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Yuan JH, Liu XN, Wang TT, Pan W, Tao QF, Zhou WP, Wang F, Sun SH. The MBNL3 splicing factor promotes hepatocellular carcinoma by increasing PXN expression through the alternative splicing of lncRNA-PXN-AS1. Nat Cell Biol 2017; 19:820-832. [PMID: 28553938 DOI: 10.1038/ncb3538] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/25/2017] [Indexed: 02/07/2023]
Abstract
Understanding the roles of splicing factors and splicing events during tumorigenesis would open new avenues for targeted therapies. Here we identify an oncofetal splicing factor, MBNL3, which promotes tumorigenesis and indicates poor prognosis of hepatocellular carcinoma patients. MBNL3 knockdown almost completely abolishes hepatocellular carcinoma tumorigenesis. Transcriptomic analysis revealed that MBNL3 induces lncRNA-PXN-AS1 exon 4 inclusion. The transcript lacking exon 4 binds to coding sequences of PXN mRNA, causes dissociation of translation elongation factors from PXN mRNA, and thereby inhibits PXN mRNA translation. In contrast, the transcript containing exon 4 preferentially binds to the 3' untranslated region of PXN mRNA, protects PXN mRNA from microRNA-24-AGO2 complex-induced degradation, and thereby increases PXN expression. Through inducing exon 4 inclusion, MBNL3 upregulates PXN, which mediates the pro-tumorigenic roles of MBNL3. Collectively, these data demonstrate detailed mechanistic links between an oncofetal splicing factor, a splicing event and tumorigenesis, and establish splicing factors and splicing events as potential therapeutic targets.
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Affiliation(s)
- Ji-Hang Yuan
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Xiao-Ning Liu
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Tian-Tian Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Wei Pan
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Qi-Fei Tao
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China
| | - Wei-Ping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China
| | - Fang Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Shu-Han Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
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202
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Rajman M, Metge F, Fiore R, Khudayberdiev S, Aksoy-Aksel A, Bicker S, Ruedell Reschke C, Raoof R, Brennan GP, Delanty N, Farrell MA, O'Brien DF, Bauer S, Norwood B, Veno MT, Krüger M, Braun T, Kjems J, Rosenow F, Henshall DC, Dieterich C, Schratt G. A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses. EMBO J 2017; 36:1770-1787. [PMID: 28487411 DOI: 10.15252/embj.201695748] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
Synaptic downscaling is a homeostatic mechanism that allows neurons to reduce firing rates during chronically elevated network activity. Although synaptic downscaling is important in neural circuit development and epilepsy, the underlying mechanisms are poorly described. We performed small RNA profiling in picrotoxin (PTX)-treated hippocampal neurons, a model of synaptic downscaling. Thereby, we identified eight microRNAs (miRNAs) that were increased in response to PTX, including miR-129-5p, whose inhibition blocked synaptic downscaling in vitro and reduced epileptic seizure severity in vivo Using transcriptome, proteome, and bioinformatic analysis, we identified the calcium pump Atp2b4 and doublecortin (Dcx) as miR-129-5p targets. Restoring Atp2b4 and Dcx expression was sufficient to prevent synaptic downscaling in PTX-treated neurons. Furthermore, we characterized a functional crosstalk between miR-129-5p and the RNA-binding protein (RBP) Rbfox1. In the absence of PTX, Rbfox1 promoted the expression of Atp2b4 and Dcx. Upon PTX treatment, Rbfox1 expression was downregulated by miR-129-5p, thereby allowing the repression of Atp2b4 and Dcx. We therefore identified a novel activity-dependent miRNA/RBP crosstalk during synaptic scaling, with potential implications for neural network homeostasis and epileptogenesis.
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Affiliation(s)
- Marek Rajman
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Franziska Metge
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, German Center for Cardiovascular Research (DZHK), University Hospital Heidelberg, Heidelberg, Germany
| | - Roberto Fiore
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Sharof Khudayberdiev
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ayla Aksoy-Aksel
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Silvia Bicker
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Rana Raoof
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gary P Brennan
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | | | - Sebastian Bauer
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Braxton Norwood
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Morten T Veno
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Marcus Krüger
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Felix Rosenow
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - David C Henshall
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, German Center for Cardiovascular Research (DZHK), University Hospital Heidelberg, Heidelberg, Germany
| | - Gerhard Schratt
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
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203
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Morriss GR, Cooper TA. Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Hum Genet 2017; 136:1247-1263. [PMID: 28484853 DOI: 10.1007/s00439-017-1807-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/28/2017] [Indexed: 12/12/2022]
Abstract
An emerging class of long noncoding RNAs (lncRNAs) function as decoy molecules that bind and sequester proteins thereby inhibiting their normal functions. Titration of proteins by lncRNAs has wide-ranging effects affecting nearly all steps in gene expression. While decoy lncRNAs play a role in normal physiology, RNAs expressed from alleles containing nucleotide repeat expansions can be pathogenic due to protein sequestration resulting in disruption of normal functions. This review focuses on commonalities between decoy lncRNAs that regulate gene expression by competitive inhibition of protein function through sequestration and specific examples of nucleotide repeat expansion disorders mediated by toxic RNA that sequesters RNA-binding proteins and impedes their normal functions. Understanding how noncoding RNAs compete with various RNA and DNA molecules for binding of regulatory proteins will provide insight into how similar mechanisms contribute to disease pathogenesis.
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Affiliation(s)
- Ginny R Morriss
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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204
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Faulty RNA splicing: consequences and therapeutic opportunities in brain and muscle disorders. Hum Genet 2017; 136:1215-1235. [DOI: 10.1007/s00439-017-1802-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
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205
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Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
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Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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206
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Donlin-Asp PG, Rossoll W, Bassell GJ. Spatially and temporally regulating translation via mRNA-binding proteins in cellular and neuronal function. FEBS Lett 2017; 591:1508-1525. [PMID: 28295262 DOI: 10.1002/1873-3468.12621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/20/2022]
Abstract
Coordinated regulation of mRNA localization and local translation are essential steps in cellular asymmetry and function. It is increasingly evident that mRNA-binding proteins play critical functions in controlling the fate of mRNA, including when and where translation occurs. In this review, we discuss the robust and complex roles that mRNA-binding proteins play in the regulation of local translation that impact cellular function in vertebrates. First, we discuss the role of local translation in cellular polarity and possible links to vertebrate development and patterning. Next, we discuss the expanding role for local protein synthesis in neuronal development and function, with special focus on how a number of neurological diseases have given us insight into the importance of translational regulation. Finally, we discuss the ever-increasing set of tools to study regulated translation and how these tools will be vital in pushing forward and addressing the outstanding questions in the field.
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Affiliation(s)
- Paul G Donlin-Asp
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Wilfried Rossoll
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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207
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Antisense Oligonucleotides Promote Exon Inclusion and Correct the Common c.-32-13T>G GAA Splicing Variant in Pompe Disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624228 PMCID: PMC5415969 DOI: 10.1016/j.omtn.2017.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The most common variant causing Pompe disease is c.-32-13T>G (IVS1) in the acid α-glucosidase (GAA) gene, which weakens the splice acceptor of GAA exon 2 and induces partial and complete exon 2 skipping. It also allows a low level of leaky wild-type splicing, leading to a childhood/adult phenotype. We hypothesized that cis-acting splicing motifs may exist that could be blocked using antisense oligonucleotides (AONs) to promote exon inclusion. To test this, a screen was performed in patient-derived primary fibroblasts using a tiling array of U7 small nuclear RNA (snRNA)-based AONs. This resulted in the identification of a splicing regulatory element in GAA intron 1. We designed phosphorodiamidate morpholino oligomer-based AONs to this element, and these promoted exon 2 inclusion and enhanced GAA enzyme activity to levels above the disease threshold. These results indicate that the common IVS1 GAA splicing variant in Pompe disease is subject to negative regulation, and inhibition of a splicing regulatory element using AONs is able to restore canonical GAA splicing and endogenous GAA enzyme activity.
