roles in cellular processes including abiotic stress responses. Physcomitrella patens serves as a representative of the first terrestrial plants and can recover from serious dehydration. To assess the possible relationship between P. patens Hsp70s and dehydration tolerance, we analyzed the P. patens genome and found at least 21 genes encoding Hsp70s. Gene structure and motif composition were relatively conserved in each subfamily. The intron-exon structure of PpcpHsp70-2 was different from that of other PpcpHsp70s; this gene exhibits several forms of intron retention, indicating that introns may play important roles in regulating gene expression. We observed expansion of Hsp70s in P. patens, which may reflect adaptations related to development and dehydration tolerance, and results mainly from tandem and segmental duplications. Expression profiles of rice, Arabidopsis and P. patens Hsp70 genes revealed that more than half of the Hsp70 genes were responsive to ABA, salt and drought. The presence of overrepresented cis-elements (DOFCOREZM and GCCCORE) among stress-responsive Hsp70s suggests that they share a common regulatory pathway. Moss plants overexpressing PpcpHsp70-2 showed salt and dehydration tolerance, further supporting a role in adaptation to land. This work highlights directions for future functional analyses of Hsp70s.
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Mishima T, Sadovsky E, Gegick ME, Sadovsky Y. Determinants of effective lentivirus-driven microRNA expression in vivo. Sci Rep 2016; 6:33345. [PMID: 27627961 PMCID: PMC5024309 DOI: 10.1038/srep33345] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/24/2016] [Indexed: 01/08/2023] Open
Abstract
Manipulation of microRNA (miRNA) levels, including overexpression of mature species, has become an important biological tool, even motivating miRNA-based therapeutics. To assess key determinants of miRNA overexpression in a mammalian system in vivo, we sought to bypass the laborious generation of a transgenic animal by exploiting placental trophoblast-specific gene manipulation using lentiviral vectors, which has been instrumental in elucidating trophoblast biology. We examined the impact of several key components of miRNA stem loops and their flanking sequences on the efficiency of mature miRNA expression in vivo. By combining established and novel approaches for miRNA expression, we engineered lentivirus-driven miRNA expression plasmids, which we tested in the mouse placenta. We found that reverse sense inserts minimized single-strand splicing and degradation, and that maintaining longer, poly-A-containing arms flanking the miRNA stem-loop markedly enhanced transgenic miRNA expression. Additionally, we accomplished overexpression of diverse mammalian, drosophila, or C. elegans miRNAs, either based on native context or using a “cassette” replacement of the mature miRNA sequence. Together, we have identified primary miRNA sequences that are paramount for effective expression of mature miRNAs, and validated their role in mice. Principles established by our findings may guide the design of efficient miRNA vectors for in vivo use.
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Affiliation(s)
- Takuya Mishima
- Magee-Womens Research Institute, Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213 USA
| | - Elena Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213 USA
| | - Margaret E Gegick
- Magee-Womens Research Institute, Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213 USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213 USA
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Sneddon WB, Ruiz GW, Gallo LI, Xiao K, Zhang Q, Rbaibi Y, Weisz OA, Apodaca GL, Friedman PA. Convergent Signaling Pathways Regulate Parathyroid Hormone and Fibroblast Growth Factor-23 Action on NPT2A-mediated Phosphate Transport. J Biol Chem 2016; 291:18632-42. [PMID: 27432882 PMCID: PMC5009241 DOI: 10.1074/jbc.m116.744052] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Indexed: 12/18/2022] Open
Abstract
