1
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Jiang Y, Conradt B. A genetic screen identifies C. elegans eif-3.H and hrpr-1 as pro-apoptotic genes and potential activators of egl-1 expression. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001126. [PMID: 38434221 PMCID: PMC10905296 DOI: 10.17912/micropub.biology.001126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024]
Abstract
During C. elegans development, 1090 somatic cells are generated of which 131 reproducibly die, many through apoptosis. The C. elegans BH3-only gene egl-1 is the key activator of apoptosis in somatic tissues, and it is predominantly expressed in 'cell death' lineages i.e. lineages in which apoptotic cell death occurs. egl-1 expression is regulated at the transcriptional and post-transcriptional level. For example, we previously showed that the miR-35 and miR-58 families of miRNAs repress egl-1 expression in mothers of 'unwanted' cells by binding to the 3' UTR of egl-1 mRNA, thereby increasing egl-1 mRNA turnover. In a screen for RNA-binding proteins with a role in the post-transcriptional control of egl-1 expression, we identified EIF-3.H (ortholog of human eIF3H) and HRPR-1 (ortholog human hnRNP R/Q) as potential activators of egl-1 expression. In addition, we demonstrate that the knockdown of the eif-3.H or hrpr-1 gene by RNA-mediated interference (RNAi) results in the inappropriate survival of unwanted cells during C. elegans development. Our study provides novel insight into how egl-1 expression is controlled to cause the reproducible pattern of cell death observed during C. elegans development.
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Affiliation(s)
- Yanwen Jiang
- Cell and Developmental Biology, University College London
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2
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Herrejon Chavez F, Luo H, Cifani P, Pine A, Chu KL, Joshi S, Barin E, Schurer A, Chan M, Chang K, Han GYQ, Pierson AJ, Xiao M, Yang X, Kuehm LM, Hong Y, Nguyen DTT, Chiosis G, Kentsis A, Leslie C, Vu LP, Kharas MG. RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nat Commun 2023; 14:2290. [PMID: 37085479 PMCID: PMC10121618 DOI: 10.1038/s41467-023-38001-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Tissue homeostasis is maintained after stress by engaging and activating the hematopoietic stem and progenitor compartments in the blood. Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here, using a conditional knockout mouse model, we revealed that the RNA-binding protein SYNCRIP is required for maintenance of blood homeostasis especially after regenerative stress due to defects in HSCs and progenitors. Mechanistically, we find that SYNCRIP loss results in a failure to maintain proteome homeostasis that is essential for HSC maintenance. SYNCRIP depletion results in increased protein synthesis, a dysregulated epichaperome, an accumulation of misfolded proteins and induces endoplasmic reticulum stress. Additionally, we find that SYNCRIP is required for translation of CDC42 RHO-GTPase, and loss of SYNCRIP results in defects in polarity, asymmetric segregation, and dilution of unfolded proteins. Forced expression of CDC42 recovers polarity and in vitro replating activities of HSCs. Taken together, we uncovered a post-transcriptional regulatory program that safeguards HSC self-renewal capacity and blood homeostasis.
