651
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Almon RR, Dubois DC, Sukumaran S, Wang X, Xue B, Nie J, Jusko WJ. Effects of high fat feeding on liver gene expression in diabetic goto-kakizaki rats. GENE REGULATION AND SYSTEMS BIOLOGY 2012; 6:151-68. [PMID: 23236253 PMCID: PMC3516129 DOI: 10.4137/grsb.s10371] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Effects of high fat diet (HFD) on obesity and, subsequently, on diabetes are highly variable and modulated by genetics in both humans and rodents. In this report, we characterized the response of Goto-Kakizaki (GK) rats, a spontaneous polygenic model for lean diabetes and healthy Wistar-Kyoto (WKY) controls, to high fat feeding from weaning to 20 weeks of age. Animals fed either normal diet or HFD were sacrificed at 4, 8, 12, 16 and 20 weeks of age and a wide array of physiological measurements were made along with gene expression profiling using Affymetrix gene array chips. Mining of the microarray data identified differentially regulated genes (involved in inflammation, metabolism, transcription regulation, and signaling) in diabetic animals, as well as the response of both strains to HFD. Functional annotation suggested that HFD increased inflammatory differences between the two strains. Chronic inflammation driven by heightened innate immune response was identified to be present in GK animals regardless of diet. In addition, compensatory mechanisms by which WKY animals on HFD resisted the development of diabetes were identified, thus illustrating the complexity of diabetes disease progression.
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Affiliation(s)
- Richard R Almon
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA. ; Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA. ; New York State Center of Excellence in Bioinformatics and Life Sciences
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652
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Zhang Y, Madl T, Bagdiul I, Kern T, Kang HS, Zou P, Mäusbacher N, Sieber SA, Krämer A, Sattler M. Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition. Nucleic Acids Res 2012; 41:1343-54. [PMID: 23175611 PMCID: PMC3553976 DOI: 10.1093/nar/gks1097] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recognition of the 3'-splice site is a key step in pre-mRNA splicing and accomplished by a dynamic complex comprising splicing factor 1 (SF1) and the U2 snRNP auxiliary factor 65-kDa subunit (U2AF65). Both proteins mediate protein-protein and protein-RNA interactions for cooperative RNA-binding during spliceosome assembly. Here, we report the solution structure of a novel helix-hairpin domain in the N-terminal region of SF1 (SF1(NTD)). The nuclear magnetic resonance- and small-angle X-ray scattering-derived structure of a complex of the SF1(NTD) with the C-terminal U2AF homology motif domain of U2AF65 (U2AF65(UHM)) reveals that, in addition to the known U2AF65(UHM)-SF1 interaction, the helix-hairpin domain forms a secondary, hydrophobic interface with U2AF65(UHM), which locks the orientation of the two subunits. Mutational analysis shows that the helix hairpin is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. We further show that tandem serine phosphorylation of a conserved Ser80-Pro81-Ser82-Pro83 motif rigidifies a long unstructured linker in the SF1 helix hairpin. Phosphorylation does not significantly alter the overall conformations of SF1, SF1-U2AF65 or the SF1-U2AF65-RNA complexes, but slightly enhances RNA binding. Our results indicate that the helix-hairpin domain of SF1 is required for cooperative 3'-splice site recognition presumably by stabilizing a unique quaternary arrangement of the SF1-U2AF65-RNA complex.
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Affiliation(s)
- Yun Zhang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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653
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Sehdev P, Crews G, Soto AM. Effect of Helix Stability on the Formation of Loop–Loop Complexes. Biochemistry 2012; 51:9612-23. [DOI: 10.1021/bi300481v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Preeti Sehdev
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
| | - Gordon Crews
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
| | - Ana Maria Soto
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
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654
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Singh NN, Seo J, Rahn SJ, Singh RN. A multi-exon-skipping detection assay reveals surprising diversity of splice isoforms of spinal muscular atrophy genes. PLoS One 2012. [PMID: 23185376 PMCID: PMC3501452 DOI: 10.1371/journal.pone.0049595] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Humans have two near identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with the predominant skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a neurodegenerative disease. SMA patient cells devoid of SMN1 provide a powerful system to examine splicing pattern of various SMN2 exons. Until now, similar system to examine splicing of SMN1 exons was unavailable. We have recently screened several patient cell lines derived from various diseases, including SMA, Alzheimer’s disease, Parkinson’s disease and Batten disease. Here we report a Batten disease cell line that lacks functional SMN2, as an ideal system to examine pre-mRNA splicing of SMN1. We employ a multiple-exon-skipping detection assay (MESDA) to capture simultaneously skipping of multiple exons. Our results show surprising diversity of splice isoforms and reveal novel splicing events that include skipping of exon 4 and co-skipping of three adjacent exons of SMN. Contrary to the general belief, MESDA captured oxidative-stress induced skipping of SMN1 exon 5 in several cell types, including non-neuronal cells. We further demonstrate that the predominant SMN2 exon 7 skipping induced by oxidative stress is modulated by a combinatorial control that includes promoter sequence, endogenous context, and the weak splice sites. We also show that an 8-mer antisense oligonucleotide blocking a recently described GC-rich sequence prevents SMN2 exon 7 skipping under the conditions of oxidative stress. Our findings bring new insight into splicing regulation of an essential housekeeping gene linked to neurodegeneration and infant mortality.
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Affiliation(s)
- Natalia N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Sarah J. Rahn
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Ravindra N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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655
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Perez-Santangelo S, Schlaen RG, Yanovsky MJ. Genomic analysis reveals novel connections between alternative splicing and circadian regulatory networks. Brief Funct Genomics 2012; 12:13-24. [DOI: 10.1093/bfgp/els052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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656
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Tolino M, Köhrmann M, Kiebler MA. RNA-binding proteins involved in RNA localization and their implications in neuronal diseases. Eur J Neurosci 2012; 35:1818-36. [PMID: 22708593 DOI: 10.1111/j.1460-9568.2012.08160.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Very often, developmental abnormalities or subtle disturbances of neuronal function may yield brain diseases even if they become obvious only late in life. It is therefore our intention to highlight fundamental mechanisms of neuronal cell biology with a special emphasis on dendritic mRNA localization including local protein synthesis at the activated synapse. Furthermore, we would like to point out possible links to neuronal or synaptic dysfunction. In particular, we will focus on a series of well-known RNA-binding proteins that are involved in these processes and outline how their dysfunction might yield neurodevelopmental, neurodegenerative or neuropsychiatric disorders. We are convinced that increasing our understanding of RNA biology in general and the mechanisms underlying mRNA transport and subsequent translation at the synapse will ultimately generate important novel RNA-based tools in the near future that will allow us to hopefully treat some of these devastating diseases.
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Affiliation(s)
- Marco Tolino
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
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657
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Ward LD, Kellis M. Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol 2012; 30:1095-106. [PMID: 23138309 PMCID: PMC3703467 DOI: 10.1038/nbt.2422] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/16/2012] [Indexed: 12/13/2022]
Abstract
Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has primarily focused on protein-coding variants, due to the difficulty of interpreting non-coding mutations. This picture has changed with advances in the systematic annotation of functional non-coding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs, and molecular quantitative trait loci all provide complementary information about non-coding function. These functional maps can help prioritize variants on risk haplotypes, filter mutations encountered in the clinic, and perform systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable dataset integration to reveal pathways shared across loci and alleles, and richer regulatory models can guide the search for epistatic interactions. Lastly, new massively parallel reporter experiments can systematically validate regulatory predictions. Ultimately, advances in regulatory and systems genomics can help unleash the value of whole-genome sequencing for personalized genomic risk assessment, diagnosis, and treatment.
