Research Topics
Genomes and Genes
| alternative splicingSummarySummary: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different. Top Publications
Research Grants
| Scientific Experts
|
Detail Information
Publications
Mapping and quantifying mammalian transcriptomes by RNA-SeqAli Mortazavi
Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
Nat Methods 5:621-8. 2008..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
Expansion of the eukaryotic proteome by alternative splicingTimothy W Nilsen
Center for RNA Molecular Biology, Department of Biochemistry, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
Nature 463:457-63. 2010..It is now clear that the 'missing' information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be ..- Alternative isoform regulation in human tissue transcriptomesEric T Wang
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 456:470-6. 2008..in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, 86% with a minor isoform frequency of 15% or more... - The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylationVidisha Tripathi
Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Mol Cell 39:925-38. 2010b>Alternative splicing (AS) of pre-mRNA is utilized by higher eukaryotes to achieve increased transcriptome and proteomic complexity... - Regulation of alternative splicing by histone modificationsReini F Luco
National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Science 327:996-1000. 2010b>Alternative splicing of pre-mRNA is a prominent mechanism to generate protein diversity, yet its regulation is poorly understood. We demonstrated a direct role for histone modifications in alternative splicing... - Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencingQun Pan
Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
Nat Genet 40:1413-5. 2008We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in approximately 20% of multiexon genes, many of which are tissue specific... - A global view of gene activity and alternative splicing by deep sequencing of the human transcriptomeMarc Sultan
Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
Science 321:956-60. 2008..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing. - RNA processing and its regulation: global insights into biological networksDonny D Licatalosi
Howard Hughes Medical Institute, Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York 10021, USA
Nat Rev Genet 11:75-87. 2010..are revealing increasingly complete descriptions of RNA regulation and complexity; for example, through alternative splicing, alternative polyadenylation and RNA editing... - HITS-CLIP yields genome-wide insights into brain alternative RNA processingDonny D Licatalosi
Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
Nature 456:464-9. 2008..footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo... - Genome-wide mapping of alternative splicing in Arabidopsis thalianaSergei A Filichkin
Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
Genome Res 20:45-58. 2010b>Alternative splicing can enhance transcriptome plasticity and proteome diversity... 
Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17M Hutton
Mayo Clinic Jacksonville, Florida 32224, USA
Nature 393:702-5. 1998..mutations all destabilize a potential stem-loop structure which is probably involved in regulating the alternative splicing of exon10...- Mechanisms of alternative splicing regulation: insights from molecular and genomics approachesMo Chen
Department of Biological Sciences, Columbia University, New York, New York 10027, USA
Nat Rev Mol Cell Biol 10:741-54. 2009b>Alternative splicing of mRNA precursors provides an important means of genetic control and is a crucial step in the expression of most genes... - Splicing in disease: disruption of the splicing code and the decoding machineryGuey Shin Wang
Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
Nat Rev Genet 8:749-61. 2007..b>Alternative splicing generates a highly dynamic human proteome through networks of coordinated splicing events... - Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cellsChristine Mayr
Howard Hughes Medical Institute, USA
Cell 138:673-84. 2009..The high incidence of APA in cancer cells, with consequent loss of 3'UTR repressive elements, suggests a pervasive role for APA in oncogene activation without genetic alteration... - Deciphering the splicing codeYoseph Barash
Biomedical Engineering, Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto M5S 3G4, Canada
Nature 465:53-9. 2010b>Alternative splicing has a crucial role in the generation of biological complexity, and its misregulation is often involved in human disease... - The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicingEugene V Makeyev
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Mol Cell 27:435-48. 2007..These events culminate in the transition from non-NS to NS-specific alternative splicing patterns... - The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growthHeather R Christofk