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208
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Zhang Z, Lu L, Zhang Y, Hua Li C, Wang CX, Zhang XY, Tan JJ. A combinatorial scoring function for protein-RNA docking. Proteins 2017; 85:741-752. [PMID: 28120375 DOI: 10.1002/prot.25253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
Protein-RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near-native structures from the incorrect ones. To solve the problem, we have constructed a knowledge-based residue-nucleotide pairwise potential with secondary structure information considered for nonribosomal protein-RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics-based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics-based method derived potential ITScore-PR, and the united atom-based statistical potentials QUASI-RNP and DARS-RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near-native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long-range electrostatic attractive energy plays an important role in distinguishing near-native structures from the incorrect ones. This work can be helpful for the development of protein-RNA docking methods and for the understanding of protein-RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741-752. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhao Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Lin Lu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Yue Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Cun Xin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Xiao Yi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Jian Jun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
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209
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deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA. Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility. J Biol Chem 2017; 292:4350-4357. [PMID: 28130447 DOI: 10.1074/jbc.m116.770768] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/25/2017] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 2 is a genetic neuromuscular disease caused by the expression of expanded CCUG repeat RNAs from the non-coding region of the CCHC-type zinc finger nucleic acid-binding protein (CNBP) gene. These CCUG repeats bind and sequester a family of RNA-binding proteins known as Muscleblind-like 1, 2, and 3 (MBNL1, MBNL2, and MBNL3), and sequestration plays a significant role in pathogenicity. MBNL proteins are alternative splicing regulators that bind to the consensus RNA sequence YGCY (Y = pyrimidine). This consensus sequence is found in the toxic RNAs (CCUG repeats) and in cellular RNA substrates that MBNL proteins have been shown to bind. Replacing the uridine in CCUG repeats with pseudouridine (Ψ) resulted in a modest reduction of MBNL1 binding. Interestingly, Ψ modification of a minimally structured RNA containing YGCY motifs resulted in more robust inhibition of MBNL1 binding. The different levels of inhibition between CCUG repeat and minimally structured RNA binding appear to be due to the ability to modify both pyrimidines in the YGCY motif, which is not possible in the CCUG repeats. Molecular dynamic studies of unmodified and pseudouridylated minimally structured RNAs suggest that reducing the flexibility of the minimally structured RNA leads to reduced binding by MBNL1.
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Affiliation(s)
- Elaine deLorimier
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - Melissa N Hinman
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - Jeremy Copperman
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - Kausiki Datta
- the Center for NeuroGenetics, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610-3010
| | - Marina Guenza
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - J Andrew Berglund
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and .,the Center for NeuroGenetics, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610-3010
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210
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Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol 2016; 13:188-193. [PMID: 27941760 DOI: 10.1038/nchembio.2251] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023]
Abstract
Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context.
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211
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Gómez-Salinero JM, López-Olañeta MM, Ortiz-Sánchez P, Larrasa-Alonso J, Gatto A, Felkin LE, Barton PJR, Navarro-Lérida I, Del Pozo MÁ, García-Pavía P, Sundararaman B, Giovinazo G, Yeo GW, Lara-Pezzi E. The Calcineurin Variant CnAβ1 Controls Mouse Embryonic Stem Cell Differentiation by Directing mTORC2 Membrane Localization and Activation. Cell Chem Biol 2016; 23:1372-1382. [PMID: 27746127 DOI: 10.1016/j.chembiol.2016.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 08/28/2016] [Accepted: 09/02/2016] [Indexed: 12/11/2022]
Abstract
Embryonic stem cells (ESC) have the potential to generate all the cell lineages that form the body. However, the molecular mechanisms underlying ESC differentiation and especially the role of alternative splicing in this process remain poorly understood. Here, we show that the alternative splicing regulator MBNL1 promotes generation of the atypical calcineurin Aβ variant CnAβ1 in mouse ESCs (mESC). CnAβ1 has a unique C-terminal domain that drives its localization mainly to the Golgi apparatus by interacting with Cog8. CnAβ1 regulates the intracellular localization and activation of the mTORC2 complex. CnAβ1 knockdown results in delocalization of mTORC2 from the membrane to the cytoplasm, inactivation of the AKT/GSK3β/β-catenin signaling pathway, and defective mesoderm specification. In summary, here we unveil the structural basis for the mechanism of action of CnAβ1 and its role in the differentiation of mESCs to the mesodermal lineage.
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Affiliation(s)
- Jesús M Gómez-Salinero
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Marina M López-Olañeta
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Paula Ortiz-Sánchez
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Larrasa-Alonso
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Alberto Gatto
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK; NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust, London SW7 2AZ, UK
| | - Inmaculada Navarro-Lérida
- Vascular Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Miguel Ángel Del Pozo
- Vascular Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Pablo García-Pavía
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain
| | - Balaji Sundararaman
- Sanford Consortium for Regenerative Medicine, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - Giovanna Giovinazo
- Pluripotent Cell Technology Unit, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Gene W Yeo
- Sanford Consortium for Regenerative Medicine, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - Enrique Lara-Pezzi
- Myocardial Pathophysiology Program, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK.
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212
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Danan-Gotthold M, Guyon C, Giraud M, Levanon EY, Abramson J. Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells. Genome Biol 2016; 17:219. [PMID: 27776542 PMCID: PMC5078920 DOI: 10.1186/s13059-016-1079-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/05/2016] [Indexed: 01/28/2023] Open
Abstract
Background In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. This educational program is, to a large extent, mediated by medullary thymic epithelial cells that have a unique capacity to express, and subsequently present, a large fraction of body antigens. While the scope of promiscuously expressed genes by medullary thymic epithelial cells is well-established, relatively little is known about the expression of variants that are generated by co-transcriptional and post-transcriptional processes. Results Our study reveals that in comparison to other cell types, medullary thymic epithelial cells display significantly higher levels of alternative splicing, as well as A-to-I and C-to-U RNA editing, which thereby further expand the diversity of their self-antigen repertoire. Interestingly, Aire, the key mediator of promiscuous gene expression in these cells, plays a limited role in the regulation of these transcriptional processes. Conclusions Our results highlight RNA processing as another layer by which the immune system assures a comprehensive self-representation in the thymus which is required for the establishment of self-tolerance and prevention of autoimmunity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1079-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Clotilde Guyon
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Matthieu Giraud
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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213
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Sznajder ŁJ, Michalak M, Taylor K, Cywoniuk P, Kabza M, Wojtkowiak-Szlachcic A, Matłoka M, Konieczny P, Sobczak K. Mechanistic determinants of MBNL activity. Nucleic Acids Res 2016; 44:10326-10342. [PMID: 27733504 PMCID: PMC5137450 DOI: 10.1093/nar/gkw915] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are critical RNA processing factors in development. MBNL activity is disrupted in the neuromuscular disease myotonic dystrophy type 1 (DM1), due to the instability of a non-coding microsatellite in the DMPK gene and the expression of CUG expansion (CUGexp) RNAs. Pathogenic interactions between MBNL and CUGexp RNA lead to the formation of nuclear complexes termed foci and prevent MBNL function in pre-mRNA processing. The existence of multiple MBNL genes, as well as multiple protein isoforms, raises the question of whether different MBNL proteins possess unique or redundant functions. To address this question, we coexpressed three MBNL paralogs in cells at equivalent levels and characterized both specific and redundant roles of these proteins in alternative splicing and RNA foci dynamics. When coexpressed in the same cells, MBNL1, MBNL2 and MBNL3 bind the same RNA motifs with different affinities. While MBNL1 demonstrated the highest splicing activity, MBNL3 showed the lowest. When forming RNA foci, MBNL1 is the most mobile paralog, while MBNL3 is rather static and the most densely packed on CUGexp RNA. Therefore, our results demonstrate that MBNL paralogs and gene-specific isoforms possess inherent functional differences, an outcome that could be enlisted to improve therapeutic strategies for DM1.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Michalak
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Kabza
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Agnieszka Wojtkowiak-Szlachcic
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Magdalena Matłoka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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214
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Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB. RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation. Mol Cell 2016; 64:294-306. [PMID: 27720642 DOI: 10.1016/j.molcel.2016.08.035] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/01/2016] [Accepted: 08/30/2016] [Indexed: 10/20/2022]
Abstract
Many RNA binding proteins (RBPs) bind specific RNA sequence motifs, but only a small fraction (∼15%-40%) of RBP motif occurrences are occupied in vivo. To determine which contextual features discriminate between bound and unbound motifs, we performed an in vitro binding assay using 12,000 mouse RNA sequences with the RBPs MBNL1 and RBFOX2. Surprisingly, the strength of binding to motif occurrences in vitro was significantly correlated with in vivo binding, developmental regulation, and evolutionary age of alternative splicing. Multiple lines of evidence indicate that the primary context effect that affects binding in vitro and in vivo is RNA secondary structure. Large-scale combinatorial mutagenesis of unfavorable sequence contexts revealed a consistent pattern whereby mutations that increased motif accessibility improved protein binding and regulatory activity. Our results indicate widespread inhibition of motif binding by local RNA secondary structure and suggest that mutations that alter sequence context commonly affect RBP binding and regulation.