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Affiliation(s)
- Lucas D Ward
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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658
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Janga SC. From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks. Brief Funct Genomics 2012; 11:505-21. [PMID: 23124862 DOI: 10.1093/bfgp/els046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulation of gene expression occurs at several levels in eukaryotic organisms and is a highly controlled process. Although RNAs have been traditionally viewed as passive molecules in the pathway from transcription to translation, there is mounting evidence that their metabolism is controlled by a class of proteins called RNA-binding proteins (RBPs), as well as a number of small RNAs. In this review, I provide an overview of the recent developments in our understanding of the repertoire of RBPs across diverse model systems, and discuss the computational and experimental approaches currently available for the construction of posttranscriptional networks governed by them. I also present an overview of the different roles played by RBPs in the cellular context, based on their cis-regulatory modules identified in the literature and discuss how their interplay can result in the dynamic, spatial and tissue-specific expression maps of RNAs. I finally present the concept of posttranscriptional network of RBPs and their cognate RNA targets and discuss their cross-talk with other important posttranscriptional regulatory molecules such as microRNAs s, resulting in diverse functional network motifs. I argue that with rapid developments in the genome-wide elucidation of posttranscriptional networks it would not only be possible to gain a deeper understanding of regulation at a level that has been under-appreciated in the past, but would also allow us to use the newly developed high-throughput approaches to interrogate the prevalence of these phenomena in different states, and thereby study their relevance to physiology and disease across organisms.
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Affiliation(s)
- Sarath Chandra Janga
- School of Informatics, Indiana University Purdue University, Indianapolis, Indiana, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave Ste 319, Walker Plaza Building, IN 46202, USA.
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659
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Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, Gregory BD. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. THE PLANT CELL 2012; 24:4346-59. [PMID: 23150631 PMCID: PMC3531838 DOI: 10.1105/tpc.112.104232] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/22/2012] [Accepted: 10/25/2012] [Indexed: 05/19/2023]
Abstract
The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.
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Affiliation(s)
- Fan Li
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Qi Zheng
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Lee E. Vandivier
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Matthew R. Willmann
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ying Chen
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Address correspondence to
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660
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Saini S, Robinson PN, Singh JR, Vanita V. A novel 7 bp deletion in PRPF31 associated with autosomal dominant retinitis pigmentosa with incomplete penetrance in an Indian family. Exp Eye Res 2012; 104:82-8. [DOI: 10.1016/j.exer.2012.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 09/09/2012] [Accepted: 09/24/2012] [Indexed: 01/18/2023]
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661
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Wang ET, Cody NAL, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 2012; 150:710-24. [PMID: 22901804 DOI: 10.1016/j.cell.2012.06.041] [Citation(s) in RCA: 372] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 04/30/2012] [Accepted: 06/20/2012] [Indexed: 11/17/2022]
Abstract
The muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in myotonic dystrophy (DM), in which expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts by using RNA-seq and CLIP-seq approaches. This analysis identified several hundred splicing events whose regulation depended on Mbnl function in a pattern indicating functional interchangeability between Mbnl1 and Mbnl2. A nucleotide resolution RNA map associated repression or activation of exon splicing with Mbnl binding near either 3' splice site or near the downstream 5' splice site, respectively. Transcriptomic analysis of subcellular compartments uncovered a global role for Mbnls in regulating localization of mRNAs in both mouse and Drosophila cells, and Mbnl-dependent translation and protein secretion were observed for a subset of mRNAs with Mbnl-dependent localization. These findings hold several new implications for DM pathogenesis.
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Affiliation(s)
- Eric T Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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662
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Disney MD, Liu B, Yang WY, Sellier C, Tran T, Charlet-Berguerand N, Childs-Disney JL. A small molecule that targets r(CGG)(exp) and improves defects in fragile X-associated tremor ataxia syndrome. ACS Chem Biol 2012; 7:1711-8. [PMID: 22948243 DOI: 10.1021/cb300135h] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of small molecule chemical probes or therapeutics that target RNA remains a significant challenge despite the great interest in such compounds. The most significant barrier to compound development is defining which chemical and RNA motif spaces interact specifically. Herein, we describe a bioactive small molecule probe that targets expanded r(CGG) repeats, or r(CGG)(exp), that causes Fragile X-associated Tremor Ataxia Syndrome (FXTAS). The compound was identified by using information on the chemotypes and RNA motifs that interact. Specifically, 9-hydroxy-5,11-dimethyl-2-(2-(piperidin-1-yl)ethyl)-6H-pyrido[4,3-b]carbazol-2-ium binds the 5'CGG/3'GGC motifs in r(CGG)(exp) and disrupts a toxic r(CGG)(exp)-protein complex in vitro. Structure-activity relationship studies determined that the alkylated pyridyl and phenolic side chains are important chemotypes that drive molecular recognition of r(CGG)(exp). Importantly, the compound is efficacious in FXTAS model cellular systems as evidenced by its ability to improve FXTAS-associated pre-mRNA splicing defects and to reduce the size and number of r(CGG)(exp)-containing nuclear foci. This approach may establish a general strategy to identify lead ligands that target RNA while also providing a chemical probe to dissect the varied mechanisms by which r(CGG)(exp) promotes toxicity.
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Affiliation(s)
- Matthew D. Disney
- Department of Chemistry, The Kellogg School of Science and Engineering, The Scripps Research Institute, Scripps Florida, 130
Scripps Way 3A1, Jupiter, Florida 33458, United States
| | - Biao Liu
- Department of Chemistry, The Kellogg School of Science and Engineering, The Scripps Research Institute, Scripps Florida, 130
Scripps Way 3A1, Jupiter, Florida 33458, United States
| | - Wang-Yong Yang
- Department of Chemistry, The Kellogg School of Science and Engineering, The Scripps Research Institute, Scripps Florida, 130
Scripps Way 3A1, Jupiter, Florida 33458, United States
| | - Chantal Sellier
- Institut de Génétique
et de Biologie Moléculaire et Cellulaire (IGBMC), Institut
National de la Santé et de la Recherche Médicale (INSERM)
U964, Centre National de la Recherche Scientifique (CNRS) UMR7104, University of Strasbourg, Illkirch, France
| | - Tuan Tran
- Department of Chemistry, The Kellogg School of Science and Engineering, The Scripps Research Institute, Scripps Florida, 130
Scripps Way 3A1, Jupiter, Florida 33458, United States
- Department of Chemistry, University at Buffalo, Buffalo, New York 14620, United
States
| | - Nicolas Charlet-Berguerand
- Institut de Génétique
et de Biologie Moléculaire et Cellulaire (IGBMC), Institut
National de la Santé et de la Recherche Médicale (INSERM)
U964, Centre National de la Recherche Scientifique (CNRS) UMR7104, University of Strasbourg, Illkirch, France
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Kellogg School of Science and Engineering, The Scripps Research Institute, Scripps Florida, 130
Scripps Way 3A1, Jupiter, Florida 33458, United States
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663
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Charizanis K, Lee KY, Batra R, Goodwin M, Zhang C, Yuan Y, Shiue L, Cline M, Scotti MM, Xia G, Kumar A, Ashizawa T, Clark HB, Kimura T, Takahashi MP, Fujimura H, Jinnai K, Yoshikawa H, Gomes-Pereira M, Gourdon G, Sakai N, Nishino S, Foster TC, Ares M, Darnell RB, Swanson MS. Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron 2012; 75:437-50. [PMID: 22884328 DOI: 10.1016/j.neuron.2012.05.029] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2012] [Indexed: 02/06/2023]
Abstract
The RNA-mediated disease model for myotonic dystrophy (DM) proposes that microsatellite C(C)TG expansions express toxic RNAs that disrupt splicing regulation by altering MBNL1 and CELF1 activities. While this model explains DM manifestations in muscle, less is known about the effects of C(C)UG expression on the brain. Here, we report that Mbnl2 knockout mice develop several DM-associated central nervous system (CNS) features including abnormal REM sleep propensity and deficits in spatial memory. Mbnl2 is prominently expressed in the hippocampus and Mbnl2 knockouts show a decrease in NMDA receptor (NMDAR) synaptic transmission and impaired hippocampal synaptic plasticity. While Mbnl2 loss did not significantly alter target transcript levels in the hippocampus, misregulated splicing of hundreds of exons was detected using splicing microarrays, RNA-seq, and HITS-CLIP. Importantly, the majority of the Mbnl2-regulated exons examined were similarly misregulated in DM. We propose that major pathological features of the DM brain result from disruption of the MBNL2-mediated developmental splicing program.