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 452:230-3. 2008..These results demonstrate that M2 expression is necessary for aerobic glycolysis and that this metabolic phenotype provides a selective growth advantage for tumour cells in vivo... - RNA and diseaseThomas A Cooper
Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
Cell 136:777-93. 2009..b>Alternative splicing provides cells with an exquisite capacity to fine-tune their transcriptome and proteome in response to cues... - Alternative splicing and evolution: diversification, exon definition and functionHadas Keren
Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
Nat Rev Genet 11:345-55. 2010Over the past decade, it has been shown that alternative splicing (AS) is a major mechanism for the enhancement of transcriptome and proteome diversity, particularly in mammals... - Transcriptome genetics using second generation sequencing in a Caucasian populationStephen B Montgomery
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211 Switzerland
Nature 464:773-7. 2010..number of variants that influence the structure of mature transcripts indicating variants responsible for alternative splicing. Finally, measures of allele-specific expression allowed the identification of rare eQTLs and allelic .. - An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transitionClaude C Warzecha
Renal Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
EMBO J 29:3286-300. 2010b>Alternative splicing achieves coordinated changes in post-transcriptional gene expression programmes through the activities of diverse RNA-binding proteins... - Statistical significance for genomewide studiesJohn D Storey
Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 100:9440-5. 2003..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage... - Genome-wide analysis of transcript isoform variation in humansTony Kwan
Department of Human Genetics, McGill University, 740 Dr Penfield, Room 7210, Montreal, Quebec H3A 1A4, Canada
Nat Genet 40:225-31. 2008..This extra layer of molecular diversity may account for natural phenotypic variation and disease susceptibility... - Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skippingYuanchao Xue
Wuhan University, Hubei, China
Mol Cell 36:996-1006. 2009Recent transcriptome analysis indicates that > 90% of human genes undergo alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells... - Alternative splicing and diseaseJamal Tazi
University of Montpellier II, Institute of Molecular Genetics, Centre Nationale de Recherche Scientifique, 1919 Route de Mende, France
Biochim Biophys Acta 1792:14-26. 2009Almost all protein-coding genes are spliced and their majority is alternatively spliced. Alternative splicing is a key element in eukaryotic gene expression that increases the coding capacity of the human genome and an increasing number .. - Sex-specific and lineage-specific alternative splicing in primatesRan Blekhman
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 20:180-9. 2010..Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the .. - Nucleosomes are well positioned in exons and carry characteristic histone modificationsRobin Andersson
The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
Genome Res 19:1732-41. 2009..Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes... - HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancerCharles J David
Department of Biological Sciences, Columbia University, New York, New York 10027, USA
Nature 463:364-8. 2010..These two isoforms result from mutually exclusive alternative splicing of the PKM pre-mRNA, reflecting inclusion of either exon 9 (PKM1) or exon 10 (PKM2)... - An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cellsGene W Yeo
Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
Nat Struct Mol Biol 16:130-7. 2009..These findings suggest that FOX2 functions as a critical regulator of a splicing network, and we further show that FOX2 is important for the survival of human embryonic stem cells... - AltAnalyze and DomainGraph: analyzing and visualizing exon expression dataDorothea Emig
Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
Nucleic Acids Res 38:W755-62. 2010b>Alternative splicing is an important mechanism for increasing protein diversity. However, its functional effects are largely unknown... - Prediction of alternative isoforms from exon expression levels in RNA-Seq experimentsHugues Richard
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
Nucleic Acids Res 38:e112. 2010b>Alternative splicing, polyadenylation of pre-messenger RNA molecules and differential promoter usage can produce a variety of transcript isoforms whose respective expression levels are regulated in time and space, thus contributing .. - A methyl transferase links the circadian clock to the regulation of alternative splicingSabrina E Sanchez