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Affiliation(s)
- Florisela Herrejon Chavez
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alli Pine
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell School of Medical Sciences, New York, NY, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Program of the Weill Cornell Graduate School of Medicine Sciences, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grace Y Q Han
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aspen J Pierson
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Xiao
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Diu T T Nguyen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
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4
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Riccioni V, Trionfetti F, Montaldo C, Garbo S, Marocco F, Battistelli C, Marchetti A, Strippoli R, Amicone L, Cicchini C, Tripodi M. SYNCRIP Modulates the Epithelial-Mesenchymal Transition in Hepatocytes and HCC Cells. Int J Mol Sci 2022; 23:ijms23020913. [PMID: 35055098 PMCID: PMC8780347 DOI: 10.3390/ijms23020913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) control gene expression by acting at multiple levels and are often deregulated in epithelial tumors; however, their roles in the fine regulation of cellular reprogramming, specifically in epithelial–mesenchymal transition (EMT), remain largely unknown. Here, we focused on the hnRNP-Q (also known as SYNCRIP), showing by molecular analysis that in hepatocytes it acts as a “mesenchymal” gene, being induced by TGFβ and modulating the EMT. SYNCRIP silencing limits the induction of the mesenchymal program and maintains the epithelial phenotype. Notably, in HCC invasive cells, SYNCRIP knockdown induces a mesenchymal–epithelial transition (MET), negatively regulating their mesenchymal phenotype and significantly impairing their migratory capacity. In exploring possible molecular mechanisms underlying these observations, we identified a set of miRNAs (i.e., miR-181-a1-3p, miR-181-b1-3p, miR-122-5p, miR-200a-5p, and miR-let7g-5p), previously shown to exert pro- or anti-EMT activities, significantly impacted by SYNCRIP interference during EMT/MET dynamics and gathered insights, suggesting the possible involvement of this RNA binding protein in their transcriptional regulation.
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Affiliation(s)
- Veronica Riccioni
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Flavia Trionfetti
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Claudia Montaldo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Sabrina Garbo
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Francesco Marocco
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Cecilia Battistelli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Alessandra Marchetti
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Raffaele Strippoli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Laura Amicone
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Carla Cicchini
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- Correspondence: (C.C.); (M.T.)
| | - Marco Tripodi
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
- Correspondence: (C.C.); (M.T.)
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5
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Chen S, Miao B, Chen N, Chen C, Shao T, Zhang X, Chang L, Zhang X, Du Q, Huang Y, Tong D. SYNCRIP facilitates porcine parvovirus viral DNA replication through the alternative splicing of NS1 mRNA to promote NS2 mRNA formation. Vet Res 2021; 52:73. [PMID: 34034820 PMCID: PMC8152309 DOI: 10.1186/s13567-021-00938-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/19/2021] [Indexed: 11/10/2022] Open
Abstract
Porcine Parvovirus (PPV), a pathogen causing porcine reproductive disorders, encodes two capsid proteins (VP1 and VP2) and three nonstructural proteins (NS1, NS2 and SAT) in infected cells. The PPV NS2 mRNA is from NS1 mRNA after alternative splicing, yet the corresponding mechanism is unclear. In this study, we identified a PPV NS1 mRNA binding protein SYNCRIP, which belongs to the hnRNP family and has been identified to be involved in host pre-mRNA splicing by RNA-pulldown and mass spectrometry approaches. SYNCRIP was found to be significantly up-regulated by PPV infection in vivo and in vitro. We confirmed that it directly interacts with PPV NS1 mRNA and is co-localized at the cytoplasm in PPV-infected cells. Overexpression of SYNCRIP significantly reduced the NS1 mRNA and protein levels, whereas deletion of SYNCRIP significantly reduced NS2 mRNA and protein levels and the ratio of NS2 to NS1, and further impaired replication of the PPV. Furthermore, we found that SYNCRIP was able to bind the 3'-terminal site of NS1 mRNA to promote the cleavage of NS1 mRNA into NS2 mRNA. Taken together, the results presented here demonstrate that SYNCRIP is a critical molecule in the alternative splicing process of PPV mRNA, while revealing a novel function for this protein and providing a potential target of antiviral intervention for the control of porcine parvovirus disease.