Parathyroid hormone (PTH) and FGF23 are the primary hormones regulating acute phosphate homeostasis. Human renal proximal tubule cells (RPTECs) were used to characterize the mechanism and signaling pathways of PTH and FGF23 on phosphate transport and the role of the PDZ protein NHERF1 in mediating PTH and FGF23 effects. RPTECs express the NPT2A phosphate transporter, αKlotho, FGFR1, FGFR3, FGFR4, and the PTH receptor. FGFR1 isoforms are formed from alternate splicing of exon 3 and of exon 8 or 9 in Ir-like loop 3. Exon 3 was absent, but mRNA containing both exons 8 and 9 is present in cytoplasm. Using an FGFR1c-specific antibody together with mass spectrometry analysis, we show that RPTECs express FGFR-β1C. The data are consistent with regulated FGFR1 splicing involving a novel cytoplasmic mechanism. PTH and FGF23 inhibited phosphate transport in a concentration-dependent manner. At maximally effective concentrations, PTH and FGF23 equivalently decreased phosphate uptake and were not additive, suggesting a shared mechanism of action. Protein kinase A or C blockade prevented PTH but not FGF23 actions. Conversely, inhibiting SGK1, blocking FGFR dimerization, or knocking down Klotho expression disrupted FGF23 actions but did not interfere with PTH effects. C-terminal FGF23(180-251) competitively and selectively blocked FGF23 action without disrupting PTH effects. However, both PTH and FGF23-sensitive phosphate transport were abolished by NHERF1 shRNA knockdown. Extended treatment with PTH or FGF23 down-regulated NPT2A without affecting NHERF1. We conclude that FGFR1c and PTHR signaling pathways converge on NHERF1 to inhibit PTH- and FGF23-sensitive phosphate transport and down-regulate NPT2A.
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MESH Headings
- Cell Line, Transformed
- Fibroblast Growth Factor-23
- Fibroblast Growth Factors/genetics
- Fibroblast Growth Factors/metabolism
- Glucuronidase/biosynthesis
- Glucuronidase/genetics
- Humans
- Klotho Proteins
- Parathyroid Hormone/genetics
- Parathyroid Hormone/metabolism
- Phosphates/metabolism
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/biosynthesis
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 4/biosynthesis
- Receptor, Fibroblast Growth Factor, Type 4/genetics
- Receptor, Parathyroid Hormone, Type 1/genetics
- Receptor, Parathyroid Hormone, Type 1/metabolism
- Signal Transduction/physiology
- Sodium-Hydrogen Exchangers/genetics
- Sodium-Hydrogen Exchangers/metabolism
- Sodium-Phosphate Cotransporter Proteins, Type IIa/genetics
- Sodium-Phosphate Cotransporter Proteins, Type IIa/metabolism
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Affiliation(s)
- W Bruce Sneddon
- From the Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology and
| | - Giovanni W Ruiz
- Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Luciana I Gallo
- Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Kunhong Xiao
- From the Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology and
| | - Qiangmin Zhang
- From the Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology and
| | - Youssef Rbaibi
- Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Ora A Weisz
- Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261 Cell Biology, and
| | - Gerard L Apodaca
- Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261 Cell Biology, and
| | - Peter A Friedman
- From the Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology and the Departments of Structural Biology,
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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Proteostasis and RNA Binding Proteins in Synaptic Plasticity and in the Pathogenesis of Neuropsychiatric Disorders. Neural Plast 2016; 2016:3857934. [PMID: 26904297 PMCID: PMC4745388 DOI: 10.1155/2016/3857934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 12/30/2022] Open
Abstract
Decades of research have demonstrated that rapid alterations in protein abundance are required for synaptic plasticity, a cellular correlate for learning and memory. Control of protein abundance, known as proteostasis, is achieved across a complex neuronal morphology that includes a tortuous axon as well as an extensive dendritic arbor supporting thousands of individual synaptic compartments. To regulate the spatiotemporal synthesis of proteins, neurons must efficiently coordinate the transport and metabolism of mRNAs. Among multiple levels of regulation, transacting RNA binding proteins (RBPs) control proteostasis by binding to mRNAs and mediating their transport and translation in response to synaptic activity. In addition to synthesis, protein degradation must be carefully balanced for optimal proteostasis, as deviations resulting in excess or insufficient abundance of key synaptic factors produce pathologies. As such, mutations in components of the proteasomal or translational machinery, including RBPs, have been linked to the pathogenesis of neurological disorders such as Fragile X Syndrome (FXS), Fragile X Tremor Ataxia Syndrome (FXTAS), and Autism Spectrum Disorders (ASD). In this review, we summarize recent scientific findings, highlight ongoing questions, and link basic molecular mechanisms to the pathogenesis of common neuropsychiatric disorders.