IFEVA, Facultad de Agronomia, UBA CONICET, C1417DSE Buenos Aires, Argentina
Nature 468:112-6. 2010..residues present in histones and Sm spliceosomal proteins, links the circadian clock to the control of alternative splicing in plants... - Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicingIgnacio E Schor
Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE UBA Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
Proc Natl Acad Sci U S A 106:4325-30. 2009In search for physiological pathways affecting alternative splicing through its kinetic coupling with transcription, we found that membrane depolarization of neuronal cells triggers the skipping of exon 18 from the neural cell adhesion .. - Functional and evolutionary insights into human brain development through global transcriptome analysisMatthew B Johnson
Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
Neuron 62:494-509. 2009..These data reveal a large number of specific gene expression and alternative splicing patterns, as well as coexpression networks, associated with distinct regions and neurodevelopmental .. - Alternative splicing: global insightsMartina Hallegger
Department of Biochemistry, University of Cambridge, UK
FEBS J 277:856-66. 2010..splicing in 1977, it was quickly realized that splicing together of different combinations of splice sites--alternative splicing--allows individual genes to generate more than one mRNA isoform... - Sam68 regulates EMT through alternative splicing-activated nonsense-mediated mRNA decay of the SF2/ASF proto-oncogeneCristina Valacca
Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche IGM CNR, 27100 Pavia, Italy
J Cell Biol 191:87-99. 2010..Using an in vitro model, we now show that SF2/ASF is also regulated during EMT/MET by alternative splicing associated with the nonsense-mediated mRNA decay pathway (AS-NMD)... - A slow RNA polymerase II affects alternative splicing in vivoManuel De la Mata
Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, Buenos Aires, Argentina
Mol Cell 12:525-32. 2003..been shown to modify the splicing pattern of several genes, evidencing a coupling between transcription and alternative splicing. It has been proposed that the promoter effect involves modulation of RNA pol II elongation rates... - The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing eventsClaude C Warzecha
Renal Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
RNA Biol 6:546-62. 2009Cell-type and tissue-specific alternative splicing events are regulated by combinatorial control involving both abundant RNA binding proteins as well as those with more discrete expression and specialized functions... - The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicingShivendra Kishore
Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
Hum Mol Genet 19:1153-64. 2010..We recently found that the C/D box snoRNA HBII-52 changes the alternative splicing of the serotonin receptor 2C pre-mRNA, which is different from the traditional C/D box snoRNA function in .. - Co-transcriptional splicing of constitutive and alternative exonsAmy Pandya-Jones
Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
RNA 15:1896-908. 2009..Thus, we demonstrate that the decision to include or skip an alternative exon is made during transcription and not post-transcriptionally... - Structure of PTB bound to RNA: specific binding and implications for splicing regulationFlorian C Oberstrass
Institute for Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology, Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
Science 309:2054-7. 2005..Thus, PTB will induce RNA looping when bound to two separated pyrimidine tracts within the same RNA. This leads to structural models for how PTB functions as an alternative-splicing repressor... - ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicingClaude C Warzecha
Department of Medicine, Renal Division, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Mol Cell 33:591-601. 2009..These studies suggest that Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2) are coordinators of an epithelial cell-type-specific splicing program... - Splicing regulation: from a parts list of regulatory elements to an integrated splicing codeZefeng Wang
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
RNA 14:802-13. 2008b>Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels... - A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heartAuinash Kalsotra
Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 105:20333-8. 2008From a large-scale screen using splicing microarrays and RT-PCR, we identified 63 alternative splicing (AS) events that are coordinated in 3 distinct temporal patterns during mouse heart development... - Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in DrosophilaKasper Daniel Hansen
Division of Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA, USA