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Affiliation(s)
- J Matthew Taliaferro
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nicole J Lambert
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Peter H Sudmant
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Daniel Dominguez
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jason J Merkin
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maria S Alexis
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Cassandra Bazile
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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215
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Hartley SW, Mullikin JC, Klein DC, Park M, Coon SL. Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation. PLoS One 2016; 11:e0163590. [PMID: 27684375 PMCID: PMC5042479 DOI: 10.1371/journal.pone.0163590] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/12/2016] [Indexed: 01/23/2023] Open
Abstract
Alternative isoform regulation (AIR) vastly increases transcriptome diversity and plays an important role in numerous biological processes and pathologies. However, the detection and analysis of isoform-level differential regulation is difficult, particularly in the face of complex and incompletely-annotated transcriptomes. Here we have used Illumina short-read/high-throughput RNA-Seq to identify 55 genes that exhibit neurally-regulated AIR in the pineal gland, and then used two other complementary experimental platforms to further study and characterize the Ttc8 gene, which is involved in Bardet-Biedl syndrome and non-syndromic retinitis pigmentosa. Use of the JunctionSeq analysis tool led to the detection of several novel exons and splice junctions in this gene, including two novel alternative transcription start sites which were found to display disproportionately strong neurally-regulated differential expression in several independent experiments. These high-throughput sequencing results were validated and augmented via targeted qPCR and long-read Pacific Biosciences SMRT sequencing. We confirmed the existence of numerous novel splice junctions and the selective upregulation of the two novel start sites. In addition, we identified more than 20 novel isoforms of the Ttc8 gene that are co-expressed in this tissue. By using information from multiple independent platforms we not only greatly reduce the risk of errors, biases, and artifacts influencing our results, we also are able to characterize the regulation and splicing of the Ttc8 gene more deeply and more precisely than would be possible via any single platform. The hybrid method outlined here represents a powerful strategy in the study of the transcriptome.
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Affiliation(s)
- Stephen W. Hartley
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
| | - James C. Mullikin
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - David C. Klein
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Morgan Park
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, 20852, United States of America
| | - NISC Comparative Sequencing Program
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, 20852, United States of America
| | - Steven L. Coon
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
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216
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Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy. PLoS Genet 2016; 12:e1006316. [PMID: 27681373 PMCID: PMC5082313 DOI: 10.1371/journal.pgen.1006316] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 08/23/2016] [Indexed: 01/23/2023] Open
Abstract
Alternative splicing is a regulated process that results in expression of
specific mRNA and protein isoforms. Alternative splicing factors determine the
relative abundance of each isoform. Here we focus on MBNL1, a splicing factor
misregulated in the disease myotonic dystrophy. By altering the concentration of
MBNL1 in cells across a broad dynamic range, we show that different splicing
events require different amounts of MBNL1 for half-maximal response, and respond
more or less steeply to MBNL1. Motifs around MBNL1 exon 5 were studied to assess
how cis-elements mediate the MBNL1 dose-dependent splicing
response. A framework was developed to estimate MBNL concentration using
splicing responses alone, validated in the cell-based model, and applied to
myotonic dystrophy patient muscle. Using this framework, we evaluated the
ability of individual and combinations of splicing events to predict functional
MBNL concentration in human biopsies, as well as their performance as biomarkers
to assay mild, moderate, and severe cases of DM. Our studies provide insight into the mechanisms of myotonic dystrophy, the most
common adult form of muscular dystrophy. In this disease, a family of RNA
binding proteins is sequestered by toxic RNA, which leads to mis-regulation and
disease symptoms. We have created a cellular model with one of these family
members to study how these RNA binding proteins function in the absence of the
toxic RNA. In parallel, we analyzed transcriptomic data from over 50 individuals
(44 affected by myotonic dystrophy) with a range of disease severity. The
results from the transcriptomic data provide a rational approach to select
biomarkers for clinical research and therapeutic trials.
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217
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Jazurek M, Ciesiolka A, Starega-Roslan J, Bilinska K, Krzyzosiak WJ. Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases. Nucleic Acids Res 2016; 44:9050-9070. [PMID: 27625393 PMCID: PMC5100574 DOI: 10.1093/nar/gkw803] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
RNA–protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA–protein networks. Extensive efforts have been made to purify in vivo-assembled RNA–protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA–protein interactions that result in the development of many neurological diseases.
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Affiliation(s)
- Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Bilinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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218
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Oddo JC, Saxena T, McConnell OL, Berglund JA, Wang ET. Conservation of context-dependent splicing activity in distant Muscleblind homologs. Nucleic Acids Res 2016; 44:8352-62. [PMID: 27557707 PMCID: PMC5041496 DOI: 10.1093/nar/gkw735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/11/2016] [Indexed: 12/15/2022] Open
Abstract
The Muscleblind (MBL) protein family is a deeply conserved family of RNA binding proteins that regulate alternative splicing, alternative polyadenylation, RNA stability and RNA localization. Their inactivation due to sequestration by expanded CUG repeats causes symptoms in the neuromuscular disease myotonic dystrophy. MBL zinc fingers are the most highly conserved portion of these proteins, and directly interact with RNA. We identified putative MBL homologs in Ciona intestinalis and Trichoplax adhaerens, and investigated their ability, as well as that of MBL homologs from human/mouse, fly and worm, to regulate alternative splicing. We found that all homologs can regulate alternative splicing in mouse cells, with some regulating over 100 events. The cis-elements through which each homolog exerts its splicing activities are likely to be highly similar to mammalian Muscleblind-like proteins (MBNLs), as suggested by motif analyses and the ability of expanded CUG repeats to inactivate homolog-mediated splicing. While regulation of specific target exons by MBL/MBNL has not been broadly conserved across these species, genes enriched for MBL/MBNL binding sites in their introns may play roles in cell adhesion, ion transport and axon guidance, among other biological pathways, suggesting a specific, conserved role for these proteins across a broad range of metazoan species.
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Affiliation(s)
- Julia C Oddo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tanvi Saxena
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Ona L McConnell
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - J Andrew Berglund
- Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA Department of Chemistry and Biochemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Eric T Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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219
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Murphy D, Cieply B, Carstens R, Ramamurthy V, Stoilov P. The Musashi 1 Controls the Splicing of Photoreceptor-Specific Exons in the Vertebrate Retina. PLoS Genet 2016; 12:e1006256. [PMID: 27541351 PMCID: PMC4991804 DOI: 10.1371/journal.pgen.1006256] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/22/2016] [Indexed: 01/08/2023] Open
Abstract
Alternative pre-mRNA splicing expands the coding capacity of eukaryotic genomes, potentially enabling a limited number of genes to govern the development of complex anatomical structures. Alternative splicing is particularly prevalent in the vertebrate nervous system, where it is required for neuronal development and function. Here, we show that photoreceptor cells, a type of sensory neuron, express a characteristic splicing program that affects a broad set of transcripts and is initiated prior to the development of the light sensing outer segments. Surprisingly, photoreceptors lack prototypical neuronal splicing factors and their splicing profile is driven to a significant degree by the Musashi 1 (MSI1) protein. A striking feature of the photoreceptor splicing program are exons that display a "switch-like" pattern of high inclusion levels in photoreceptors and near complete exclusion outside of the retina. Several ubiquitously expressed genes that are involved in the biogenesis and function of primary cilia produce highly photoreceptor specific isoforms through use of such "switch-like" exons. Our results suggest a potential role for alternative splicing in the development of photoreceptors and the conversion of their primary cilia to the light sensing outer segments.
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Affiliation(s)
- Daniel Murphy
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Benjamin Cieply
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Russ Carstens
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Visvanathan Ramamurthy
- Departments of Biochemistry, Ophthalmology and Center for Neuroscience, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Peter Stoilov
- Department of Biochemistry and Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
- * E-mail:
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220
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Carrell ST, Carrell EM, Auerbach D, Pandey SK, Bennett CF, Dirksen RT, Thornton CA. Dmpk gene deletion or antisense knockdown does not compromise cardiac or skeletal muscle function in mice. Hum Mol Genet 2016; 25:4328-4338. [PMID: 27522499 DOI: 10.1093/hmg/ddw266] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 11/13/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a genetic disorder in which dominant-active DM protein kinase (DMPK) transcripts accumulate in nuclear foci, leading to abnormal regulation of RNA processing. A leading approach to treat DM1 uses DMPK-targeting antisense oligonucleotides (ASOs) to reduce levels of toxic RNA. However, basal levels of DMPK protein are reduced by half in DM1 patients. This raises concern that intolerance for further DMPK loss may limit ASO therapy, especially since mice with Dmpk gene deletion reportedly show cardiac defects and skeletal myopathy. We re-examined cardiac and muscle function in mice with Dmpk gene deletion, and studied post-maturity knockdown using Dmpk-targeting ASOs in mice with heterozygous deletion. Contrary to previous reports, we found no effect of Dmpk gene deletion on cardiac or muscle function, when studied on two genetic backgrounds. In heterozygous knockouts, the administration of ASOs reduced Dmpk expression in cardiac and skeletal muscle by > 90%, yet survival, electrocardiogram intervals, cardiac ejection fraction and muscle strength remained normal. The imposition of cardiac stress by pressure overload, or muscle stress by myotonia, did not unmask a requirement for DMPK. Our results support the feasibility and safety of using ASOs for post-transcriptional silencing of DMPK in muscle and heart.