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Abstract
A majority of messenger RNA precursors (pre-mRNAs) in the higher eukaryotes undergo alternative splicing to generate more than one mature product. By targeting the open reading frame region this process increases diversity of protein isoforms beyond the nominal coding capacity of the genome. However, alternative splicing also frequently controls output levels and spatiotemporal features of cellular and organismal gene expression programs. Here we discuss how these non-coding functions of alternative splicing contribute to development through regulation of mRNA stability, translational efficiency and cellular localization.
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Briese M, Saal L, Appenzeller S, Moradi M, Baluapuri A, Sendtner M. Whole transcriptome profiling reveals the RNA content of motor axons. Nucleic Acids Res 2015; 44:e33. [PMID: 26464439 PMCID: PMC4770199 DOI: 10.1093/nar/gkv1027] [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] [Received: 02/27/2015] [Accepted: 09/28/2015] [Indexed: 12/26/2022] Open
Abstract
Most RNAs within polarized cells such as neurons are sorted subcellularly in a coordinated manner. Despite advances in the development of methods for profiling polyadenylated RNAs from small amounts of input RNA, techniques for profiling coding and non-coding RNAs simultaneously are not well established. Here, we optimized a transcriptome profiling method based on double-random priming and applied it to serially diluted total RNA down to 10 pg. Read counts of expressed genes were robustly correlated between replicates, indicating that the method is both reproducible and scalable. Our transcriptome profiling method detected both coding and long non-coding RNAs sized >300 bases. Compared to total RNAseq using a conventional approach our protocol detected 70% more genes due to reduced capture of ribosomal RNAs. We used our method to analyze the RNA composition of compartmentalized motoneurons. The somatodendritic compartment was enriched for transcripts with post-synaptic functions as well as for certain nuclear non-coding RNAs such as 7SK. In axons, transcripts related to translation were enriched including the cytoplasmic non-coding RNA 7SL. Our profiling method can be applied to a wide range of investigations including perturbations of subcellular transcriptomes in neurodegenerative diseases and investigations of microdissected tissue samples such as anatomically defined fiber tracts.
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Affiliation(s)
- Michael Briese
- Institute for Clinical Neurobiology, University of Wuerzburg, 97078 Wuerzburg, Germany
| | - Lena Saal
- Institute for Clinical Neurobiology, University of Wuerzburg, 97078 Wuerzburg, Germany
| | - Silke Appenzeller
- Core Unit Systems Medicine, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Mehri Moradi
- Institute for Clinical Neurobiology, University of Wuerzburg, 97078 Wuerzburg, Germany
| | - Apoorva Baluapuri
- Institute for Clinical Neurobiology, University of Wuerzburg, 97078 Wuerzburg, Germany
| | - Michael Sendtner
- Institute for Clinical Neurobiology, University of Wuerzburg, 97078 Wuerzburg, Germany
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Casañas-Sánchez V, Pérez JA, Fabelo N, Quinto-Alemany D, Díaz ML. Docosahexaenoic (DHA) modulates phospholipid-hydroperoxide glutathione peroxidase (Gpx4) gene expression to ensure self-protection from oxidative damage in hippocampal cells. Front Physiol 2015; 6:203. [PMID: 26257655 PMCID: PMC4510835 DOI: 10.3389/fphys.2015.00203] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/03/2015] [Indexed: 01/31/2023] Open
Abstract