PLoS Genet 5:e1000525. 2009..Not all alternative splicing results in functional protein; it can also yield mRNA isoforms with premature stop codons that are degraded .. - Stochastic noise in splicing machineryEugene Melamud
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Nucleic Acids Res 37:4873-86. 2009..In this paper, we propose that most alternative splicing events are the result of noise in the splicing process... - The carboxy terminal domain of RNA polymerase II and alternative splicingManuel J Munoz
Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
Trends Biochem Sci 35:497-504. 2010b>Alternative splicing is controlled by cis-regulatory sequences present in the pre-mRNA and their cognate trans-acting factors, as well as by its coupling to RNA polymerase II (pol II) transcription... - Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophyR S Savkur
Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
Nat Genet 29:40-7. 2001..Here we demonstrate that alternative splicing of the insulin receptor (IR) pre-mRNA is aberrantly regulated in DM1 skeletal muscle tissue, resulting in .. - Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiationNathan Salomonis
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 107:10514-9. 2010..would be greatly helped by obtaining a complete picture of the RNA isoforms produced by these cells due to alternative splicing (AS) and alternative promoter selection (APS)... - Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1Rachel Spellman
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
Mol Cell 27:420-34. 2007..To identify additional PTB-regulated alternative splicing events, we used quantitative proteomic analysis of HeLa cells after knockdown of PTB... - High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicingKara Juneau
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 104:1522-7. 2007..This robust methodology can be used to explore environmentally distinct splicing responses and should be readily adaptable to the study of other organisms, including humans... - The pathobiology of splicingAmanda J Ward
Departments of Molecular and Cellular Biology and Pathology, Baylor College of Medicine, Houston, TX 77030, USA
J Pathol 220:152-63. 2010..One advantage of this architecture is that it allows alternative splicing by differential use of exons to generate multiple mRNAs from individual genes... - Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse modelYimin Hua
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Genes Dev 24:1634-44. 2010..We conclude that this MOE ASO is a promising drug candidate for SMA therapy, and, more generally, that ASOs can be used to efficiently redirect alternative splicing of target genes in the CNS. - ASTD: The Alternative Splicing and Transcript Diversity databaseGautier Koscielny
European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Genomics 93:213-20. 2009The Alternative Splicing and Transcript Diversity database (ASTD) gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data... - An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancersPhilip J Smith
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Hum Mol Genet 15:2490-508. 2006..Finally, we have derived an increased specificity score matrix that incorporates information from both of our SF2/ASF-specific matrices and that accurately predicts the exon-skipping phenotypes of deleterious point mutations... - Alternative splicing controls selective trans-synaptic interactions of the neuroligin-neurexin complexBen Chih
Department of Physiology and Cellular Biophysics, Center for Neurobiology and Behavior, Columbia University Medical Center, College of Physicians and Surgeons, P and S 11-511, 630 West 168th Street, New York, New York 10032, USA
Neuron 51:171-8. 2006..Both neuroligins and neurexins are encoded by multiple genes. Alternative splicing generates large numbers of isoforms, which may engage in selective axo-dendritic interactions... - TMEM16A, a membrane protein associated with calcium-dependent chloride channel activityAntonella Caputo
Laboratorio di Genetica Molecolare, Istituto Giannina Gaslini, Genova 16148, Italy
Science 322:590-4. 2008.... - Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAsYuan Yuan
Department of Molecular Genetics and Microbiology and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, USA
Nucleic Acids Res 35:5474-86. 2007The MBNL and CELF proteins act antagonistically to control the alternative splicing of specific exons during mammalian postnatal development... - Alternative polyadenylation: a twist on mRNA 3' end formationCarol S Lutz
Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey New JerseyMedical School, MSB E671, 185 South Orange Avenue, Newark, New Jersey 07101, USA
ACS Chem Biol 3:609-17. 2008..Alternative RNA processing events, such as alternative splicing, also have been recognized as key contributors to the complexity of mammalian gene expression... - 7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate developmentMatjaz Barboric