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Affiliation(s)
| | | | | | | | | | | | - Charles A Thornton
- Department of Neurology, University of Rochester, Rochester, New York, NY, USA and
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221
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Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N. Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. eLife 2016; 5. [PMID: 27502555 PMCID: PMC4978528 DOI: 10.7554/elife.16797] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
In contrast to transcriptional regulation, the function of alternative splicing (AS) in stem cells is poorly understood. In mammals, MBNL proteins negatively regulate an exon program specific of embryonic stem cells; however, little is known about the in vivo significance of this regulation. We studied AS in a powerful in vivo model for stem cell biology, the planarian Schmidtea mediterranea. We discover a conserved AS program comprising hundreds of alternative exons, microexons and introns that is differentially regulated in planarian stem cells, and comprehensively identify its regulators. We show that functional antagonism between CELF and MBNL factors directly controls stem cell-specific AS in planarians, placing the origin of this regulatory mechanism at the base of Bilaterians. Knockdown of CELF or MBNL factors lead to abnormal regenerative capacities by affecting self-renewal and differentiation sets of genes, respectively. These results highlight the importance of AS interactions in stem cell regulation across metazoans. DOI:http://dx.doi.org/10.7554/eLife.16797.001 Stem cells are specialized cells found in all animals that can develop into several different types of mature cells. Stem cells are therefore well suited for maintaining organs that are in heavy use, such as the intestine, and for regenerating tissues that are prone to injury, like the skin. One reason why stem cells differ from mature cell types is because they activate, or “express”, different sets of genes. In addition, many genes can be expressed as one of several versions. These variants, also known as isoforms, are generated by a process called alternative splicing. In mature cells in mammals, a group of proteins called the MBNL proteins help to prevent the expression of gene isoforms that are characteristic to stem cells. The adult flatworm Schmidtea mediterranea contains stem cells that can regenerate any part of the body. Solana, Irimia et al. have now investigated whether alternative splicing is important for controlling how the worm’s stem cells behave. After establishing which gene isoforms are expressed in the stem cells and the mature cells, the levels of different sets of proteins that control alternative splicing were experimentally reduced. The results indicate that just as seen in mammals, the MBNL proteins reduce the expression of stem cell-related gene isoforms in the flatworms. Furthermore, Solana, Irimia et al. found that another protein called CELF counteracts MBNL proteins by helping to express gene isoforms that are active in stem cells. The interplay between the MBNL and CELF proteins has also been observed in human cells. Thus, it appears that this way of controlling alternative splicing is common to flatworms and mammals and is therefore evolutionarily ancient. This suggests that other similar ways of controlling stem cells by interactions between regulatory proteins might be working in all animal stem cells. Further studies are now needed to investigate these control proteins. DOI:http://dx.doi.org/10.7554/eLife.16797.002
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Affiliation(s)
- Jordi Solana
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Salah Ayoub
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marta Rodriguez Orejuela
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Vera Zywitza
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Javier Tapial
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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222
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Choi J, Dixon DM, Dansithong W, Abdallah WF, Roos KP, Jordan MC, Trac B, Lee HS, Comai L, Reddy S. Muscleblind-like 3 deficit results in a spectrum of age-associated pathologies observed in myotonic dystrophy. Sci Rep 2016; 6:30999. [PMID: 27484195 PMCID: PMC4971533 DOI: 10.1038/srep30999] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/11/2016] [Indexed: 01/20/2023] Open
Abstract
Myotonic dystrophy type I (DM1) exhibits distinctive disease specific phenotypes and the accelerated onset of a spectrum of age-associated pathologies. In DM1, dominant effects of expanded CUG repeats result in part from the inactivation of the muscleblind-like (MBNL) proteins. To test the role of MBNL3, we deleted Mbnl3 exon 2 (Mbnl3(ΔE2)) in mice and examined the onset of age-associated diseases over 4 to 13 months of age. Accelerated onset of glucose intolerance with elevated insulin levels, cardiac systole deficits, left ventricle hypertrophy, a predictor of a later onset of heart failure and the development of subcapsular and cortical cataracts is observed in Mbnl3(ΔE2) mice. Retention of embryonic splice isoforms in adult organs, a prominent defect in DM1, is not observed in multiple RNAs including the Insulin Receptor (Insr), Cardiac Troponin T (Tnnt2), Lim Domain Binding 3 (Ldb3) RNAs in Mbnl3(ΔE2) mice. Although rare DM1-like splice errors underlying the observed phenotypes cannot be excluded, our data in conjunction with the reported absence of alternative splice errors in embryonic muscles of a similar Mbnl3(ΔE2) mouse by RNA-seq studies, suggest that mechanisms distinct from the adult retention of embryonic splice patterns may make important contributions to the onset of age-associated pathologies in DM1.
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Affiliation(s)
- Jongkyu Choi
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Donald M Dixon
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Warunee Dansithong
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Walid F Abdallah
- USC Eye Institute, Los Angeles, CA 90033, USA.,Department of Ophthalmology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Kenneth P Roos
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1751, USA
| | - Maria C Jordan
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1751, USA
| | - Brandon Trac
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Han Shin Lee
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Lucio Comai
- Department of Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Sita Reddy
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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223
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Gopinath G, Arunkumar KP, Mita K, Nagaraju J. Role of Bmznf-2, a Bombyx mori CCCH zinc finger gene, in masculinisation and differential splicing of Bmtra-2. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 75:32-44. [PMID: 27260399 DOI: 10.1016/j.ibmb.2016.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 06/05/2023]
Abstract
Deciphering the regulatory factors involved in Bombyx mori sex determination has been a puzzle, challenging researchers for nearly a century now. The pre-mRNA of B. mori doublesex (Bmdsx), a master regulator gene of sexual differentiation, is differentially spliced, producing Bmdsxm and Bmdsxf transcripts in males and females respectively. The putative proteins encoded by these differential transcripts orchestrate antagonistic functions, which lead to sexual differentiation. A recent study in B. mori illustrated the role of a W-derived fem piRNA in conferring femaleness. In females, the fem piRNA was shown to suppress the activity of a Z-linked CCCH type zinc finger (znf) gene, Masculiniser (masc), which indirectly promotes the Bmdsxm type of splicing. In this study, we report a novel autosomal (Chr 25) CCCH type znf motif encoding gene Bmznf-2 as one of the potential factors in the Bmdsx sex specific differential splicing, and we also provide insights into its role in the alternative splicing of Bmtra2 by using ovary derived BmN cells. Over-expression of Bmznf-2 induced Bmdsxm type of splicing (masculinisation) with a correspondingly reduced expression of Bmdsxf type isoform in BmN cells. Further, the site-directed mutational studies targeting the tandem CCCH znf motifs revealed their indispensability in the observed phenotype of masculinisation. Additionally, the dual luciferase assays in BmN cells using 5' UTR region of the Bmznf-2 strongly implied the existence of a translational repression over this gene. From these findings, we propose Bmznf-2 to be one of the potential factors of masculinisation similar to Masc. From the growing number of Bmdsx splicing regulators, we assume that the sex determination cascade of B. mori is quite intricate in nature; hence, it has to be further investigated for its comprehensive understanding.
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Affiliation(s)
- Gajula Gopinath
- Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500001, India.
| | - Kallare P Arunkumar
- Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500001, India.
| | - Kazuei Mita
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Javaregowda Nagaraju
- Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500001, India
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224
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Stempien-Otero A, Kim DH, Davis J. Molecular networks underlying myofibroblast fate and fibrosis. J Mol Cell Cardiol 2016; 97:153-61. [PMID: 27167848 PMCID: PMC5482716 DOI: 10.1016/j.yjmcc.2016.05.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 01/06/2023]
Abstract
Fibrotic remodeling is a hallmark of most forms of cardiovascular disease and a strong prognostic indicator of the advancement towards heart failure. Myofibroblasts, which are a heterogeneous cell-type specialized for extracellular matrix (ECM) secretion and tissue contraction, are the primary effectors of the heart's fibrotic response. This review is focused on defining myofibroblast physiology, its progenitor cell populations, and the core signaling network that orchestrates myofibroblast differentiation as a way of understanding the basic determinants of fibrotic disease in the heart and other tissues.
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Affiliation(s)
- April Stempien-Otero
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Deok-Ho Kim
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jennifer Davis
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA.
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225
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Cellular responses to HSV-1 infection are linked to specific types of alterations in the host transcriptome. Sci Rep 2016; 6:28075. [PMID: 27354008 PMCID: PMC4926211 DOI: 10.1038/srep28075] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/26/2016] [Indexed: 02/06/2023] Open
Abstract
Pathogen invasion triggers a number of cellular responses and alters the host transcriptome. Here we report that the type of changes to cellular transcriptome is related to the type of cellular functions affected by lytic infection of Herpes Simplex Virus type I in Human primary fibroblasts. Specifically, genes involved in stress responses and nuclear transport exhibited mostly changes in alternative polyadenylation (APA), cell cycle genes showed mostly alternative splicing (AS) changes, while genes in neurogenesis, rarely underwent these changes. Transcriptome wide, the infection resulted in 1,032 cases of AS, 161 incidences of APA, 1,827 events of isoform changes, and up regulation of 596 genes and down regulations of 61 genes compared to uninfected cells. Thus, these findings provided important and specific links between cellular responses to HSV-1 infection and the type of alterations to the host transcriptome, highlighting important roles of RNA processing in virus-host interactions.