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Affiliation(s)
- Songbiao Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Bichen Miao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Nannan Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Caiyi Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ting Shao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xuezhi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Lingling Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xiujuan Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qian Du
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yong Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
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6
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Identification of RNA-binding proteins that partner with Lin28a to regulate Dnmt3a expression. Sci Rep 2021; 11:2345. [PMID: 33504840 PMCID: PMC7841167 DOI: 10.1038/s41598-021-81429-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/06/2021] [Indexed: 12/28/2022] Open
Abstract
Lin28 is an evolutionary conserved RNA-binding protein that plays important roles during embryonic development and tumorigenesis. It regulates gene expression through two different post-transcriptional mechanisms. The first one is based on the regulation of miRNA biogenesis, in particular that of the let-7 family, whose expression is suppressed by Lin28. Thus, loss of Lin28 leads to the upregulation of mRNAs that are targets of let-7 species. The second mechanism is based on the direct interaction of Lin28 with a large number of mRNAs, which results in the regulation of their translation. This second mechanism remains poorly understood. To address this issue, we purified high molecular weight complexes containing Lin28a in mouse embryonic stem cells (ESCs). Numerous proteins, co-purified with Lin28a, were identified by proteomic procedures and tested for their possible role in Lin28a-dependent regulation of the mRNA encoding DNA methyltransferase 3a (Dnmt3a). The results show that Lin28a activity is dependent on many proteins, including three helicases and four RNA-binding proteins. The suppression of four of these proteins, namely Ddx3x, Hnrnph1, Hnrnpu or Syncrip, interferes with the binding of Lin28a to the Dnmt3a mRNA, thus suggesting that they are part of an oligomeric ribonucleoprotein complex that is necessary for Lin28a activity.
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7
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Chen Y, Chan J, Chen W, Li J, Sun M, Kannan GS, Mok YK, Yuan YA, Jobichen C. SYNCRIP, a new player in pri-let-7a processing. RNA (NEW YORK, N.Y.) 2020; 26:290-305. [PMID: 31907208 PMCID: PMC7025501 DOI: 10.1261/rna.072959.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
microRNAs (miRNAs), a class of small and endogenous molecules that control gene expression, are broadly involved in biological processes. Although a number of cofactors that assist or antagonize let-7 miRNA biogenesis are well-established, more auxiliary factors remain to be investigated. Here, we identified SYNCRIP (Synaptotagmin Binding Cytoplasmic RNA Interacting Protein) as a new player for let-7a miRNA. SYNCRIP interacts with pri-let-7a both in vivo and in vitro. Knockdown of SYNCRIP impairs, while overexpression of SYNCRIP promotes, the expression of let-7a miRNA. A broad miRNA profiling analysis revealed that silencing of SYNCRIP regulates the expression of a set of mature miRNAs positively or negatively. In addition, SYNCRIP is associated with microprocessor complex and promotes the processing of pri-let-7a. Strikingly, the terminal loop of pri-let-7a was shown to be the main contributor for its interaction with SYNCRIP. Functional studies demonstrated that the SYNCRIP RRM2-3 domain can promote the processing of pri-let-7a. Structure-based alignment of RRM2-3 with other RNA binding proteins identified the residues likely to participate in protein-RNA interactions. Taken together, these findings suggest the promising role that SYNCRIP plays in miRNA regulation, thus providing insights into the function of SYNCRIP in eukaryotic development.
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Affiliation(s)
- Ying Chen
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jingru Chan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Wei Chen
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jianwei Li
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Meng Sun
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Gayathiri Sathyamoorthy Kannan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yu-Keung Mok
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yuren Adam Yuan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
- National University of Singapore (Suzhou) Research Institute, Suzhou Industrial Park, Jiangsu 215123, China
| | - Chacko Jobichen
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
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8
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Rizzo F, Nizzardo M, Vashisht S, Molteni E, Melzi V, Taiana M, Salani S, Santonicola P, Di Schiavi E, Bucchia M, Bordoni A, Faravelli I, Bresolin N, Comi GP, Pozzoli U, Corti S. Key role of SMN/SYNCRIP and RNA-Motif 7 in spinal muscular atrophy: RNA-Seq and motif analysis of human motor neurons. Brain 2019; 142:276-294. [PMID: 30649277 PMCID: PMC6351774 DOI: 10.1093/brain/awy330] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 11/03/2018] [Indexed: 12/12/2022] Open
Abstract
Spinal muscular atrophy is a motor neuron disorder caused by mutations in SMN1. The reasons for the selective vulnerability of motor neurons linked to SMN (encoded by SMN1) reduction remain unclear. Therefore, we performed deep RNA sequencing on human spinal muscular atrophy motor neurons to detect specific altered gene splicing/expression and to identify the presence of a common sequence motif in these genes. Many deregulated genes, such as the neurexin and synaptotagmin families, are implicated in critical motor neuron functions. Motif-enrichment analyses of differentially expressed/spliced genes, including neurexin2 (NRXN2), revealed a common motif, motif 7, which is a target of SYNCRIP. Interestingly, SYNCRIP interacts only with full-length SMN, binding and modulating several motor neuron transcripts, including SMN itself. SYNCRIP overexpression rescued spinal muscular atrophy motor neurons, due to the subsequent increase in SMN and their downstream target NRXN2 through a positive loop mechanism and ameliorated SMN-loss-related pathological phenotypes in Caenorhabditis elegans and mouse models. SMN/SYNCRIP complex through motif 7 may account for selective motor neuron degeneration and represent a potential therapeutic target.