Department of Medicine, Rosalind Russell Medical Research Center, University of California, San Francisco, CA 94143 0703, USA
Proc Natl Acad Sci U S A 106:7798-803. 2009..that 7SK snRNP is not only critical for controlling transcription elongation, but also for regulating alternative splicing of pre-mRNAs... - Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTBMiriam Llorian
Department of Biochemistry, University of Cambridge, Cambridge, UK
Nat Struct Mol Biol 17:1114-23. 2010..Our results show that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons... - CTCF-promoted RNA polymerase II pausing links DNA methylation to splicingSanjeev Shukla
Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
Nature 479:74-9. 2011b>Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood... - A novel DNMT3B splice variant expressed in tumor and pluripotent cells modulates genomic DNA methylation patterns and displays altered DNA bindingSuhasni Gopalakrishnan
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
Mol Cancer Res 7:1622-34. 2009..Interestingly, all three DNMTs make use of alternative splicing. DNMT3B has nearly 40 known splice variants expressed in a tissue- and disease-specific manner, but very .. - Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assaysS A Bustin
Academic Department of Surgery, St Bartholomew s and the Royal London School of Medicine and Dentistry, Queen Mary and Westfield College, London E1 1BB, UK
J Mol Endocrinol 25:169-93. 2000..It illustrates the usefulness of these assays by demonstrating the significantly different levels of transcription between individuals of the housekeeping gene family, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH)... - Global impact of RNA polymerase II elongation inhibition on alternative splicing regulationJoanna Y Ip
Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
Genome Res 21:390-401. 2011..transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing (AS) is not well understood... - Internal and external paralogy in the evolution of tropomyosin genes in metazoansManuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 27:1504-17. 2010..In each case, recurrent tandem exon duplication and mutually exclusive alternative splicing of the duplicates, with further association between these alternatively spliced exons along the gene, led .. - Noisy splicing drives mRNA isoform diversity in human cellsJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 6:e1001236. 2010While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant... - Autoregulation of Fox protein expression to produce dominant negative splicing factorsAndrey Damianov
Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
RNA 16:405-16. 2010The Fox proteins are a family of regulators that control the alternative splicing of many exons in neurons, muscle, and other tissues... - Genomic features defining exonic variants that modulate splicingAdam Woolfe
Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA
Genome Biol 11:R20. 2010..In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative... - A splice code for trans-synaptic cell adhesion mediated by binding of neuroligin 1 to alpha- and beta-neurexinsAntony A Boucard
Center for Basic Neuroscience, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA4.118, Dallas, Texas 75390, USA
Neuron 48:229-36. 2005..also bind alpha-neurexins and that alpha- and beta-neurexin binding by neuroligin 1 is regulated by alternative splicing of neuroligin 1 (at splice site B) and of neurexins (at splice site 4)... - An inducible change in Fox-1/A2BP1 splicing modulates the alternative splicing of downstream neuronal target exonsJi Ann Lee
Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
Genes Dev 23:2284-93. 2009..These results reveal a novel mechanism for the slow modulation of splicing as cells adapt to chronic stimuli: The subcellular localization of a splicing regulator is controlled through its own alternative splicing. - Colocalization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophyThai H Ho
Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
J Cell Sci 118:2923-33. 2005..in transcripts of mutant DMPK form nuclear foci that recruit muscleblind-like (MBNL) proteins, a family of alternative splicing factors... - Alternative splicing isoform of tau protein kinase I/glycogen synthase kinase 3betaFumiko Mukai
Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo, Japan
J Neurochem 81:1073-83. 2002..of tau protein kinase I (TPKI)/GSK3beta with a 13 amino acid insert in the catalytic domain owing to alternative splicing. The alternative transcripts were found in the brains of the mouse, rat and human, with highly conserved .. - miR-148 targets human DNMT3b protein coding regionAnja M Duursma
Division of Tumor Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