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226
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Fish L, Pencheva N, Goodarzi H, Tran H, Yoshida M, Tavazoie SF. Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts. Genes Dev 2016; 30:386-98. [PMID: 26883358 PMCID: PMC4762424 DOI: 10.1101/gad.270645.115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Post-transcriptional deregulation is a defining feature of metastatic cancer. While many microRNAs have been implicated as regulators of metastatic progression, less is known about the roles and mechanisms of RNA-binding proteins in this process. We identified muscleblind-like 1 (MBNL1), a gene implicated in myotonic dystrophy, as a robust suppressor of multiorgan breast cancer metastasis. MBNL1 binds the 3' untranslated regions (UTRs) of DBNL (drebrin-like protein) and TACC1 (transforming acidic coiled-coil containing protein 1)-two genes that we implicate as metastasis suppressors. By enhancing the stability of these genes' transcripts, MBNL1 suppresses cell invasiveness. Consistent with these findings, elevated MBNL1 expression in human breast tumors is associated with reduced metastatic relapse likelihood. Our findings delineate a post-transcriptional network that governs breast cancer metastasis through RNA-binding protein-mediated transcript stabilization.
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Affiliation(s)
- Lisa Fish
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York 10065, USA
| | - Nora Pencheva
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York 10065, USA
| | - Hani Goodarzi
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York 10065, USA
| | - Hien Tran
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York 10065, USA
| | - Mitsukuni Yoshida
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York 10065, USA
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227
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Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics 2016; 17:338. [PMID: 27150721 PMCID: PMC4858895 DOI: 10.1186/s12864-016-2675-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/28/2016] [Indexed: 01/13/2023] Open
Abstract
Background High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. This methodology is frequently used to validate predicted targets of microRNA binding, as well as direct targets of other RNA-binding proteins. Hence, the accuracy and sensitivity of binding site identification is critical. Results We found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45 % of peaks in publicly available HITS-CLIP libraries are attributable to this mispriming artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating microRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. Conclusions Here, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact and improves the sensitivity and complexity of resulting libraries. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2675-5) contains supplementary material, which is available to authorized users.
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228
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Yeh HS, Yong J. Alternative Polyadenylation of mRNAs: 3'-Untranslated Region Matters in Gene Expression. Mol Cells 2016; 39:281-5. [PMID: 26912084 PMCID: PMC4844933 DOI: 10.14348/molcells.2016.0035] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/11/2016] [Indexed: 12/26/2022] Open
Abstract
Almost all of eukaryotic mRNAs are subjected to polyadenylation during mRNA processing. Recent discoveries showed that many of these mRNAs contain more than one polyadenylation sites in their 3' untranslated regions (UTR) and that alternative polyadenylation (APA) is prevalent among these genes. Many biological processes such as differentiation, proliferation, and tumorigenesis have been correlated to global APA events in the 3' UTR of mRNAs, suggesting that these APA events are tightly regulated and may play important physiological roles. In this review, recent discoveries in the physiological roles of APA events, as well as the known and proposed mechanisms are summarized. Perspective for future directions is also discussed.
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Affiliation(s)
- Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455,
USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455,
USA
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229
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Bargiela A, Cerro-Herreros E, Fernandez-Costa JM, Vilchez JJ, Llamusi B, Artero R. Increased autophagy and apoptosis contribute to muscle atrophy in a myotonic dystrophy type 1 Drosophila model. Dis Model Mech 2016; 8:679-90. [PMID: 26092529 PMCID: PMC4486854 DOI: 10.1242/dmm.018127] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Muscle mass wasting is one of the most debilitating symptoms of myotonic dystrophy type 1 (DM1) disease, ultimately leading to immobility, respiratory defects, dysarthria, dysphagia and death in advanced stages of the disease. In order to study the molecular mechanisms leading to the degenerative loss of adult muscle tissue in DM1, we generated an inducible Drosophila model of expanded CTG trinucleotide repeat toxicity that resembles an adult-onset form of the disease. Heat-shock induced expression of 480 CUG repeats in adult flies resulted in a reduction in the area of the indirect flight muscles. In these model flies, reduction of muscle area was concomitant with increased apoptosis and autophagy. Inhibition of apoptosis or autophagy mediated by the overexpression of DIAP1, mTOR (also known as Tor) or muscleblind, or by RNA interference (RNAi)-mediated silencing of autophagy regulatory genes, achieved a rescue of the muscle-loss phenotype. In fact, mTOR overexpression rescued muscle size to a size comparable to that in control flies. These results were validated in skeletal muscle biopsies from DM1 patients in which we found downregulated autophagy and apoptosis repressor genes, and also in DM1 myoblasts where we found increased autophagy. These findings provide new insights into the signaling pathways involved in DM1 disease pathogenesis.
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Affiliation(s)
- Ariadna Bargiela
- Translational Genomics Group, Department of Genetics, University of Valencia, Burjassot 46100, Spain INCLIVA Health Research Institute, Valencia 46010, Spain
| | - Estefanía Cerro-Herreros
- Translational Genomics Group, Department of Genetics, University of Valencia, Burjassot 46100, Spain INCLIVA Health Research Institute, Valencia 46010, Spain
| | - Juan M Fernandez-Costa
- Translational Genomics Group, Department of Genetics, University of Valencia, Burjassot 46100, Spain
| | - Juan J Vilchez
- Neurology Section, Hospital Universitari La Fe, Valencia 46026, Spain Department of Internal Medicine, University of Valencia, Valencia 46010, Spain Centro de Investigaciones Biomedicas en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute Carlos III, Ministry of Economy and Competitiveness, Madrid 28049, Spain
| | | | - Ruben Artero
- Translational Genomics Group, Department of Genetics, University of Valencia, Burjassot 46100, Spain INCLIVA Health Research Institute, Valencia 46010, Spain
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230
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Ajith S, Gazzara MR, Cole BS, Shankarling G, Martinez NM, Mallory MJ, Lynch KW. Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells. RNA Biol 2016; 13:569-81. [PMID: 27096301 PMCID: PMC4962813 DOI: 10.1080/15476286.2016.1176663] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CELF2 is an RNA binding protein that has been implicated in developmental and signal-dependent splicing in the heart, brain and T cells. In the heart, CELF2 expression decreases during development, while in T cells CELF2 expression increases both during development and in response to antigen-induced signaling events. Although hundreds of CELF2-responsive splicing events have been identified in both heart and T cells, the way in which CELF2 functions has not been broadly investigated. Here we use CLIP-Seq to identified physical targets of CELF2 in a cultured human T cell line. By comparing the results with known functional targets of CELF2 splicing regulation from the same cell line we demonstrate a generalizable position-dependence of CELF2 activity that is consistent with previous mechanistic studies of individual CELF2 target genes in heart and brain. Strikingly, this general position-dependence is sufficient to explain the bi-directional activity of CELF2 on 2 T cell targets recently reported. Therefore, we propose that the location of CELF2 binding around an exon is a primary predictor of CELF2 function in a broad range of cellular contexts.
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Affiliation(s)
- Sandya Ajith
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Matthew R Gazzara
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Brian S Cole
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Ganesh Shankarling
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Nicole M Martinez
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Michael J Mallory
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Kristen W Lynch
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
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231
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Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy. Nat Commun 2016; 7:11067. [PMID: 27063795 PMCID: PMC4831019 DOI: 10.1038/ncomms11067] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/16/2016] [Indexed: 12/11/2022] Open
Abstract
Myotonic dystrophy (DM) is caused by the expression of mutant RNAs containing expanded CUG repeats that sequester muscleblind-like (MBNL) proteins, leading to alternative splicing changes. Cardiac alterations, characterized by conduction delays and arrhythmia, are the second most common cause of death in DM. Using RNA sequencing, here we identify novel splicing alterations in DM heart samples, including a switch from adult exon 6B towards fetal exon 6A in the cardiac sodium channel, SCN5A. We find that MBNL1 regulates alternative splicing of SCN5A mRNA and that the splicing variant of SCN5A produced in DM presents a reduced excitability compared with the control adult isoform. Importantly, reproducing splicing alteration of Scn5a in mice is sufficient to promote heart arrhythmia and cardiac-conduction delay, two predominant features of myotonic dystrophy. In conclusion, misregulation of the alternative splicing of SCN5A may contribute to a subset of the cardiac dysfunctions observed in myotonic dystrophy. Patients with myotonic dystrophy (MD) suffer from severe cardiac issues of unknown aetiology. Freyermuth et al. show that fatal changes in cardiac electrophysiological properties in humans and mice with MD may arise from misregulation of the alternative splicing of the cardiac Na+ channel SCN5A transcript, resulting in expression of its fetal form.