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Affiliation(s)
- Federica Rizzo
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Monica Nizzardo
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Shikha Vashisht
- Scientific Institute IRCCS E. MEDEA, Computational Biology, Bosisio Parini, Lecco, Italy
| | - Erika Molteni
- Scientific Institute IRCCS E. MEDEA, Computational Biology, Bosisio Parini, Lecco, Italy
| | - Valentina Melzi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Michela Taiana
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Sabrina Salani
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Elia Di Schiavi
- Institute of Bioscience and BioResources, IBBR, CNR, Naples, Italy
| | - Monica Bucchia
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Andreina Bordoni
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Irene Faravelli
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Nereo Bresolin
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy.,Scientific Institute IRCCS E. MEDEA, Computational Biology, Bosisio Parini, Lecco, Italy
| | - Giacomo Pietro Comi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy.,Scientific Institute IRCCS E. MEDEA, Computational Biology, Bosisio Parini, Lecco, Italy
| | - Uberto Pozzoli
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy.,Scientific Institute IRCCS E. MEDEA, Computational Biology, Bosisio Parini, Lecco, Italy
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9
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Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes. The Central Dogma of Biology schematically highlights the transmission of genetic information stored in DNA, through RNA, to the formation of proteins. This general flow implicates RNA export from the nucleus to the cytoplasm and proper protein localization within the eukaryotic cell. Ultimately, proteins are the cell’s structural and catalytic functional units. As a result, cells differentiate into one cell type or another (such as epithelial, muscle, neuron…) and exhibit specific shape and functionality. Here we describe, in a C. elegans model, how mutations in genes involved in a general and ubiquitous mechanism, such as mRNA export, may result in tissue-specific developmental phenotypes that show up in processes that are highly demanding of cytoplasmic transcripts like epithelialization and gamete formation. A deep understanding of the mechanisms underlying the "connectors" shown in the Central Dogma of Biology is key both to unravel the general genetic control of an organism’s development and, at the same time, contribute to a better understanding of tissue-specific diseases.
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10
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Kotagama K, Schorr AL, Steber HS, Mangone M. ALG-1 Influences Accurate mRNA Splicing Patterns in the Caenorhabditis elegans Intestine and Body Muscle Tissues by Modulating Splicing Factor Activities. Genetics 2019; 212:931-951. [PMID: 31073019 PMCID: PMC6614907 DOI: 10.1534/genetics.119.302223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. To study their contribution to tissue-specific gene expression, we developed novel tools to profile putative miRNA targets in the Caenorhabditis elegans intestine and body muscle. We validated many previously described interactions and identified ∼3500 novel targets. Many of the candidate miRNA targets curated are known to modulate the functions of their respective tissues. Within our data sets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more putative miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA-binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as putative miRNA targets in our study (asd-2, hrp-2, and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3'UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10, and ret-1) is dysregulated when the miRNA pathway is disrupted. A reannotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.