Docosahexaenoic acid (DHA, 22:6n-3) is a unique polyunsaturated fatty acid particularly abundant in nerve cell membrane phospholipids. DHA is a pleiotropic molecule that, not only modulates the physicochemical properties and architecture of neuronal plasma membrane, but it is also involved in multiple facets of neuronal biology, from regulation of synaptic function to neuroprotection and modulation of gene expression. As a highly unsaturated fatty acid due to the presence of six double bonds, DHA is susceptible for oxidation, especially in the highly pro-oxidant environment of brain parenchyma. We have recently reported the ability of DHA to regulate the transcriptional program controlling neuronal antioxidant defenses in a hippocampal cell line, especially the glutathione/glutaredoxin system. Within this antioxidant system, DHA was particularly efficient in triggering the upregulation of Gpx4 gene, which encodes for the nuclear, cytosolic, and mitochondrial isoforms of phospholipid-hydroperoxide glutathione peroxidase (PH-GPx/GPx4), the main enzyme protecting cell membranes against lipid peroxidation and capable to reduce oxidized phospholipids in situ. We show here that this novel property of DHA is also significant in the hippocampus of wild-type mice and, to a lesser extent in APP/PS1 transgenic mice, a familial model of Alzheimer's disease. By doing this, DHA stimulates a mechanism to self-protect from oxidative damage even in the neuronal scenario of high aerobic metabolism and in the presence of elevated levels of transition metals, which inevitably favor the generation of reactive oxygen species. Noticeably, DHA also upregulated a Gpx4 CIRT (Cytoplasmic Intron-sequence Retaining Transcripts), a novel Gpx4 splicing variant, harboring part of the first intronic region, which according to the “sentinel RNA hypothesis” would expand the ability of Gpx4 (and DHA) to provide neuronal antioxidant defense independently of conventional nuclear splicing in cellular compartments, like dendritic zones, located away from nuclear compartment. We discuss here, the crucial role of this novel transcriptional regulation triggered by DHA in the context of normal and pathological hippocampal cell.
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Affiliation(s)
- Verónica Casañas-Sánchez
- Department of Genetics, University Institute of Tropical Diseases and Public Health, University of La Laguna La Laguna, Spain
| | - José A Pérez
- Department of Genetics, University Institute of Tropical Diseases and Public Health, University of La Laguna La Laguna, Spain
| | - Noemí Fabelo
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, University of La Laguna La Laguna, Spain
| | - David Quinto-Alemany
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, University of La Laguna La Laguna, Spain
| | - Mario L Díaz
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, University of La Laguna La Laguna, Spain
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39
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Alternative splicing mechanisms orchestrating post-transcriptional gene expression: intron retention and the intron-rich genome of apicomplexan parasites. Curr Genet 2015; 62:31-8. [PMID: 26194054 DOI: 10.1007/s00294-015-0506-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/09/2015] [Accepted: 07/09/2015] [Indexed: 12/13/2022]
Abstract
Apicomplexan parasites including Toxoplasma gondii and Plasmodium species have complex life cycles that include multiple hosts and differentiation through several morphologically distinct stages requiring marked changes in gene expression. This review highlights emerging evidence implicating regulation of mRNA splicing as a mechanism to prime these parasites for rapid gene expression upon differentiation. We summarize the most important insights in alternative splicing including its role in regulating gene expression by decreasing mRNA abundance via 'Regulated Unproductive Splicing and Translation'. As a related but less well-understood mechanism, we discuss also our recent work suggesting a role for intron retention for precluding translation of stage specific isoforms of T. gondii glycolytic enzymes. We additionally provide new evidence that intron retention might be a widespread mechanism during parasite differentiation. Supporting this notion, recent genome-wide analysis of Toxoplasma and Plasmodium suggests intron retention is more pervasive than heretofore thought. These findings parallel recent emergence of intron retention being more prevalent in mammals than previously believed, thereby adding to the established roles in plants, fungi and unicellular eukaryotes. Deeper mechanistic studies of intron retention will provide important insight into its role in regulating gene expression in apicomplexan parasites and more general in eukaryotic organisms.