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232
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Roles for RNA-binding proteins in development and disease. Brain Res 2016; 1647:1-8. [PMID: 26972534 DOI: 10.1016/j.brainres.2016.02.050] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 12/13/2022]
Abstract
RNA-binding protein activities are highly regulated through protein levels, intracellular localization, and post-translation modifications. During development, mRNA processing of specific gene sets is regulated through manipulation of functional RNA-binding protein activities. The impact of altered RNA-binding protein activities also affects human diseases in which there are either a gain-of-function or loss-of-function causes pathogenesis. We will discuss RNA-binding proteins and their normal developmental RNA metabolism and contrast how their function is disrupted in disease. This article is part of a Special Issue entitled SI:RNA Metabolism in Disease.
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233
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Gao H, Zhai Y, Wang W, Chen H, Zhou X, Zhuang Q, Yu Y, Li R. Transcriptome Analysis and Discovery of Genes Relevant to Development in Bradysia odoriphaga at Three Developmental Stages. PLoS One 2016; 11:e0146812. [PMID: 26891450 PMCID: PMC4759360 DOI: 10.1371/journal.pone.0146812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/21/2015] [Indexed: 11/18/2022] Open
Abstract
Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive (Allium tuberosum) in Asia; however, the molecular genetics are poorly understood. To explore the molecular biological mechanism of development, Illumina sequencing and de novo assembly were performed in the third-instar, fourth-instar, and pupal B. odoriphaga. The study resulted in 16.2 Gb of clean data and 47,578 unigenes (≥125 bp) contained in 7,632,430 contigs, 46.21% of which were annotated from non-redundant protein (NR), Gene Ontology (GO), Clusters of Orthologous Groups (COG), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. It was found that 19.67% of unigenes matched the homologous species mainly, including Aedes aegypti, Culex quinquefasciatus, Ceratitis capitata, and Anopheles gambiae. According to differentially expressed gene (DEG) analysis, 143, 490, and 309 DEGs were annotated as involved in the developmental process in the GO database respectively, in the comparisons of third-instar and fourth-instar larvae, third-instar larvae and pupae, and fourth-instar larvae and pupae. Twenty-five genes were closely related to these processes, including developmental process, reproduction process, and reproductive organs development and programmed cell death (PCD). The information of unigenes assembled in B. odoriphaga through transcriptome and DEG analyses could provide a detailed genetic basis and regulated information for elaborating the developmental mechanism from the larval, pre-pupal to pupal stages of B. odoriphaga.
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Affiliation(s)
- Huanhuan Gao
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wenbo Wang
- Institute of Quality Standard & Testing Technology for Agri-products, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xianhong Zhou
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qianying Zhuang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yi Yu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rumei Li
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
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234
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Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB. Distal Alternative Last Exons Localize mRNAs to Neural Projections. Mol Cell 2016; 61:821-33. [PMID: 26907613 DOI: 10.1016/j.molcel.2016.01.020] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/10/2015] [Accepted: 01/15/2016] [Indexed: 11/30/2022]
Abstract
Spatial restriction of mRNA to distinct subcellular locations enables local regulation and synthesis of proteins. However, the organizing principles of mRNA localization remain poorly understood. Here we analyzed subcellular transcriptomes of neural projections and soma of primary mouse cortical neurons and two neuronal cell lines and found that alternative last exons (ALEs) often confer isoform-specific localization. Surprisingly, gene-distal ALE isoforms were four times more often localized to neurites than gene-proximal isoforms. Localized isoforms were induced during neuronal differentiation and enriched for motifs associated with muscleblind-like (Mbnl) family RNA-binding proteins. Depletion of Mbnl1 and/or Mbnl2 reduced localization of hundreds of transcripts, implicating Mbnls in localization of mRNAs to neurites. We provide evidence supporting a model in which the linkage between genomic position of ALEs and subcellular localization enables coordinated induction of localization-competent mRNA isoforms through a post-transcriptional regulatory program that is induced during differentiation and reversed in cellular reprogramming and cancer.
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Affiliation(s)
- J Matthew Taliaferro
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Marina Vidaki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Tanvi Saxena
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Frank B Gertler
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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235
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Blech-Hermoni Y, Dasgupta T, Coram RJ, Ladd AN. Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle. PLoS One 2016; 11:e0149061. [PMID: 26866591 PMCID: PMC4750973 DOI: 10.1371/journal.pone.0149061] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/30/2015] [Indexed: 01/17/2023] Open
Abstract
CUG-BP, Elav-like family member 1 (CELF1) is a highly conserved RNA binding protein that regulates pre-mRNA alternative splicing, polyadenylation, mRNA stability, and translation. In the heart, CELF1 is expressed in the myocardium, where its levels are tightly regulated during development. CELF1 levels peak in the heart during embryogenesis, and aberrant up-regulation of CELF1 in the adult heart has been implicated in cardiac pathogenesis in myotonic dystrophy type 1, as well as in diabetic cardiomyopathy. Either inhibition of CELF activity or over-expression of CELF1 in heart muscle causes cardiomyopathy in transgenic mice. Nonetheless, many of the cardiac targets of CELF1 regulation remain unknown. In this study, to identify cardiac targets of CELF1 we performed cross-linking immunoprecipitation (CLIP) for CELF1 from embryonic day 8 chicken hearts. We identified a previously unannotated exon in MYH7B as a novel target of CELF1-mediated regulation. We demonstrated that knockdown of CELF1 in primary chicken embryonic cardiomyocytes leads to increased inclusion of this exon and decreased MYH7B levels. We also investigated global changes in the transcriptome of primary embryonic cardiomyocytes following CELF1 knockdown in a published RNA-seq dataset. Pathway and network analyses identified strong associations between CELF1 and regulation of cell cycle and translation. Important regulatory proteins, including both RNA binding proteins and a cardiac transcription factor, were affected by loss of CELF1. Together, these data suggest that CELF1 is a key regulator of cardiomyocyte gene expression.
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Affiliation(s)
- Yotam Blech-Hermoni
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Program in Cell Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Twishasri Dasgupta
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ryan J. Coram
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Andrea N. Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Program in Cell Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail:
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236
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Ladd AN. New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:125-85. [PMID: 27017008 DOI: 10.1016/bs.ircmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.
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Affiliation(s)
- A N Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America.
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Dewaele M, Tabaglio T, Willekens K, Bezzi M, Teo SX, Low DHP, Koh CM, Rambow F, Fiers M, Rogiers A, Radaelli E, Al-Haddawi M, Tan SY, Hermans E, Amant F, Yan H, Lakshmanan M, Koumar RC, Lim ST, Derheimer FA, Campbell RM, Bonday Z, Tergaonkar V, Shackleton M, Blattner C, Marine JC, Guccione E. Antisense oligonucleotide-mediated MDM4 exon 6 skipping impairs tumor growth. J Clin Invest 2016. [PMID: 26595814 DOI: 10.1172/jci82534.mdm4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
MDM4 is a promising target for cancer therapy, as it is undetectable in most normal adult tissues but often upregulated in cancer cells to dampen p53 tumor-suppressor function. The mechanisms that underlie MDM4 upregulation in cancer cells are largely unknown. Here, we have shown that this key oncogenic event mainly depends on a specific alternative splicing switch. We determined that while a nonsense-mediated, decay-targeted isoform of MDM4 (MDM4-S) is produced in normal adult tissues as a result of exon 6 skipping, enhanced exon 6 inclusion leads to expression of full-length MDM4 in a large number of human cancers. Although this alternative splicing event is likely regulated by multiple splicing factors, we identified the SRSF3 oncoprotein as a key enhancer of exon 6 inclusion. In multiple human melanoma cell lines and in melanoma patient-derived xenograft (PDX) mouse models, antisense oligonucleotide-mediated (ASO-mediated) skipping of exon 6 decreased MDM4 abundance, inhibited melanoma growth, and enhanced sensitivity to MAPK-targeting therapeutics. Additionally, ASO-based MDM4 targeting reduced diffuse large B cell lymphoma PDX growth. As full-length MDM4 is enhanced in multiple human tumors, our data indicate that this strategy is applicable to a wide range of tumor types. We conclude that enhanced MDM4 exon 6 inclusion is a common oncogenic event and has potential as a clinically compatible therapeutic target.
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238
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Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:1-28. [PMID: 27256380 DOI: 10.1007/978-3-319-29073-7_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. The recent explosion in genomics techniques has enabled transcriptome-wide profiling of RNA processing in an unbiased manner. However, it has also brought with it both experimental challenges in developing improved methods to probe distinct processing steps, as well as computational challenges in data storage, processing, and analysis tools to enable large-scale interpretation in the genomics era. In this chapter we review experimental techniques and challenges in profiling various aspects of RNA processing, as well as recent efforts to develop analyses integrating multiple data sources and techniques to infer RNA regulatory networks.