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Affiliation(s)
- Konstantinos Charizanis
- Department of Molecular Genetics and Microbiology and the Center for NeuroGenetics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
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664
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Turunen JJ, Niemelä EH, Verma B, Frilander MJ. The significant other: splicing by the minor spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:61-76. [PMID: 23074130 PMCID: PMC3584512 DOI: 10.1002/wrna.1141] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The removal of non-coding sequences, introns, from the mRNA precursors is an essential step in eukaryotic gene expression. U12-type introns are a minor subgroup of introns, distinct from the major or U2-type introns. U12-type introns are present in most eukaryotes but only account for less than 0.5% of all introns in any given genome. They are processed by a specific U12-dependent spliceosome, which is similar to, but distinct from, the major spliceosome. U12-type introns are spliced somewhat less efficiently than the major introns, and it is believed that this limits the expression of the genes containing such introns. Recent findings on the role of U12-dependent splicing in development and human disease have shown that it can also affect multiple cellular processes not directly related to the functions of the host genes of U12-type introns. At the same time, advances in understanding the regulation and phylogenetic distribution of the minor spliceosome are starting to shed light on how the U12-type introns and the minor spliceosome may have evolved. © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Janne J Turunen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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665
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Coonrod LA, Lohman JR, Berglund JA. Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix. Biochemistry 2012; 51:8330-7. [PMID: 23025897 DOI: 10.1021/bi300829w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a microsatellite expansion disorder caused by the aberrant expansion of CTG repeats in the 3'-untranslated region of the DMPK gene. When transcribed, the toxic RNA CUG repeats sequester RNA binding proteins, which leads to disease symptoms. The expanded CUG repeats can adopt a double-stranded structure, and targeting this helix is a therapeutic strategy for DM1. To improve our understanding of the 5'CUG/3'GUC motif and how it may interact with proteins and small molecules, we designed a short CUG helix attached to a GAAA tetraloop/receptor to facilitate crystal packing. Here we report the highest-resolution structure (1.95 Å) to date of a GAAA tetraloop/receptor and the CUG helix it was used to crystallize. Within the CUG helix, we identify two different forms of noncanonical U-U pairs and reconfirm that CUG repeats are essentially A-form. An analysis of all noncanonical U-U pairs in the context of CUG repeats revealed six different classes of conformations that the noncanonical U-U pairs are able to adopt.
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Affiliation(s)
- Leslie A Coonrod
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA
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666
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Blakeley BD, DePorter SM, Mohan U, Burai R, Tolbert BS, McNaughton BR. Methods for identifying and characterizing interactions involving RNA. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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667
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Spencer P, Fry RC, Kisby GE. Unraveling 50-Year-Old Clues Linking Neurodegeneration and Cancer to Cycad Toxins: Are microRNAs Common Mediators? Front Genet 2012; 3:192. [PMID: 23060898 PMCID: PMC3460211 DOI: 10.3389/fgene.2012.00192] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/09/2012] [Indexed: 01/19/2023] Open
Abstract
Recognition of overlapping molecular signaling activated by a chemical trigger of cancer and neurodegeneration is new, but the path to this discovery has been long and potholed. Six conferences (1962–1972) examined the puzzling neurotoxic and carcinogenic properties of a then-novel toxin [cycasin: methylazoxymethanol (MAM)-β-d-glucoside] in cycad plants used traditionally for food and medicine on Guam where a complex neurodegenerative disease plagued the indigenous population. Affected families showed combinations of amyotrophic lateral sclerosis (ALS), parkinsonism (P), and/or a dementia (D) akin to Alzheimer’s disease (AD). Modernization saw declining disease rates on Guam and remarkable changes in clinical phenotype (ALS was replaced by P-D and then by D) and in two genetically distinct ALS-PDC-affected populations (Kii-Japan, West Papua-Indonesia) that used cycad seed medicinally. MAM forms DNA lesions – repaired by O6-methylguanine methyltransferase (MGMT) – that perturb mouse brain development and induce malignant tumors in peripheral organs. The brains of young adult MGMT-deficient mice given a single dose of MAM show DNA lesion-linked changes in cell-signaling pathways associated with miRNA-1, which is implicated in colon, liver, and prostate cancers, and in neurological disease, notably AD. MAM is metabolized to formaldehyde, a human carcinogen. Formaldehyde-responsive miRNAs predicted to modulate MAM-associated genes in the brains of MGMT-deficient mice include miR-17-5p and miR-18d, which regulate genes involved in tumor suppression, DNA repair, amyloid deposition, and neurotransmission. These findings marry cycad-associated ALS-PDC with colon, liver, and prostate cancer; they also add to evidence linking changes in microRNA status both to ALS, AD, and parkinsonism, and to cancer initiation and progression.
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Affiliation(s)
- Peter Spencer
- Global Health Center, Oregon Health and Science University Portland, OR, USA
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668
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Alternative splicing: functional diversity among voltage-gated calcium channels and behavioral consequences. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:1522-9. [PMID: 23022282 DOI: 10.1016/j.bbamem.2012.09.018] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/15/2012] [Accepted: 09/19/2012] [Indexed: 12/14/2022]
Abstract
Neuronal voltage-gated calcium channels generate rapid, transient intracellular calcium signals in response to membrane depolarization. Neuronal Ca(V) channels regulate a range of cellular functions and are implicated in a variety of neurological and psychiatric diseases including epilepsy, Parkinson's disease, chronic pain, schizophrenia, and bipolar disorder. Each mammalian Cacna1 gene has the potential to generate tens to thousands of Ca(V) channels by alternative pre-mRNA splicing, a process that adds fine granulation to the pool of Ca(V) channel structures and functions. The precise composition of Ca(V) channel splice isoform mRNAs expressed in each cell are controlled by cell-specific splicing factors. The activity of splicing factors are in turn regulated by molecules that encode various cellular features, including cell-type, activity, metabolic states, developmental state, and other factors. The cellular and behavioral consequences of individual sites of Ca(V) splice isoforms are being elucidated, as are the cell-specific splicing factors that control splice isoform selection. Altered patterns of alternative splicing of Ca(V) pre-mRNAs can alter behavior in subtle but measurable ways, with the potential to influence drug efficacy and disease severity. This article is part of a Special Issue entitled: Calcium channels.