RNA 14:872-7. 2008..More generally, we provide evidence that coding regions of human genes can be targeted by miRNAs, and that such a mechanism might play a role in determining the relative abundance of different splice variants... - SWI/SNF associates with nascent pre-mRNPs and regulates alternative pre-mRNA processingAnu Tyagi
Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden
PLoS Genet 5:e1000470. 2009.... - The splicing factor SC35 has an active role in transcriptional elongationShengrong Lin
Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0651, USA
Nat Struct Mol Biol 15:819-26. 2008..Recombinant SC35 is sufficient to rescue this defect in nuclear run-on experiments. These findings suggest a reciprocal functional relationship between the transcription and splicing machineries during gene expression... - Regulation of TMEM16A chloride channel properties by alternative splicingLoretta Ferrera
Laboratory of Molecular Genetics, Istituto Giannina Gaslini, Largo G Gaslini 5, 16147 Genova
J Biol Chem 284:33360-8. 2009..TMEM16A primary transcript undergoes alternative splicing. thus resulting in the generation of multiple isoforms... - Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursorsNathan Salomonis
Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
PLoS Comput Biol 5:e1000553. 2009The role of alternative splicing in self-renewal, pluripotency and tissue lineage specification of human embryonic stem cells (hESCs) is largely unknown... - Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptomeGuojie Zhang
Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
Genome Res 20:646-54. 2010..An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in approximately 33% of all rice .. - SnapShot: The splicing regulatory machineryMathieu Gabut
Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
Cell 133:192.e1. 2008 - iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolutionJulian König
Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
Nat Struct Mol Biol 17:909-15. 2010..Integration of transcriptome-wide iCLIP data and alternative splicing profiles into an 'RNA map' indicates how the positioning of hnRNP particles determines their effect on the .. - Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platformsPeter A C 't Hoen
The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Nucleic Acids Res 36:e141. 2008..We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies... - Alternative splicing of neuroligin regulates the rate of presynaptic differentiationHanson Lee
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
J Neurosci 30:11435-46. 2010..Indeed, we find that NLG-1DeltaB recruits more axonal alpha-NRX. Our results suggest that the engagement of alpha-NRX is a key to rapid induction of synapses at new sites of axo-dendritic contact... - Global regulation of alternative splicing during myogenic differentiationChristopher S Bland
Department of Pathology and Immunology, Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Nucleic Acids Res 38:7651-64. 2010Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues... - SARP, a new alternatively spliced protein phosphatase 1 and DNA interacting proteinGareth J Browne
Medical Research Council Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
Biochem J 402:187-96. 2007..The presence of a leucine zipper near the C-terminus of SARP1 and SARP2, and the binding of mammalian DNA to SARP2, suggests that SARP1 and SARP2 may be transcription factors or DNA-associated proteins that modulate gene expression... - Alternative splicing: regulation of HIV-1 multiplication as a target for therapeutic actionJamal Tazi
Université Montpellier 2 Université Montpellier 1 CNRS, Institut de Genetique Moleculaire de Montpellier, UMR5535, IFR122, Montpellier, France
FEBS J 277:867-76. 2010..In this review we will summarize the current acknowledge about the HIV-1 alternative splicing mechanism and will describe how this malleable process can help further understanding of infection, spread .. - hnRNP H1 and intronic G runs in the splicing control of the human rpL3 geneAnnapina Russo
Dipartimento di Biochimica e Biotecnologie Mediche, Universita Federico II, Napoli 80131, Italy
Biochim Biophys Acta 1799:419-28. 2010By generating mRNA containing a premature termination codon (PTC), alternative splicing (AS) can quantitatively regulate the expression of genes that are degraded by nonsense-mediated mRNA decay (NMD)... - Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controlsChaolin Zhang
Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Science 329:439-43. 2010The control of RNA alternative splicing is critical for generating biological diversity. Despite emerging genome-wide technologies to study RNA complexity, reliable and comprehensive RNA-regulatory networks have not been defined... - A catalog of SCN1A variantsChristoph Lossin
Department of Neurology, University of California, Davis, 4635 2nd Avenue, Room 1004A, Sacramento, CA 95817, USA