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239
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MBNL1-mediated regulation of differentiation RNAs promotes myofibroblast transformation and the fibrotic response. Nat Commun 2015; 6:10084. [PMID: 26670661 PMCID: PMC4703843 DOI: 10.1038/ncomms10084] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 11/02/2015] [Indexed: 02/06/2023] Open
Abstract
The differentiation of fibroblasts into myofibroblasts mediates tissue wound healing and fibrotic remodelling, although the molecular programme underlying this process remains poorly understood. Here we perform a genome-wide screen for genes that control myofibroblast transformation, and identify the RNA-binding protein muscleblind-like1 (MBNL1). MBNL1 overexpression promotes transformation of fibroblasts into myofibroblasts, whereas loss of Mbnl1 abrogates transformation and impairs the fibrotic phase of wound healing in mouse models of myocardial infarction and dermal injury. Mechanistically, MBNL1 directly binds to and regulates a network of differentiation-specific and cytoskeletal/matrix-assembly transcripts to promote myofibroblast differentiation. One of these transcripts is the nodal transcriptional regulator serum response factor (SRF), whereas another is calcineurin Aβ. CRISPR-Cas9-mediated gene-editing of the MBNL1-binding site within the Srf 3′UTR impairs myofibroblast differentiation, whereas in vivo deletion of Srf in fibroblasts impairs wound healing and fibrosis. These data establish a new RNA-dependent paradigm for myofibroblast formation through MBNL1. Fibroblast-to-myofibroblast differentiation is crucial for wound healing and regeneration. Davis et al. describe a new regulatory mechanism underlying myofibroblast differentiation via the RNA-binding protein MBNL1, which promotes the maturation of certain mRNA transcripts that are integral nodes in fibroblast differentiation.
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240
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Hong SE, Nho KJ, Song HK, Kim DH. Deep sequencing-generated modules demonstrate coherent expression patterns for various cardiac diseases. Gene 2015; 574:53-60. [PMID: 26232333 DOI: 10.1016/j.gene.2015.07.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 07/24/2015] [Indexed: 11/30/2022]
Abstract
As sequencing technology rapidly develops, gene annotations have also become increasingly sophisticated with incorporation of information regarding the temporal-spatial context of alternative splicing patterns, developmental stages, and tissue specificity. The present study aimed to identify the heart-enriched genes based on next-generation sequencing data and to investigate the gene modules demonstrating coherent expression patterns for various cardiac disease-related perturbations. Seven gene modules, including 382 heart-enriched genes, were identified. At least two modules containing differentially expressed genes were experimentally confirmed to be highly sensitive to various cardiac diseases. Transcription factors regulating the gene modules were then analyzed based on knowledgebase information; the expression of eight transcription factors changed significantly during pressure-overload cardiac hypertrophy, suggesting possible regulation of the modules by the identified transcription factors. Collectively, our results contribute to the classification of heart-enriched genes and their modules and would aid in identification of the transcription factors involved in cardiac pathogenesis in the future.
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Affiliation(s)
- Seong-Eui Hong
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Kyoung Jin Nho
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Hong Ki Song
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Do Han Kim
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
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241
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Nakamori M, Taylor K, Mochizuki H, Sobczak K, Takahashi MP. Oral administration of erythromycin decreases RNA toxicity in myotonic dystrophy. Ann Clin Transl Neurol 2015; 3:42-54. [PMID: 26783549 PMCID: PMC4704483 DOI: 10.1002/acn3.271] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/04/2015] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE Myotonic dystrophy type 1 (DM1) is caused by the expansion of a CTG repeat in the 3' untranslated region of DMPK. The transcripts containing an expanded CUG repeat (CUG (exp)) result in a toxic gain-of-function by forming ribonuclear foci that sequester the alternative splicing factor muscleblind-like 1 (MBNL1). Although several small molecules reportedly ameliorate RNA toxicity, none are ready for clinical use because of the lack of safety data. Here, we undertook a drug-repositioning screen to identify a safe and effective small molecule for upcoming clinical trials of DM1. METHODS We examined the potency of small molecules in inhibiting the interaction between CUG (exp) and MBNL1 by in vitro sequestration and fluorescent titration assays. We studied the effect of lead compounds in DM1 model cells by evaluating foci reduction and splicing rescue. We also tested their effects on missplicing and myotonia in DM1 model mice. RESULTS Of the 20 FDA-approved small molecules tested, erythromycin showed the highest affinity to CUG (exp) and a capacity to inhibit its binding to MBNL1. Erythromycin decreased foci formation and rescued missplicing in DM1 cell models. Both systemic and oral administration of erythromycin in the DM1 model mice showed splicing reversal and improvement of myotonia with no toxicity. Long-term oral administration of erythromycin at the dose used in humans also improved the splicing abnormality in the DM1 model mice. INTERPRETATION Oral erythromycin treatment, which has been widely used in humans with excellent tolerability, may be a promising therapy for DM1.
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Affiliation(s)
- Masayuki Nakamori
- Department of Neurology Osaka University Graduate School of Medicine Osaka Japan
| | - Katarzyna Taylor
- Department of Gene Expression Institute of Molecular Biology and Biotechnology Adam Mickiewicz University Posnan Poland
| | - Hideki Mochizuki
- Department of Neurology Osaka University Graduate School of Medicine Osaka Japan
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology Adam Mickiewicz University Posnan Poland
| | - Masanori P Takahashi
- Department of Neurology Osaka University Graduate School of Medicine Osaka Japan
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242
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Actinomycin D Specifically Reduces Expanded CUG Repeat RNA in Myotonic Dystrophy Models. Cell Rep 2015; 13:2386-2394. [PMID: 26686629 DOI: 10.1016/j.celrep.2015.11.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 09/10/2015] [Accepted: 11/06/2015] [Indexed: 01/16/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is an inherited disease characterized by the inability to relax contracted muscles. Affected individuals carry large CTG expansions that are toxic when transcribed. One possible treatment approach is to reduce or eliminate transcription of CTG repeats. Actinomycin D (ActD) is a potent transcription inhibitor and FDA-approved chemotherapeutic that binds GC-rich DNA with high affinity. Here, we report that ActD decreased CUG transcript levels in a dose-dependent manner in DM1 cell and mouse models at significantly lower concentrations (nanomolar) compared to its use as a general transcription inhibitor or chemotherapeutic. ActD also significantly reversed DM1-associated splicing defects in a DM1 mouse model, and did so within the currently approved human treatment range. RNA-seq analyses showed that low concentrations of ActD did not globally inhibit transcription in a DM1 mouse model. These results indicate that transcription inhibition of CTG expansions is a promising treatment approach for DM1.
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243
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Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nat Struct Mol Biol 2015; 23:16-23. [PMID: 26641712 DOI: 10.1038/nsmb.3140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 11/12/2015] [Indexed: 12/11/2022]
Abstract
Unkempt is an evolutionarily conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. Here we determined the X-ray crystal structure of mouse Unkempt and show that its six CCCH zinc fingers (ZnFs) form two compact clusters, ZnF1-3 and ZnF4-6, that recognize distinct trinucleotide RNA substrates. Both ZnF clusters adopt a similar overall topology and use distinct recognition principles to target specific RNA sequences. Structure-guided point mutations reduce the RNA binding affinity of Unkempt both in vitro and in vivo, ablate Unkempt's translational control and impair the ability of Unkempt to induce a bipolar cellular morphology. Our study unravels a new mode of RNA sequence recognition by clusters of CCCH ZnFs that is critical for post-transcriptional control of neuronal morphology.
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244
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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245
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Abstract
The human transcriptome is composed of a vast RNA population that undergoes further diversification by splicing. Detecting specific splice sites in this large sequence pool is the responsibility of the major and minor spliceosomes in collaboration with numerous splicing factors. This complexity makes splicing susceptible to sequence polymorphisms and deleterious mutations. Indeed, RNA mis-splicing underlies a growing number of human diseases with substantial societal consequences. Here, we provide an overview of RNA splicing mechanisms followed by a discussion of disease-associated errors, with an emphasis on recently described mutations that have provided new insights into splicing regulation. We also discuss emerging strategies for splicing-modulating therapy.