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669
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Licatalosi DD, Yano M, Fak JJ, Mele A, Grabinski SE, Zhang C, Darnell RB. Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev 2012; 26:1626-42. [PMID: 22802532 DOI: 10.1101/gad.191338.112] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by Ptbp2. To define the roles of Ptbp2 in the nervous system, we generated two independent Ptbp2-null strains, unexpectedly revealing that Ptbp2 is expressed in neuronal progenitors and is essential for postnatal survival. A HITS-CLIP (high-throughput sequencing cross-linking immunoprecipitation)-generated map of reproducible Ptbp2-RNA interactions in the developing mouse neocortex, combined with results from splicing-sensitive microarrays, demonstrated that the major action of Ptbp2 is to inhibit adult-specific alternative exons by binding pyrimidine-rich sequences upstream of and/or within them. These regulated exons are present in mRNAs encoding proteins associated with control of cell fate, proliferation, and the actin cytoskeleton, suggesting a role for Ptbp2 in neurogenesis. Indeed, neuronal progenitors in the Ptbp2-null brain exhibited an aberrant polarity and were associated with regions of premature neurogenesis and reduced progenitor pools. Thus, Ptbp2 inhibition of a discrete set of adult neuronal exons underlies early brain development prior to neuronal differentiation and is essential for postnatal survival.
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Affiliation(s)
- Donny D Licatalosi
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA
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670
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Arslan AD, He X, Wang M, Rumschlag-Booms E, Rong L, Beck WT. A high-throughput assay to identify small-molecule modulators of alternative pre-mRNA splicing. ACTA ACUST UNITED AC 2012; 18:180-90. [PMID: 22972848 DOI: 10.1177/1087057112459901] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alternative splicing (AS) is an efficient mechanism that involves the generation of transcriptome and protein diversity from a single gene. Defects in pre-messenger RNA (mRNA) splicing are an important cause of numerous diseases, including cancer. AS of pre-mRNA as a target for cancer therapy has not been well studied. We have reported previously that a splicing factor, polypyrimidine tract-binding protein (PTB), is overexpressed in ovarian tumors compared with matched normal controls, and knockdown of PTB expression by short-hairpin RNA impairs ovarian tumor cell growth, colony formation, and invasiveness. Given the complexity of PTB's molecular functions, a chemical method for controlling PTB activity might provide a therapeutic and experimental tool. However, no commercially available PTB inhibitors have yet been described. To expand our ability to find novel inhibitors, we developed a robust, fluorometric, cell-based high-throughput screening assay in 96-well plates that reports on the splicing activity of PTB. In an attempt to use the cells for large-scale chemical screens to identify PTB modulators, we established cell lines stably expressing the reporter gene. Our results suggest that this high-throughput assay could be used to identify small-molecule modulators of PTB activity. Based on these findings and the role that upregulated PTB has on cell proliferation and malignant properties of tumors, targeting PTB for inhibition with small molecules offers a promising strategy for cancer therapy.
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Affiliation(s)
- Ahmet Dirim Arslan
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
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671
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Koval AP, Gogolevskaya IK, Tatosyan KA, Kramerov DA. Complementarity of end regions increases the lifetime of small RNAs in mammalian cells. PLoS One 2012; 7:e44157. [PMID: 22984470 PMCID: PMC3440375 DOI: 10.1371/journal.pone.0044157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/30/2012] [Indexed: 11/22/2022] Open
Abstract
Two RNAs (4.5SH and 4.5SI) with unknown functions share a number of features: short length (about 100 nt), transcription by RNA polymerase III, predominately nuclear localization, the presence in various tissues, and relatively narrow taxonomic distribution (4 and 3 rodent families, respectively). It was reported that 4.5SH RNA turns over rapidly, whereas 4.5SI RNA is stable in the cell, but their lifetimes remained unknown. We showed that 4.5SH is indeed short-lived (t1/2∼18 min) and 4.5SI is long-lived (t1/2∼22 h) in Krebs ascites carcinoma cells. The RNA structures specifying rapid or slow decay of different small cellular RNAs remain unstudied. We searched for RNA structural features that determine the short lifetime of 4.5SH in comparison with the long lifetime of 4.5SI RNA. The sequences of genes of 4.5SH and 4.5SI RNAs were altered and human cells (HeLa) were transfected with these genes. The decay rate of the original and altered RNAs was measured. The complementarity of 16-nt end regions of 4.5SI RNA proved to contribute to its stability in cells, whereas the lack of such complementarity in 4.5SH RNA caused its rapid decay. Possible mechanisms of the phenomenon are discussed.
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Affiliation(s)
| | | | | | - Dmitri A. Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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672
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Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol 2012; 19:998-1004. [PMID: 22961379 DOI: 10.1038/nsmb.2373] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/02/2012] [Indexed: 12/29/2022]
Abstract
Argonaute proteins play a major part in transcriptional gene silencing in many organisms, but their role in the nucleus of somatic mammalian cells remains elusive. Here, we have immunopurified human Argonaute-1 and Argonaute-2 (AGO1 and AGO2) chromatin-embedded proteins and found them associated with chromatin modifiers and, notably, with splicing factors. Using the CD44 gene as a model, we show that AGO1 and AGO2 facilitate spliceosome recruitment and modulate RNA polymerase II elongation rate, thereby affecting alternative splicing. Proper AGO1 and AGO2 recruitment to CD44 transcribed regions required the endonuclease Dicer and the chromobox protein HP1γ, and resulted in increased histone H3 lysine 9 methylation on variant exons. Our data thus uncover a new model for the regulation of alternative splicing, in which Argonaute proteins couple RNA polymerase II elongation to chromatin modification.
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673
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Vogel G, Richard S. Emerging roles for Sam68 in adipogenesis and neuronal development. RNA Biol 2012; 9:1129-33. [PMID: 23018781 DOI: 10.4161/rna.21409] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sam68, the Src-associated substrate during mitosis of 68 kDa, belongs to the large class of heteronuclear ribonucleoprotein particle K (hnRNP K) homology (KH) domain family of RNA-binding proteins. Sam68 contains a single KH domain harboring conserved N- and C-terminal sequences required for RNA binding and homodimerization. The KH domain is one of the most prevalent RNA binding domains that directly contacts single-stranded RNA. Sam68 has been implicated in numerous aspects of RNA metabolism including alternative splicing and polysomal recruitment of mRNAs. Studies in mice have revealed physiological roles linking Sam68 to osteoporosis, obesity, cancer, infertility and ataxia. Recent publications have greatly enhanced our understanding of Sam68 mechanism of action in addition to its cellular role. Herein, we will discuss the latest advances in the literature pertaining to obesity and neuronal development.