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Affiliation(s)
- Kasuen Kotagama
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Anna L Schorr
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Hannah S Steber
- Barrett, The Honors College, Arizona State University, Tempe, Arizona 85281
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona
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11
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Martinez JR, Dhawan A, Farach-Carson MC. Modular Proteoglycan Perlecan/ HSPG2: Mutations, Phenotypes, and Functions. Genes (Basel) 2018; 9:E556. [PMID: 30453502 PMCID: PMC6266596 DOI: 10.3390/genes9110556] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 02/08/2023] Open
Abstract
Heparan sulfate proteoglycan 2 (HSPG2) is an essential, highly conserved gene whose expression influences many developmental processes including the formation of the heart and brain. The gene is widely expressed throughout the musculoskeletal system including cartilage, bone marrow and skeletal muscle. The HSPG2 gene product, perlecan is a multifunctional proteoglycan that preserves the integrity of extracellular matrices, patrols tissue borders, and controls various signaling pathways affecting cellular phenotype. Given HSPG2's expression pattern and its role in so many fundamental processes, it is not surprising that relatively few gene mutations have been identified in viable organisms. Mutations to the perlecan gene are rare, with effects ranging from a relatively mild condition to a more severe and perinatally lethal form. This review will summarize the important studies characterizing mutations and variants of HSPG2 and discuss how these genomic modifications affect expression, function and phenotype. Additionally, this review will describe the clinical findings of reported HSPG2 mutations and their observed phenotypes. Finally, the evolutionary aspects that link gene integrity to function are discussed, including key findings from both in vivo animal studies and in vitro systems. We also hope to facilitate discussion about perlecan/HSPG2 and its role in normal physiology, to explain how mutation can lead to pathology, and to point out how this information can suggest pathways for future mechanistic studies.
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Affiliation(s)
- Jerahme R Martinez
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Akash Dhawan
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA.
| | - Mary C Farach-Carson
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA.
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12
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Fu R, Zhu Y, Jiang X, Li Y, Zhu M, Dong M, Huang Z, Wang C, Labouesse M, Zhang H. CCAR-1 affects hemidesmosome biogenesis by regulating unc-52/perlecan alternative splicing in the C. elegans epidermis. J Cell Sci 2018; 131:jcs.214379. [PMID: 29748380 DOI: 10.1242/jcs.214379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/02/2018] [Indexed: 12/31/2022] Open
Abstract
Hemidesmosomes are epithelial-specific attachment structures that maintain tissue integrity and resist tension. Despite their importance, how hemidesmosomes are regulated at the post-transcriptional level is poorly understood. Caenorhabditiselegans hemidesmosomes (CeHDs) have a similar structure and composition to their mammalian counterparts, making C. elegans an ideal model for studying hemidesmosomes. Here, we focus on the transcription regulator CCAR-1, identified in a previous genetic screen searching for enhancers of mutations in the conserved hemidesmosome component VAB-10A (known as plectin in mammals). Loss of CCAR-1 function in a vab-10(e698) background results in CeHD disruption and muscle detachment from the epidermis. CCAR-1 regulates CeHD biogenesis, not by controlling the transcription of CeHD-related genes, but by affecting the alternative splicing of unc-52 (known as perlecan or HSPG2 in mammals), the predicted basement extracellular matrix (ECM) ligand of CeHDs. CCAR-1 physically interacts with HRP-2 (hnRNPR in mammals), a splicing factor known to mediate unc-52 alternative splicing to control the proportions of different UNC-52 isoforms and stabilize CeHDs. Our discovery underlines the importance of post-transcriptional regulation in hemidesmosome reorganization. It also uncovers previously unappreciated roles of CCAR-1 in alternative splicing and hemidesmosome biogenesis, shedding new light on the mechanisms through which mammalian CCAR1 functions in tumorigenesis.