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40
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Smalheiser NR. The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0504. [PMID: 25135965 PMCID: PMC4142025 DOI: 10.1098/rstb.2013.0504] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
If mRNAs were the only RNAs made by a neuron, there would be a simple mapping of mRNAs to proteins. However, microRNAs and other non-coding RNAs (ncRNAs; endo-siRNAs, piRNAs, BC1, BC200, antisense and long ncRNAs, repeat-related transcripts, etc.) regulate mRNAs via effects on protein translation as well as transcriptional and epigenetic mechanisms. Not only are genes ON or OFF, but their ability to be translated can be turned ON or OFF at the level of synapses, supporting an enormous increase in information capacity. Here, I review evidence that ncRNAs are expressed pervasively within dendrites in mammalian brain; that some are activity-dependent and highly enriched near synapses; and that synaptic ncRNAs participate in plasticity responses including learning and memory. Ultimately, ncRNAs can be viewed as the post-it notes of the neuron. They have no literal meaning of their own, but derive their functions from where (and to what) they are stuck. This may explain, in part, why ncRNAs differ so dramatically from protein-coding genes, both in terms of the usual indicators of functionality and in terms of evolutionary constraints. ncRNAs do not appear to be direct mediators of synaptic transmission in the manner of neurotransmitters or receptors, yet they orchestrate synaptic plasticity—and may drive species-specific changes in cognition.
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Affiliation(s)
- Neil R Smalheiser
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA
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41
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Mammalian introns: when the junk generates molecular diversity. Int J Mol Sci 2015; 16:4429-52. [PMID: 25710723 PMCID: PMC4394429 DOI: 10.3390/ijms16034429] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 01/14/2023] Open
Abstract
Introns represent almost half of the human genome, yet their vast majority is eliminated from eukaryotic transcripts through RNA splicing. Nevertheless, they feature key elements and functions that deserve further interest. At the level of DNA, introns are genomic segments that can shelter independent transcription units for coding and non-coding RNAs which transcription may interfere with that of the host gene, and regulatory elements that can influence gene expression and splicing itself. From the RNA perspective, some introns can be subjected to alternative splicing. Intron retention appear to provide some plasticity to the nature of the protein produced, its distribution in a given cell type and timing of its translation. Intron retention may also serve as a switch to produce coding or non-coding RNAs from the same transcription unit. Conversely, splicing of introns has been directly implicated in the production of small regulatory RNAs. Hence, splicing of introns also appears to provide plasticity to the type of RNA produced from a genetic locus (coding, non-coding, short or long). We addressed these aspects to add to our understanding of mechanisms that control the fate of introns and could be instrumental in regulating genomic output and hence cell fate.
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42
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Chen FC. Alternative RNA structure-coupled gene regulations in tumorigenesis. Int J Mol Sci 2014; 16:452-75. [PMID: 25551597 PMCID: PMC4307256 DOI: 10.3390/ijms16010452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative RNA structures (ARSs), or alternative transcript isoforms, are critical for regulating cellular phenotypes in humans. In addition to generating functionally diverse protein isoforms from a single gene, ARS can alter the sequence contents of 5'/3' untranslated regions (UTRs) and intronic regions, thus also affecting the regulatory effects of these regions. ARS may introduce premature stop codon(s) into a transcript, and render the transcript susceptible to nonsense-mediated decay, which in turn can influence the overall gene expression level. Meanwhile, ARS can regulate the presence/absence of upstream open reading frames and microRNA targeting sites in 5'UTRs and 3'UTRs, respectively, thus affecting translational efficiencies and protein expression levels. Furthermore, since ARS may alter exon-intron structures, it can influence the biogenesis of intronic microRNAs and indirectly affect the expression of the target genes of these microRNAs. The connections between ARS and multiple regulatory mechanisms underline the importance of ARS in determining cell fate. Accumulating evidence indicates that ARS-coupled regulations play important roles in tumorigenesis. Here I will review our current knowledge in this field, and discuss potential future directions.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan.