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Affiliation(s)
- Gillian Vogel
- Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, QC Canada
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674
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Dichmann DS, Harland RM. fus/TLS orchestrates splicing of developmental regulators during gastrulation. Genes Dev 2012; 26:1351-63. [PMID: 22713872 DOI: 10.1101/gad.187278.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we investigated the function of the atypical RNA-binding protein fus/TLS (fused in sarcoma/translocated in sarcoma) during early frog development. We found that fus is necessary for proper mRNA splicing of a set of developmental regulatory genes during early frog development and gastrulation. Upon fus knockdown, embryos fail to gastrulate and show mesodermal differentiation defects that we connect to intron retention in fgf8 (fibroblast growth factor 8) and fgfr2 (fgf receptor 2) transcripts. During gastrulation, the animal and marginal regions dissociate, and we show that this is caused, at least in part, by intron retention in cdh1 transcripts. We confirm the specificity of splicing defects at a genomic level using analysis of RNA sequencing (RNA-seq) and show that 3%-5% of all transcripts display intron retention throughout the pre-mRNA. By analyzing gene ontology slim annotations, we show that the affected genes are enriched for developmental regulators and therefore represent a biologically coherent set of targets for fus regulation in embryogenesis. This shows that fus is central to embryogenesis and may provide information on its function in neurodegenerative disease.
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Affiliation(s)
- Darwin S Dichmann
- Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California at Berkeley, Berkeley, California 94720, USA
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675
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Boucas J, Riabinska A, Jokic M, Herter-Sprie GS, Chen S, Höpker K, Reinhardt HC. Posttranscriptional regulation of gene expression-adding another layer of complexity to the DNA damage response. Front Genet 2012; 3:159. [PMID: 22936947 PMCID: PMC3427493 DOI: 10.3389/fgene.2012.00159] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/06/2012] [Indexed: 12/13/2022] Open
Abstract
In response to DNA damage, cells activate a complex, kinase-based signaling network to arrest the cell cycle and allow time for DNA repair, or, if the extend of damage is beyond repair capacity, induce apoptosis. This signaling network, which is collectively referred to as the DNA damage response (DDR), is primarily thought to consist of two components—a rapid phosphorylation-driven signaling cascade that results in immediate inhibition of Cdk/cyclin complexes and a delayed transcriptional response that promotes a prolonged cell cycle arrest through the induction of Cdk inhibitors, such as p21. In recent years a third layer of complexity has emerged that involves potent posttranscriptional regulatory mechanisms that control the cellular response to DNA damage. Although much has been written on the relevance of the DDR in cancer and on the post-transcriptional role of microRNAs (miRs) in cancer, the post-transcriptional regulation of the DDR by non-coding RNAs and RNA-binding proteins (RBPs) still remains elusive in large parts. Here, we review the recent developments in this exciting new area of research in the cellular response to genotoxic stress. We put specific emphasis on the role of RBPs and the control of their function through DNA damage-activated protein kinases.
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Affiliation(s)
- Jorge Boucas
- Division of Hematology and Oncology, Center for Internal Medicine, University Hospital of Cologne Cologne, Germany
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676
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Lombès T, Moumné R, Larue V, Prost E, Catala M, Lecourt T, Dardel F, Micouin L, Tisné C. Investigation of RNA-Ligand Interactions by 19F NMR Spectroscopy Using Fluorinated Probes. Angew Chem Int Ed Engl 2012; 51:9530-4. [DOI: 10.1002/anie.201204083] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 01/08/2023]
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677
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Lombès T, Moumné R, Larue V, Prost E, Catala M, Lecourt T, Dardel F, Micouin L, Tisné C. Investigation of RNA-Ligand Interactions by 19F NMR Spectroscopy Using Fluorinated Probes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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678
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Weigand JE, Boeckel JN, Gellert P, Dimmeler S. Hypoxia-induced alternative splicing in endothelial cells. PLoS One 2012; 7:e42697. [PMID: 22876330 PMCID: PMC3411717 DOI: 10.1371/journal.pone.0042697] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/11/2012] [Indexed: 01/12/2023] Open
Abstract
Background Adaptation to low oxygen by changing gene expression is vitally important for cell survival and tissue development. The sprouting of new blood vessels, initiated from endothelial cells, restores the oxygen supply of ischemic tissues. In contrast to the transcriptional response induced by hypoxia, which is mainly mediated by members of the HIF family, there are only few studies investigating alternative splicing events. Therefore, we performed an exon array for the genome-wide analysis of hypoxia-related changes of alternative splicing in endothelial cells. Methodology/Principal findings Human umbilical vein endothelial cells (HUVECs) were incubated under hypoxic conditions (1% O2) for 48 h. Genome-wide transcript and exon expression levels were assessed using the Affymetrix GeneChip Human Exon 1.0 ST Array. We found altered expression of 294 genes after hypoxia treatment. Upregulated genes are highly enriched in glucose metabolism and angiogenesis related processes, whereas downregulated genes are mainly connected to cell cycle and DNA repair. Thus, gene expression patterns recapitulate known adaptations to low oxygen supply. Alternative splicing events, until now not related to hypoxia, are shown for nine genes: six which are implicated in angiogenesis-mediated cytoskeleton remodeling (cask, itsn1, larp6, sptan1, tpm1 and robo1); one, which is involved in the synthesis of membrane-anchors (pign) and two universal regulators of gene expression (cugbp1 and max). Conclusions/Significance For the first time, this study investigates changes in splicing in the physiological response to hypoxia on a genome-wide scale. Nine alternative splicing events, until now not related to hypoxia, are reported, considerably expanding the information on splicing changes due to low oxygen supply. Therefore, this study provides further knowledge on hypoxia induced gene expression changes and presents new starting points to study the hypoxia adaptation of endothelial cells.
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Affiliation(s)
- Julia E Weigand
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe University Frankfurt, Frankfurt am Main, Germany.
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679
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Robinson TJ, Forte E, Salinas RE, Puri S, Marengo M, Garcia-Blanco MA, Luftig MA. SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data. RNA (NEW YORK, N.Y.) 2012; 18:1435-1445. [PMID: 22736799 PMCID: PMC3404365 DOI: 10.1261/rna.033621.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/04/2012] [Indexed: 06/01/2023]
Abstract
The key postulate that one gene encodes one protein has been overhauled with the discovery that one gene can generate multiple RNA transcripts through alternative mRNA processing. In this study, we describe SplicerEX, a novel and uniquely motivated algorithm designed for experimental biologists that (1) detects widespread changes in mRNA isoforms from both conventional and splice sensitive microarray data, (2) automatically categorizes mechanistic changes in mRNA processing, and (3) mitigates known technological artifacts of exon array-based detection of alternative splicing resulting from 5' and 3' signal attenuation, background detection limits, and saturation of probe set signal intensity. In this study, we used SplicerEX to compare conventional and exon-based Affymetrix microarray data in a model of EBV transformation of primary human B cells. We demonstrated superior detection of 3'-located changes in mRNA processing by the Affymetrix U133 GeneChip relative to the Human Exon Array. SplicerEX-identified exon-level changes in the EBV infection model were confirmed by RT-PCR and revealed a novel set of EBV-regulated mRNA isoform changes in caspases 6, 7, and 8. Finally, SplicerEX as compared with MiDAS analysis of publicly available microarray data provided more efficiently categorized mRNA isoform changes with a significantly higher proportion of hits supported by previously annotated alternative processing events. Therefore, SplicerEX provides an important tool for the biologist interested in studying changes in mRNA isoform usage from conventional or splice-sensitive microarray platforms, especially considering the expansive amount of archival microarray data generated over the past decade. SplicerEX is freely available upon request.