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Affiliation(s)
- Rong Fu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yi Zhu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaowan Jiang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yuanbao Li
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Mengqiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhaohui Huang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Chunxia Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Michel Labouesse
- Institut de Biologie Paris Seine, Université Pierre et Marie Curie, Paris 75005, France
| | - Huimin Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
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13
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Hobor F, Dallmann A, Ball NJ, Cicchini C, Battistelli C, Ogrodowicz RW, Christodoulou E, Martin SR, Castello A, Tripodi M, Taylor IA, Ramos A. A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets. Nat Commun 2018; 9:831. [PMID: 29483512 PMCID: PMC5827114 DOI: 10.1038/s41467-018-03182-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/25/2018] [Indexed: 01/18/2023] Open
Abstract
Exosomal miRNA transfer is a mechanism for cell-cell communication that is important in the immune response, in the functioning of the nervous system and in cancer. Syncrip/hnRNPQ is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. Here, we report that Syncrip's amino-terminal domain, which was previously thought to mediate protein-protein interactions, is a cryptic, conserved and sequence-specific RNA-binding domain, designated NURR (N-terminal unit for RNA recognition). The NURR domain mediates the specific recognition of a short hEXO sequence defining Syncrip exosomal miRNA targets, and is coupled by a non-canonical structural element to Syncrip's RRM domains to achieve high-affinity miRNA binding. As a consequence, Syncrip-mediated selection of the target miRNAs implies both recognition of the hEXO sequence by the NURR domain and binding of the RRM domains 5' to this sequence. This structural arrangement enables Syncrip-mediated selection of miRNAs with different seed sequences.
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Affiliation(s)
- Fruzsina Hobor
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andre Dallmann
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Street 2, 12489, Berlin, Germany
| | - Neil J Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Carla Cicchini
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Cecilia Battistelli
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Roksana W Ogrodowicz
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Marco Tripodi
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK.
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14
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Kulkarni S, Ramsuran V, Rucevic M, Singh S, Lied A, Kulkarni V, O'hUigin C, Le Gall S, Carrington M. Posttranscriptional Regulation of HLA-A Protein Expression by Alternative Polyadenylation Signals Involving the RNA-Binding Protein Syncrip. THE JOURNAL OF IMMUNOLOGY 2017; 199:3892-3899. [PMID: 29055006 DOI: 10.4049/jimmunol.1700697] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/25/2017] [Indexed: 01/15/2023]
Abstract
Genomic variation in the untranslated region (UTR) has been shown to influence HLA class I expression level and associate with disease outcomes. Sequencing of the 3'UTR of common HLA-A alleles indicated the presence of two polyadenylation signals (PAS). The proximal PAS is conserved, whereas the distal PAS is disrupted within certain alleles by sequence variants. Using 3'RACE, we confirmed expression of two distinct forms of the HLA-A 3'UTR based on use of either the proximal or the distal PAS, which differ in length by 100 bp. Specific HLA-A alleles varied in the usage of the proximal versus distal PAS, with some alleles using only the proximal PAS, and others using both the proximal and distal PAS to differing degrees. We show that the short and the long 3'UTR produced similar mRNA expression levels. However, the long 3'UTR conferred lower luciferase activity as compared with the short form, indicating translation inhibition of the long 3'UTR. RNA affinity pull-down followed by mass spectrometry analysis as well as RNA coimmunoprecipitation indicated differential binding of Syncrip to the long versus short 3'UTR. Depletion of Syncrip by small interfering RNA increased surface expression of an HLA-A allotype that uses primarily the long 3'UTR, whereas an allotype expressing only the short form was unaffected. Furthermore, specific blocking of the proximal 3'UTR reduced surface expression without decreasing mRNA expression. These data demonstrate HLA-A allele-specific variation in PAS usage, which modulates their cell surface expression posttranscriptionally.