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43
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Talhouarne GJS, Gall JG. Lariat intronic RNAs in the cytoplasm of Xenopus tropicalis oocytes. RNA (NEW YORK, N.Y.) 2014; 20:1476-87. [PMID: 25051970 PMCID: PMC4138330 DOI: 10.1261/rna.045781.114] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We previously demonstrated that the oocyte nucleus (germinal vesicle or GV) of Xenopus tropicalis contains a population of stable RNA molecules derived from the introns of most expressed genes. Here we show that similar stable intronic sequence (sis) RNAs occur in the oocyte cytoplasm. About 9000 cytoplasmic sisRNAs have been identified, all of which are resistant to the exonuclease RNase R. About half have been confirmed as lariat molecules and the rest are presumed to be lariats, whereas nuclear sisRNAs are a mixture of lariat and linear molecules. Cytoplasmic sisRNAs are more abundant on a molar basis than nuclear sisRNAs and are derived from short introns, mostly under 1 kb in length. Both nuclear and cytoplasmic sisRNAs are transmitted intact to the egg at GV breakdown and persist until at least the blastula stage of embryogenesis, when zygotic transcription begins. We compared cytoplasmic sisRNAs derived from orthologous genes of X. tropicalis and X. laevis, and found that the specific introns from which sisRNAs are derived are not conserved. The existence of sisRNAs in the cytoplasm of the oocyte, their transmission to the fertilized egg, and their persistence during early embryogenesis suggest that they might play a regulatory role in mRNA translation.
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Affiliation(s)
- Gaëlle J S Talhouarne
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA Department of Biology, Mudd Hall, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA Department of Biology, Mudd Hall, Johns Hopkins University, Baltimore, Maryland 21218, USA
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44
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Casañas-Sánchez V, Pérez JA, Fabelo N, Herrera-Herrera AV, Fernández C, Marín R, González-Montelongo MC, Díaz M. Addition of docosahexaenoic acid, but not arachidonic acid, activates glutathione and thioredoxin antioxidant systems in murine hippocampal HT22 cells: potential implications in neuroprotection. J Neurochem 2014; 131:470-83. [DOI: 10.1111/jnc.12833] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 07/12/2014] [Accepted: 07/21/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Verónica Casañas-Sánchez
- Department of Genetics; University Institute of Tropical Diseases and Public Health; University of La Laguna; Tenerife Spain
| | - José A. Pérez
- Department of Genetics; University Institute of Tropical Diseases and Public Health; University of La Laguna; Tenerife Spain
| | - Noemí Fabelo
- Laboratory of Membrane Physiology and Biophysics; Department of Animal Biology; University of La Laguna; Tenerife Spain
| | | | - Cecilia Fernández
- Laboratory of Cellular Neurobiology; Department of Physiology; University of La Laguna; Tenerife Spain
| | - Raquel Marín
- Laboratory of Cellular Neurobiology; Department of Physiology; University of La Laguna; Tenerife Spain
| | - María C. González-Montelongo
- Laboratory of Membrane Physiology and Biophysics; Department of Animal Biology; University of La Laguna; Tenerife Spain
| | - Mario Díaz
- Laboratory of Membrane Physiology and Biophysics; Department of Animal Biology; University of La Laguna; Tenerife Spain
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45
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Jung H, Gkogkas CG, Sonenberg N, Holt CE. Remote control of gene function by local translation. Cell 2014; 157:26-40. [PMID: 24679524 PMCID: PMC3988848 DOI: 10.1016/j.cell.2014.03.005] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/04/2014] [Accepted: 03/04/2014] [Indexed: 12/12/2022]
Abstract
The subcellular position of a protein is a key determinant of its function. Mounting evidence indicates that RNA localization, where specific mRNAs are transported subcellularly and subsequently translated in response to localized signals, is an evolutionarily conserved mechanism to control protein localization. On-site synthesis confers novel signaling properties to a protein and helps to maintain local proteome homeostasis. Local translation plays particularly important roles in distal neuronal compartments, and dysregulated RNA localization and translation cause defects in neuronal wiring and survival. Here, we discuss key findings in this area and possible implications of this adaptable and swift mechanism for spatial control of gene function.
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Affiliation(s)
- Hosung Jung
- Department of Anatomy, Brain Research Institute, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, South Korea
| | - Christos G Gkogkas
- Patrick Wild Centre, Centre for Integrative Physiology, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada.
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, Anatomy Building, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK.
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