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Affiliation(s)
| | | | | | - Shaan Puri
- Department of Molecular Genetics and Microbiology
| | - Matthew Marengo
- Department of Molecular Genetics and Microbiology
- Center for RNA Biology
| | - Mariano A. Garcia-Blanco
- Department of Molecular Genetics and Microbiology
- Center for RNA Biology
- Department of Medicine, and
- Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology
- Center for RNA Biology
- Department of Medicine, and
- Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
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680
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Chamberlain CM, Ranum LPW. Mouse model of muscleblind-like 1 overexpression: skeletal muscle effects and therapeutic promise. Hum Mol Genet 2012; 21:4645-54. [PMID: 22846424 DOI: 10.1093/hmg/dds306] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Myotonic dystrophy (DM) is a multisystemic disease caused by CTG or CCTG expansion mutations. There is strong evidence that DM1 CUG and DM2 CCUG expansion transcripts sequester muscleblind-like (MBNL) proteins and that loss of MBNL function causes alternative splicing abnormalities that contribute to disease. Because MBNL1 loss is thought to play an important role in disease and localized AAV delivery of MBNL1 partially rescues skeletal muscle pathology in DM mice, there is strong interest in MBNL1 overexpression as a therapeutic strategy. We developed the first transgenic MBNL1 overexpression mouse model (MBNL1-OE) to test the safety and efficacy of multisystemic MBNL1 overexpression. First, we demonstrate that MBNL1 overexpression is generally well-tolerated in skeletal muscle. Second, we show the surprising result that premature shifts in alternative splicing of MBNL1-regulated genes in multiple organ systems are compatible with life and do not cause embryonic lethality. Third, we show for the first time that early and long-term MBNL1 overexpression prevents CUG-induced myotonia, myopathy and alternative splicing abnormalities in DM1 mice. In summary, MBNL1 overexpression may be a valuable strategy for treating the skeletal muscle features of DM.
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681
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RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nat Med 2012; 18:766-73. [PMID: 22466703 DOI: 10.1038/nm.2693] [Citation(s) in RCA: 405] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/31/2012] [Indexed: 01/15/2023]
Abstract
Alternative splicing has a major role in cardiac adaptive responses, as exemplified by the isoform switch of the sarcomeric protein titin, which adjusts ventricular filling. By positional cloning using a previously characterized rat strain with altered titin mRNA splicing, we identified a loss-of-function mutation in the gene encoding RNA binding motif protein 20 (Rbm20) as the underlying cause of pathological titin isoform expression. The phenotype of Rbm20-deficient rats resembled the pathology seen in individuals with dilated cardiomyopathy caused by RBM20 mutations. Deep sequencing of the human and rat cardiac transcriptome revealed an RBM20-dependent regulation of alternative splicing. In addition to titin (TTN), we identified a set of 30 genes with conserved splicing regulation between humans and rats. This network is enriched for genes that have previously been linked to cardiomyopathy, ion homeostasis and sarcomere biology. Our studies emphasize the key role of post-transcriptional regulation in cardiac function and provide mechanistic insights into the pathogenesis of human heart failure.
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682
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Kaida D, Schneider-Poetsch T, Yoshida M. Splicing in oncogenesis and tumor suppression. Cancer Sci 2012; 103:1611-6. [PMID: 22691055 DOI: 10.1111/j.1349-7006.2012.02356.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/04/2012] [Accepted: 06/07/2012] [Indexed: 12/23/2022] Open
Abstract
Post-transcriptional modifications, such as 5' end capping, 3' end polyadenylation and splicing, are necessary for the precise regulation of gene expression and transcriptome integrity. Therefore, it is not surprising that abnormalities of these post-transcriptional modifications prompt numerous diseases, including cancer. In fact, many studies revealed that misregulation of mRNA processing, especially splicing, are observed in a variety of cancer cells. In this review we describe how changes within RNA splicing regulatory elements or mutations in the processing factors alter the expression of tumor suppressors or oncogenes with pathological consequences. In addition, we show how several small molecules that bind to spliceosomal components and splicing regulators inhibit or modulate splicing activity. These compounds have anticancer activity and further development of small molecule modulators has potential in next generation cancer therapy.
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Affiliation(s)
- Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Japan
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683
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The Caenorhabditis elegans gene mfap-1 encodes a nuclear protein that affects alternative splicing. PLoS Genet 2012; 8:e1002827. [PMID: 22829783 PMCID: PMC3400559 DOI: 10.1371/journal.pgen.1002827] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/25/2012] [Indexed: 12/02/2022] Open
Abstract
RNA splicing is a major regulatory mechanism for controlling eukaryotic gene expression. By generating various splice isoforms from a single pre–mRNA, alternative splicing plays a key role in promoting the evolving complexity of metazoans. Numerous splicing factors have been identified. However, the in vivo functions of many splicing factors remain to be understood. In vivo studies are essential for understanding the molecular mechanisms of RNA splicing and the biology of numerous RNA splicing-related diseases. We previously isolated a Caenorhabditis elegans mutant defective in an essential gene from a genetic screen for suppressors of the rubberband Unc phenotype of unc-93(e1500) animals. This mutant contains missense mutations in two adjacent codons of the C. elegans microfibrillar-associated protein 1 gene mfap-1. mfap-1(n4564 n5214) suppresses the Unc phenotypes of different rubberband Unc mutants in a pattern similar to that of mutations in the splicing factor genes uaf-1 (the C. elegans U2AF large subunit gene) and sfa-1 (the C. elegans SF1/BBP gene). We used the endogenous gene tos-1 as a reporter for splicing and detected increased intron 1 retention and exon 3 skipping of tos-1 transcripts in mfap-1(n4564 n5214) animals. Using a yeast two-hybrid screen, we isolated splicing factors as potential MFAP-1 interactors. Our studies indicate that C. elegans mfap-1 encodes a splicing factor that can affect alternative splicing. RNA splicing removes intervening intronic sequences from pre–mRNA transcripts and joins adjacent exonic sequences to generate functional messenger RNAs. The in vivo functions of numerous factors that regulate splicing remain to be understood. From a genetic screen for suppressors of the rubberband Unc phenotype caused by the Caenorhabditis elegans unc-93(e1500) mutation, we isolated a mutation that affects a highly conserved essential gene, mfap-1. MFAP-1 is a nuclear protein that is broadly expressed. MFAP-1 can affect the alternative splicing of tos-1, an endogenous reporter gene for splicing, and is required for the altered splicing at a cryptic 3′ splice site of tos-1. mfap-1 enhances the effects of the gene uaf-1 (splicing factor U2AF large subunit) in suppressing the rubberband Unc phenotype of unc-93(e1500) animals. Our studies provide in vivo evidence that MFAP-1 functions as a splicing factor.