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Affiliation(s)
- Smita Kulkarni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139; .,Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Veron Ramsuran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139.,Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702.,KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.,Centre for the AIDS Programme of Research in South Africa, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; and
| | | | - Sukhvinder Singh
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Alexandra Lied
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Viraj Kulkarni
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227
| | - Colm O'hUigin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139.,Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
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15
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Gracida X, Norris AD, Calarco JA. Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:229-61. [DOI: 10.1007/978-3-319-29073-7_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Wigington CP, Williams KR, Meers MP, Bassell GJ, Corbett AH. Poly(A) RNA-binding proteins and polyadenosine RNA: new members and novel functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:601-22. [PMID: 24789627 PMCID: PMC4332543 DOI: 10.1002/wrna.1233] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/07/2014] [Accepted: 03/06/2014] [Indexed: 02/05/2023]
Abstract
Poly(A) RNA-binding proteins (Pabs) bind with high affinity and specificity to polyadenosine RNA. Textbook models show a nuclear Pab, PABPN1, and a cytoplasmic Pab, PABPC, where the nuclear PABPN1 modulates poly(A) tail length and the cytoplasmic PABPC stabilizes poly(A) RNA in the cytoplasm and also enhances translation. While these conventional roles are critically important, the Pab family has expanded recently both in number and in function. A number of novel roles have emerged for both PAPBPN1 and PABPC that contribute to the fine-tuning of gene expression. Furthermore, as the characterization of the nucleic acid binding properties of RNA-binding proteins advances, additional proteins that show high affinity and specificity for polyadenosine RNA are being discovered. With this expansion of the Pab family comes a concomitant increase in the potential for Pabs to modulate gene expression. Further complication comes from an expansion of the potential binding sites for Pab proteins as revealed by an analysis of templated polyadenosine stretches present within the transcriptome. Thus, Pabs could influence mRNA fate and function not only by binding to the nontemplated poly(A) tail but also to internal stretches of adenosine. Understanding the diverse functions of Pab proteins is not only critical to understand how gene expression is regulated but also to understand the molecular basis for tissue-specific diseases that occur when Pab proteins are altered. Here we describe both conventional and recently emerged functions for PABPN1 and PABPC and then introduce and discuss three new Pab family members, ZC3H14, hnRNP-Q1, and LARP4.
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Affiliation(s)
- Callie P. Wigington
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kathryn R. Williams
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P. Meers
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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17
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Abstract
The RNA-binding protein hnRNP Q has been implicated in neuronal mRNA metabolism. Here, we show that knockdown of hnRNP Q increased neurite complexity in cultured rat cortical neurons and induced filopodium formation in mouse neuroblastoma cells. Reexpression of hnRNP Q1 in hnRNP Q-depleted cells abrogated the morphological changes of neurites, indicating a specific role for hnRNP Q1 in neuronal morphogenesis. A search for mRNA targets of hnRNP Q1 identified functionally coherent sets of mRNAs encoding factors involved in cellular signaling or cytoskeletal regulation and determined its preferred binding sequences. We demonstrated that hnRNP Q1 bound to a set of identified mRNAs encoding the components of the actin nucleation-promoting Cdc42/N-WASP/Arp2/3 complex and was in part colocalized with Cdc42 mRNA in granules. Using subcellular fractionation and immunofluorescence, we showed that knockdown of hnRNP Q reduced the level of some of those mRNAs in neurites and redistributed their encoded proteins from neurite tips to soma to different extents. Overexpression of dominant negative mutants of Cdc42 or N-WASP compromised hnRNP Q depletion-induced neurite complexity. Together, our results suggest that hnRNP Q1 may participate in localization of mRNAs encoding Cdc42 signaling factors in neurites, and thereby may regulate actin dynamics and control neuronal morphogenesis.
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18
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Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA (NEW YORK, N.Y.) 2011; 17:1884-94. [PMID: 21865603 PMCID: PMC3185920 DOI: 10.1261/rna.2696311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 07/08/2011] [Indexed: 05/22/2023]
Abstract
RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5' and 3' splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes.
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Affiliation(s)
- Angela N. Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Julie L. Aspden
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
| | - Anna I. Podgornaia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Donald C. Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Corresponding author.E-mail .