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Affiliation(s)
- Marina M Scotti
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32610-3610 USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32610-3610 USA
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246
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Dewaele M, Tabaglio T, Willekens K, Bezzi M, Teo SX, Low DHP, Koh CM, Rambow F, Fiers M, Rogiers A, Radaelli E, Al-Haddawi M, Tan SY, Hermans E, Amant F, Yan H, Lakshmanan M, Koumar RC, Lim ST, Derheimer FA, Campbell RM, Bonday Z, Tergaonkar V, Shackleton M, Blattner C, Marine JC, Guccione E. Antisense oligonucleotide-mediated MDM4 exon 6 skipping impairs tumor growth. J Clin Invest 2015; 126:68-84. [PMID: 26595814 DOI: 10.1172/jci82534] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/09/2015] [Indexed: 12/27/2022] Open
Abstract
MDM4 is a promising target for cancer therapy, as it is undetectable in most normal adult tissues but often upregulated in cancer cells to dampen p53 tumor-suppressor function. The mechanisms that underlie MDM4 upregulation in cancer cells are largely unknown. Here, we have shown that this key oncogenic event mainly depends on a specific alternative splicing switch. We determined that while a nonsense-mediated, decay-targeted isoform of MDM4 (MDM4-S) is produced in normal adult tissues as a result of exon 6 skipping, enhanced exon 6 inclusion leads to expression of full-length MDM4 in a large number of human cancers. Although this alternative splicing event is likely regulated by multiple splicing factors, we identified the SRSF3 oncoprotein as a key enhancer of exon 6 inclusion. In multiple human melanoma cell lines and in melanoma patient-derived xenograft (PDX) mouse models, antisense oligonucleotide-mediated (ASO-mediated) skipping of exon 6 decreased MDM4 abundance, inhibited melanoma growth, and enhanced sensitivity to MAPK-targeting therapeutics. Additionally, ASO-based MDM4 targeting reduced diffuse large B cell lymphoma PDX growth. As full-length MDM4 is enhanced in multiple human tumors, our data indicate that this strategy is applicable to a wide range of tumor types. We conclude that enhanced MDM4 exon 6 inclusion is a common oncogenic event and has potential as a clinically compatible therapeutic target.
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247
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Chakraborty M, Selma-Soriano E, Magny E, Couso JP, Pérez-Alonso M, Charlet-Berguerand N, Artero R, Llamusi B. Pentamidine rescues contractility and rhythmicity in a Drosophila model of myotonic dystrophy heart dysfunction. Dis Model Mech 2015; 8:1569-78. [PMID: 26515653 PMCID: PMC4728315 DOI: 10.1242/dmm.021428] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/19/2015] [Indexed: 02/01/2023] Open
Abstract
Up to 80% of individuals with myotonic dystrophy type 1 (DM1) will develop cardiac abnormalities at some point during the progression of their disease, the most common of which is heart blockage of varying degrees. Such blockage is characterized by conduction defects and supraventricular and ventricular tachycardia, and carries a high risk of sudden cardiac death. Despite its importance, very few animal model studies have focused on the heart dysfunction in DM1. Here, we describe the characterization of the heart phenotype in a Drosophila model expressing pure expanded CUG repeats under the control of the cardiomyocyte-specific driver GMH5-Gal4. Morphologically, expression of 250 CUG repeats caused abnormalities in the parallel alignment of the spiral myofibrils in dissected fly hearts, as revealed by phalloidin staining. Moreover, combined immunofluorescence and in situ hybridization of Muscleblind and CUG repeats, respectively, confirmed detectable ribonuclear foci and Muscleblind sequestration, characteristic features of DM1, exclusively in flies expressing the expanded CTG repeats. Similarly to what has been reported in humans with DM1, heart-specific expression of toxic RNA resulted in reduced survival, increased arrhythmia, altered diastolic and systolic function, reduced heart tube diameters and reduced contractility in the model flies. As a proof of concept that the fly heart model can be used for in vivo testing of promising therapeutic compounds, we fed flies with pentamidine, a compound previously described to improve DM1 phenotypes. Pentamidine not only released Muscleblind from the CUG RNA repeats and reduced ribonuclear formation in the Drosophila heart, but also rescued heart arrhythmicity and contractility, and improved fly survival in animals expressing 250 CUG repeats.
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Affiliation(s)
- Mouli Chakraborty
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, Burjasot 46100, Spain
| | - Estela Selma-Soriano
- Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, Burjasot 46100, Spain
| | - Emile Magny
- School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex, BN1 9QG, UK
| | - Juan Pablo Couso
- School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex, BN1 9QG, UK
| | - Manuel Pérez-Alonso
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, Burjasot 46100, Spain
| | - Nicolas Charlet-Berguerand
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67400 Illkirch-Graffenstaden, France
| | - Ruben Artero
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, Burjasot 46100, Spain
| | - Beatriz Llamusi
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, Burjasot 46100, Spain
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248
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Iachettini S, Valaperta R, Marchesi A, Perfetti A, Cuomo G, Fossati B, Vaienti L, Costa E, Meola G, Cardani R. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1. Eur J Histochem 2015; 59:2562. [PMID: 26708183 PMCID: PMC4698615 DOI: 10.4081/ejh.2015.2562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/25/2015] [Accepted: 10/03/2015] [Indexed: 01/30/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by a CTG repeat expansion in 3'UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA) muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.
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249
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Abstract
Alternative pre-mRNA processing greatly increases the coding capacity of the human genome and regulatory factors involved in RNA processing play critical roles in tissue development and maintenance. Indeed, abnormal functions of RNA processing factors have been associated with a wide range of human diseases from cancer to neurodegenerative disorders. While many studies have emphasized the importance of alternative splicing (AS), recent high-throughput sequencing efforts have also allowed global surveys of alternative polyadenylation (APA). For the majority of pre-mRNAs, as well as some non-coding transcripts such as lncRNAs, APA selects different 3'-ends and thus modulates the availability of regulatory sites recognized by trans-acting regulatory effectors, including miRs and RNA binding proteins (RBPs). Here, we compare the available technologies for assessing global polyadenylation patterns, summarize the roles of auxiliary factors on APA, and discuss the impact of differential polyA site (pA) selection in the determination of cell fate, transformation and disease.
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Affiliation(s)
- Ranjan Batra
- a Department of Cellular and Molecular Medicine ; Institute for Genomic Medicine; UCSD Stem Cell Program; University of California ; San Diego , CA USA
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250
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Coram RJ, Stillwagon SJ, Guggilam A, Jenkins MW, Swanson MS, Ladd AN. Muscleblind-like 1 is required for normal heart valve development in vivo. BMC DEVELOPMENTAL BIOLOGY 2015; 15:36. [PMID: 26472242 PMCID: PMC4608261 DOI: 10.1186/s12861-015-0087-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/09/2015] [Indexed: 12/26/2022]
Abstract
Background Development of the valves and septa of the heart depends on the formation and remodeling of the endocardial cushions in the atrioventricular canal and outflow tract. These cushions are populated by mesenchyme produced from the endocardium by epithelial-mesenchymal transition (EMT). The endocardial cushions are remodeled into the valves at post-EMT stages via differentiation of the mesenchyme and changes in the extracellular matrix (ECM). Transforming growth factor β (TGFβ) signaling has been implicated in both the induction of EMT in the endocardial cushions and the remodeling of the valves at post-EMT stages. We previously identified the RNA binding protein muscleblind-like 1 (MBNL1) as a negative regulator of TGFβ signaling and EMT in chicken endocardial cushions ex vivo. Here, we investigate the role of MBNL1 in endocardial cushion development and valvulogenesis in Mbnl1∆E3/∆E3 mice, which are null for MBNL1 protein. Methods Collagen gel invasion assays, histology, immunohistochemistry, real-time RT-PCR, optical coherence tomography, and echocardiography were used to evaluate EMT and TGFβ signaling in the endocardial cushions, and morphogenesis, ECM composition, and function of the heart valves. Results As in chicken, the loss of MBNL1 promotes precocious TGFβ signaling and EMT in the endocardial cushions. Surprisingly, this does not lead to the production of excess mesenchyme, but later valve morphogenesis is aberrant. Adult Mbnl1∆E3/∆E3 mice exhibit valve dysmorphia with elevated TGFβ signaling, changes in ECM composition, and increased pigmentation. This is accompanied by a high incidence of regurgitation across both inflow and outflow valves. Mbnl1∆E3/∆E3 mice also have a high incidence of ostium secundum septal defects accompanied by atrial communication, but do not develop overt cardiomyopathy. Conclusions Together, these data indicate that MBNL1 plays a conserved role in negatively regulating TGFβ signaling, and is required for normal valve morphogenesis and homeostasis in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0087-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan J Coram
- Department of Cellular & Molecular Medicine, Lerner Research Institute, 9500 Euclid Ave. NC10, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Present Address: Ohio University Heritage College of Osteopathic Medicine, Athens, OH, 45701, USA.
| | - Samantha J Stillwagon
- Department of Cellular & Molecular Medicine, Lerner Research Institute, 9500 Euclid Ave. NC10, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Present Address: Department of Obstetrics and Gynecology, Women's Health Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
| | - Anuradha Guggilam
- Department of Cellular & Molecular Medicine, Lerner Research Institute, 9500 Euclid Ave. NC10, Cleveland Clinic, Cleveland, OH, 44195, USA.
| | - Michael W Jenkins
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Maurice S Swanson
- Department of Molecular Genetics & Microbiology, College of Medicine, Center for NeuroGenetics and the Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Andrea N Ladd
- Department of Cellular & Molecular Medicine, Lerner Research Institute, 9500 Euclid Ave. NC10, Cleveland Clinic, Cleveland, OH, 44195, USA.
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