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684
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Pre-mRNA splicing in disease and therapeutics. Trends Mol Med 2012; 18:472-82. [PMID: 22819011 DOI: 10.1016/j.molmed.2012.06.006] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 06/12/2012] [Accepted: 06/18/2012] [Indexed: 01/18/2023]
Abstract
In metazoans, alternative splicing of genes is essential for regulating gene expression and contributing to functional complexity. Computational predictions, comparative genomics, and transcriptome profiling of normal and diseased tissues indicate that an unexpectedly high fraction of diseases are caused by mutations that alter splicing. Mutations in cis elements cause missplicing of genes that alter gene function and contribute to disease pathology. Mutations of core spliceosomal factors are associated with hematolymphoid neoplasias, retinitis pigmentosa, and microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Mutations in the trans regulatory factors that control alternative splicing are associated with autism spectrum disorder, amyotrophic lateral sclerosis (ALS), and various cancers. In addition to discussing the disorders caused by these mutations, this review summarizes therapeutic approaches that have emerged to correct splicing of individual genes or target the splicing machinery.
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685
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Abstract
Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.
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Affiliation(s)
| | - Jan Attig
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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686
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Abstract
Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.
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687
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Pérez-Valle J, Vilardell J. Intronic features that determine the selection of the 3' splice site. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:707-17. [PMID: 22807288 DOI: 10.1002/wrna.1131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Most eukaryotic primary transcripts include segments, or introns, that will be accurately removed during RNA biogenesis. This process, known as pre-messenger RNA splicing, is catalyzed by the spliceosome, accurately selecting a set of intronic marks from others apparently equivalent. This identification is critical, as incorrectly spliced RNAs can be toxic for the organism. One of these marks, the dinucleotide AG, signals the intronic 3' end, or 3' splice site (ss). In this review we will focus on those intronic features that have an impact on 3' ss selection. These include the location and type of neighboring sequences, and their distance to the 3' end. We will see that their interplay is needed to select the right intronic end, and that this can be modulated by additional intronic elements that contribute to alternative splicing, whereby diverse RNAs can be generated from identical precursors. This complexity, still poorly understood, is fundamental for the accuracy of gene expression. In addition, a clear knowledge of 3' ss selection is needed to fully decipher the coding potential of genomes.
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Affiliation(s)
- Jorge Pérez-Valle
- Department of Molecular Genòmics, Institute of Molecular Biology of Barcelona (IBMB), Barcelona, Spain
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688
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Bolisetty MT, Beemon KL. Splicing of internal large exons is defined by novel cis-acting sequence elements. Nucleic Acids Res 2012; 40:9244-54. [PMID: 22790982 PMCID: PMC3467050 DOI: 10.1093/nar/gks652] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Human internal exons have an average size of 147 nt, and most are <300 nt. This small size is thought to facilitate exon definition. A small number of large internal exons have been identified and shown to be alternatively spliced. We identified 1115 internal exons >1000 nt in the human genome; these were found in 5% of all protein-coding genes, and most were expressed and translated. Surprisingly, 40% of these were expressed at levels similar to the flanking exons, suggesting they were constitutively spliced. While all of the large exons had strong splice sites, the constitutively spliced large exons had a higher ratio of splicing enhancers/silencers and were more conserved across mammals than the alternatively spliced large exons. We asked if large exons contain specific sequences that promote splicing and identified 38 sequences enriched in the large exons relative to small exons. The consensus sequence is C-rich with a central invariant CA dinucleotide. Mutation of these sequences in a candidate large exon indicated that these are important for recognition of large exons by the splicing machinery. We propose that these sequences are large exon splicing enhancers (LESEs).
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Affiliation(s)
- Mohan T Bolisetty
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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689
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Yee JK, Lin RJ. Antisense oligonucleotides shed new light on the pathogenesis and treatment of spinal muscular atrophy. Mol Ther 2012; 20:8-10. [PMID: 22215052 DOI: 10.1038/mt.2011.275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jiing-Kuan Yee
- Department of Virology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California 91010, USA.
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690
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Decorsière A, Toulas C, Fouque F, Tilkin-Mariamé AF, Selves J, Guimbaud R, Chipoulet E, Delmas C, Rey JM, Pujol P, Favre G, Millevoi S, Vagner S. Decreased efficiency of MSH6 mRNA polyadenylation linked to a 20-base-pair duplication in Lynch syndrome families. Cell Cycle 2012; 11:2578-80. [DOI: 10.4161/cc.20625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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691
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Kanhoush R, Beenders B, Perrin C, Moreau J, Bellini M, Penrad-Mobayed M. Novel domains in the hnRNP G/RBMX protein with distinct roles in RNA binding and targeting nascent transcripts. Nucleus 2012; 1:109-22. [PMID: 21327109 DOI: 10.4161/nucl.1.1.10857] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 12/06/2009] [Accepted: 12/06/2009] [Indexed: 11/19/2022] Open
Abstract
The heterogenous nuclear ribonucleoprotein G (hnRNP G) controls the alternative splicing of several pre-mRNas. While hnRNP G displays an amino terminal RNA recognition motif (RRM), we find that this motif is paradoxically not implicated in the recruitment of hnRNP G to nascent transcripts in amphibian oocytes. In fact, a deletion analysis revealed that targeting of hnRNP G to active transcription units depends on another domain, centrally positioned, and consisting of residues 186-236. We show that this domain acts autonomously and thus is named NTD for nascent transcripts targeting domain. Furthermore, using an RNA probe previously characterized in vitro as an RNA that interacts specifically with hnRNP G, we demonstrate a new auxiliary RNA binding domain (RBD). It corresponds to a short region of 58 residues positioned at the carboxyl terminal end of the protein, which recognizes an RNA motif predicted to adopt an hairpin structure. The fact that the NTD acts independently from both the RRM and the RBD strongly suggests that the initial recruitment of hnRNP G to nascent pre-mRNAs is independent of its sequence-specific RNA binding properties. Together, these findings highlight the modular organization of hnRNP G and offer new insights into its multifunctional roles.
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Affiliation(s)
- Rasha Kanhoush
- Institut Jacques Monod, CNRS and Université Paris-Diderot, Paris, France
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692
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Wei WJ, Mu SR, Heiner M, Fu X, Cao LJ, Gong XF, Bindereif A, Hui J. YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts. Nucleic Acids Res 2012; 40:8622-36. [PMID: 22730292 PMCID: PMC3458536 DOI: 10.1093/nar/gks579] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The human Y box-binding protein-1 (YB-1) is a deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein with pleiotropic functions. Besides its roles in the regulation of transcription and translation, several recent studies indicate that YB-1 is a spliceosome-associated protein and is involved in alternative splicing, but the underlying mechanism has remained elusive. Here, we define both CAUC and CACC as high-affinity binding motifs for YB-1 by systematic evolution of ligands by exponential enrichment (SELEX) and demonstrate that these newly defined motifs function as splicing enhancers. Interestingly, on the endogenous CD44 gene, YB-1 appears to mediate a network interaction to activate exon v5 inclusion via multiple CAUC motifs in both the alternative exon and its upstream polypyrimidine tract. We provide evidence that YB-1 activates splicing by facilitating the recruitment of U2AF65 to weak polypyrimidine tracts through direct protein–protein interactions. Together, these findings suggest a vital role of YB-1 in activating a subset of weak 3′ splice sites in mammalian cells.