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19
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Abstract
MicroRNAs (miRNAs) are short single-stranded RNA molecules that regulate gene expression. MiRNAs originate from large primary (pri) and precursor (pre) transcripts that undergo various processing steps along their biogenesis pathway till they reach their mature and functional form. It is not clear, however, whether all miRNAs are processed similarly. Here we show that the ratio between pre-miRNA and mature miRNA forms varies between different miRNAs. Moreover, over-expression of several factors involved in miRNA biogenesis, including Exportin-5, Drosha, NF90a, NF45 and KSRP, displayed bidirectional effects on pre/mature miRNA ratios, suggesting their intricate biogenesis sensitivity. In an attempt to identify additional factors that might explain the versatility in miRNA biogenesis we have analyzed the contribution of two hnRNP family members, hnRNPH1 and hnRNPR. Knock-down or over-expression of these genes suggested that hnRNPR inhibits, whereas hnRNPH1 facilitates, miRNA processing. Overall, our results emphasize that miRNA biogenesis is versatile.
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20
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Xie W, Denman RB. Protein methylation and stress granules: posttranslational remodeler or innocent bystander? Mol Biol Int 2011; 2011:137459. [PMID: 22091395 PMCID: PMC3196864 DOI: 10.4061/2011/137459] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 01/10/2011] [Indexed: 01/06/2023] Open
Abstract
Stress granules contain a large number of post-translationally modified proteins, and studies have shown that these modifications serve as recruitment tags for specific proteins and even control the assembly and disassembly of the granules themselves. Work originating from our laboratory has focused on the role protein methylation plays in stress granule composition and function. We have demonstrated that both asymmetrically and symmetrically dimethylated proteins are core constituents of stress granules, and we have endeavored to understand when and how this occurs. Here we seek to integrate this data into a framework consisting of the currently known post-translational modifications affecting stress granules to produce a model of stress granule dynamics that, in turn, may serve as a benchmark for understanding and predicting how post-translational modifications regulate other granule types.
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Affiliation(s)
- Wen Xie
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY 1065, USA
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21
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Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, Lee LJ, Morris Q, Blencowe BJ, Zhen M, Fraser AG. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res 2011; 21:342-8. [PMID: 21177968 PMCID: PMC3032936 DOI: 10.1101/gr.114645.110] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 12/07/2010] [Indexed: 11/24/2022]
Abstract
Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provide the most comprehensive set of annotated splice variants in C. elegans to date, and are therefore expected to facilitate focused, high resolution in vivo functional assays of AS function.
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Affiliation(s)
- Arun K. Ramani
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - John A. Calarco
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Qun Pan
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
| | - Sepand Mavandadi
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
| | - Ying Wang
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrew C. Nelson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, United Kingdom
| | - Leo J. Lee
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
| | - Quaid Morris
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Benjamin J. Blencowe
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Mei Zhen
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrew G. Fraser
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
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22
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Wen J, Chiba A, Cai X. Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq. Nucleic Acids Res 2010; 38:7895-907. [PMID: 20685814 PMCID: PMC3001057 DOI: 10.1093/nar/gkq679] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Tissue-specific alternative splicing is a key mechanism for generating tissue-specific proteomic diversity in eukaryotes. Splicing regulatory elements (SREs) in pre-mature messenger RNA play a very important role in regulating alternative splicing. In this article, we use mouse RNA-Seq data to determine a positive data set where SREs are over-represented and a reliable negative data set where the same SREs are most likely under-represented for a specific tissue and then employ a powerful discriminative approach to identify SREs. We identified 456 putative splicing enhancers or silencers, of which 221 were predicted to be tissue-specific. Most of our tissue-specific SREs are likely different from constitutive SREs, since only 18% of our exonic splicing enhancers (ESEs) are contained in constitutive RESCUE-ESEs. A relatively small portion (20%) of our SREs is included in tissue-specific SREs in human identified in two recent studies. In the analysis of position distribution of SREs, we found that a dozen of SREs were biased to a specific region. We also identified two very interesting SREs that can function as an enhancer in one tissue but a silencer in another tissue from the same intronic region. These findings provide insight into the mechanism of tissue-specific alternative splicing and give a set of valuable putative SREs for further experimental investigations.
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Affiliation(s)
- Ji Wen
- Department of Electrical and Computer Engineering, University of Miami, 1251 Memorial Drive, Coral Gables, FL 33146, USA
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