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Affiliation(s)
- Wen-Juan Wei
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
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693
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The Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus. Mol Cell 2012; 47:422-33. [PMID: 22727668 DOI: 10.1016/j.molcel.2012.05.014] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/09/2012] [Accepted: 05/10/2012] [Indexed: 11/21/2022]
Abstract
Pre-mRNA splicing is regulated by developmental and environmental cues, but little is known about how specific signals are transduced in mammalian cells to regulate this critical gene expression step. Here, we report massive reprogramming of alternative splicing in response to EGF signaling. By blocking individual branches in EGF signaling, we found that Akt activation plays a major role, while other branches, such as the JAK/STAT and ERK pathways, make minor contributions to EGF-induced splicing. Activated Akt next branches to SR protein-specific kinases, rather than mTOR, by inducing SRPK autophosphorylation that switches the splicing kinases from Hsp70- to Hsp90-containing complexes. This leads to enhanced SRPK nuclear translocation and SR protein phosphorylation. These findings reveal a major signal transduction pathway for regulated splicing and place SRPKs in a central position in the pathway, consistent with their reputed roles in a large number of human cancers.
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694
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Cao W, Razanau A, Feng D, Lobo VG, Xie J. Control of alternative splicing by forskolin through hnRNP K during neuronal differentiation. Nucleic Acids Res 2012; 40:8059-71. [PMID: 22684629 PMCID: PMC3439897 DOI: 10.1093/nar/gks504] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The molecular basis of cell signal-regulated alternative splicing at the 3′ splice site remains largely unknown. We isolated a protein kinase A-responsive ribonucleic acid (RNA) element from a 3′ splice site of the synaptosomal-associated protein 25 (Snap25) gene for forskolin-inhibited splicing during neuronal differentiation of rat pheochromocytoma PC12 cells. The element binds specifically to heterogeneous nuclear ribonucleo protein (hnRNP) K in a phosphatase-sensitive way, which directly competes with the U2 auxiliary factor U2AF65, an essential component of early spliceosomes. Transcripts with similarly localized hnRNP K target motifs upstream of alternative exons are enriched in genes often associated with neurological diseases. We show that such motifs upstream of the Runx1 exon 6 also bind hnRNP K, and importantly, hnRNP K is required for forskolin-induced repression of the exon. Interestingly, this exon encodes the peptide domain that determines the switch of the transcriptional repressor/activator activity of Runx1, a change known to be critical in specifying neuron lineages. Consistent with an important role of the target genes in neurons, knocking down hnRNP K severely disrupts forskolin-induced neurite growth. Thus, through hnRNP K, the neuronal differentiation stimulus forskolin targets a critical 3′ splice site component of the splicing machinery to control alternative splicing of crucial genes. This also provides a regulated direct competitor of U2AF65 for cell signal control of 3′ splice site usage.
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Affiliation(s)
- Wenguang Cao
- Department of Physiology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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695
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Herzog A, Hartung R, Reuser AJJ, Hermanns P, Runz H, Karabul N, Gökce S, Pohlenz J, Kampmann C, Lampe C, Beck M, Mengel E. A cross-sectional single-centre study on the spectrum of Pompe disease, German patients: molecular analysis of the GAA gene, manifestation and genotype-phenotype correlations. Orphanet J Rare Dis 2012; 7:35. [PMID: 22676651 PMCID: PMC3479421 DOI: 10.1186/1750-1172-7-35] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/07/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pompe disease (Glycogen storage disease type II, GSD II, acid alpha-glucosidase deficiency, acid maltase deficiency, OMIM # 232300) is an autosomal-recessive lysosomal storage disorder due to a deficiency of acid alpha-glucosidase (GAA, acid maltase, EC 3.2.1.20, Swiss-Prot P10253). Clinical manifestations are dominated by progressive weakness of skeletal muscle throughout the clinical spectrum. In addition, the classic infantile form is characterised by hypertrophic cardiomyopathy. METHODS In a cross-sectional single-centre study we clinically assessed 3 patients with classic infantile Pompe disease and 39 patients with non-classic presentations, measured their acid alpha-glucosidase activities and analysed their GAA genes. RESULTS Classic infantile patients had nearly absent residual enzyme activities and a typical clinical course with hypertrophic cardiomyopathy until the beginning of therapy. The disease manifestations in non-classic patients were heterogeneous. There was a broad variability in the decline of locomotive and respiratory function. The age of onset ranged from birth to late adulthood and correlated with enzyme activities. Molecular analysis revealed as many as 33 different mutations, 14 of which are novel. All classic infantile patients had two severe mutations. The most common mutation in the non-classic group was c.-32-13T>G. It was associated with a milder course in this subgroup. CONCLUSIONS Disease manifestation strongly correlates with the nature of the GAA mutations, while the variable progression in non-classic Pompe disease is likely to be explained by yet unknown modifying factors. This study provides the first comprehensive dataset on the clinical course and the mutational spectrum of Pompe disease in Germany.
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Affiliation(s)
- Andreas Herzog
- Center for Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
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696
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Redelsperger F, Lekbaby B, Mandouri Y, Giang E, Duriez M, Desire N, Roque Afonso AM, Brichler S, Dubreuil P, Dobrin A, Perlemuter G, Prevot S, Bacon N, Grange JD, Zatla F, Le Pendeven C, Pol S, Strick-Marchand H, Di Santo J, Kremsdorf D, Soussan P. Production of hepatitis B defective particles is dependent on liver status. Virology 2012; 431:21-8. [PMID: 22664356 DOI: 10.1016/j.virol.2012.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 05/09/2012] [Indexed: 02/07/2023]
Abstract
Defective hepatitis B virus (dHBV) generated from spliced RNA is detected in the sera of HBV-chronic carriers. Our study was designed to determine whether the proportion of dHBV changed during the course of infection, and to investigate whether dHBV might interfere with HBV replication. To achieve this, HBV wild-type and dHBV levels were determined by Q-PCR in sera from 56 untreated chronic patients and 23 acute patients, in sequential samples from 4 treated-patients and from liver-humanized mice after HBV infection. The proportion of dHBV was higher in patients with severe compared to null/moderate liver disease or with acute infection. Follow-up showed that the proportion of dHBV increased during disease progression. By contrast, a low and stable proportion of dHBV was observed in the humanized-mouse model of HBV infection. Our results highlight a regulation of the proportion of dHBV during liver disease progression that is independent of interference with viral replication.
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Affiliation(s)
- Francois Redelsperger
- Inserm U845, Pathogenèse des Hépatites Virales B et Immunothérapie, 156 Rue de Vaugirard, 75015 Paris, France
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697
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Alternative splicing interference by xenobiotics. Toxicology 2012; 296:1-12. [DOI: 10.1016/j.tox.2012.01.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/21/2012] [Accepted: 01/23/2012] [Indexed: 12/21/2022]
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698
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de Almeida SF, Carmo-Fonseca M. Design principles of interconnections between chromatin and pre-mRNA splicing. Trends Biochem Sci 2012; 37:248-53. [DOI: 10.1016/j.tibs.2012.02.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/01/2012] [Accepted: 02/06/2012] [Indexed: 11/24/2022]
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699
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Alternative splicing: decoding an expansive regulatory layer. Curr Opin Cell Biol 2012; 24:323-32. [DOI: 10.1016/j.ceb.2012.03.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/27/2012] [Accepted: 03/08/2012] [Indexed: 12/14/2022]
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700
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Mackereth CD, Sattler M. Dynamics in multi-domain protein recognition of RNA. Curr Opin Struct Biol 2012; 22:287-96. [DOI: 10.1016/j.sbi.2012.03.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/25/2012] [Indexed: 12/28/2022]
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