Brain Dev 31:114-30. 2009..1 variants so as to provide a platform from which future mutation analyses can be started without need for up-front data normalization. An online resource--SCN1A infobase--is introduced... - Nonsense-mediated RNA decay regulation by cellular stress: implications for tumorigenesisLawrence B Gardner
Division of Hematology, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
Mol Cancer Res 8:295-308. 2010.... - DARPP-32 binds to tra2-beta1 and influences alternative splicingNatalya Benderska
University of Erlangen Nuremberg, Institute for Biochemistry, Fahrstrasse 17, 91054 Erlangen, Germany
Biochim Biophys Acta 1799:448-53. 2010The majority of human genes undergo alternative splicing, which is frequently altered in response to physiological stimuli. DARPP-32 (dopamine and cAMP regulated phosphoprotein, 32kDa) is a component of PKA-dependent signaling pathways... - Human RBMY regulates germline-specific splicing events by modulating the function of the serine/arginine-rich proteins 9G8 and Tra2-{beta}Natacha Dreumont
IGBMC Department of Functional Genomics, Illkirch, France
J Cell Sci 123:40-50. 2010RBMY is a male germline RNA binding protein and potential alternative splicing regulator, but the lack of a convenient biological system has made its cellular functions elusive... - Molecular cloning of the chicken ST2 gene and a novel variant form of the ST2 gene product, ST2LVHiroyuki Iwahana
Department of Biochemistry, Jichi Medical School, 3311 1 Yakushiji, Minamikawachi Machi, Kawachi gun, Tochigi 329 0498, Japan
Biochim Biophys Acta 1681:1-14. 2004..Three types of ST2 gene products, ST2, ST2L, and ST2V, can be produced by alternative splicing. In the course of cloning the chicken ST2 and ST2L cDNAs, we identified a novel variant cDNA other than ST2,.. - Identification and molecular characterization of three GnRH ligands and five GnRH receptors in the spotted green pufferfishT Ikemoto
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
Mol Cell Endocrinol 242:67-79. 2005..b>Alternative splicing was also observed for some receptor subtypes... - Molecular cloning and characterization of two novel truncated isoforms of human Na+/Ca2+ exchanger 3, expressed in fetal brainRose Marie Lindgren
Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE 751 85 Uppsala, Sweden
Gene 348:143-55. 2005The human gene encoding the Na+/Ca2+ exchanger family member 3 (NCX3) undergoes extensive alternative splicing, with four variants previously identified... - Expression of interferon-inducible RNA adenosine deaminase ADAR1 during pathogen infection and mouse embryo development involves tissue-selective promoter utilization and alternative splicingCyril X George
Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA
J Biol Chem 280:15020-8. 2005.... - Genetic and molecular analysis of phytochromes from the filamentous fungus Neurospora crassaAllan C Froehlich
Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
Eukaryot Cell 4:2140-52. 2005..Strains containing deletions of phy-1 and phy-2, either singly or in tandem, were not compromised in any known photoresponses in Neurospora, leaving their function(s) unclear... - Differential transcription initiation and alternative RNA splicing of Knox7, a class 2 homeobox gene of maizeMarie Christine Morère-Le Paven
UMR INRA 1191, Physiologie Moléculaire des Semences, University of Angers, 2 Bd Lavoisier 49045 Angers cedex 01 France
Gene 401:71-9. 2007..to ORFs of both Knox7 alternative transcripts showed that seven cDNA clones were probably generated by alternative splicing of Knox7L... - Alternative splicing of the WNT-2B/WNT-13 geneM Katoh
Genetics and Cell Biology Section, Genetics Division, National Cancer Center Research Institute, Tsukiji 5 chome, Chuo Ku, Tokyo, 104 0045, Japan
Biochem Biophys Res Commun 275:209-16. 2000..These results indicate that the WNT-2B1 and WNT-2B2 mRNAs are transcribed due to alternative splicing with distinct expression profile... - Identification of three mouse mu-opioid receptor (MOR) gene (Oprm1) splice variants containing a newly identified alternatively spliced exonGlenn A Doyle
The Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
Gene 388:135-47. 2007..In summary, we have identified three brain expressed, alternatively spliced mouse MOR splice variants containing a novel exon and encoding new putative MOR isoforms, MOR-1V and MOR-1W... - Structure and evolution of RIM-BP genes: identification of a novel family memberTobias Mittelstaedt
Department of Neuropathology and Epileptology, University of Bonn, Sigmund Freud Str 25, D 53105 Bonn, Germany
Gene 403:70-9. 2007..The modular domain structure of RIM-BPs, their expression pattern and the conservative expansion during evolution shown here support their potential role as important molecular adaptors...
Research Grants
- Use of alternative splicing and rAAV for longterm control of transgene expressionKYSON CHOU; Fiscal Year: 2007..To avoid the drawback, we are exploring a novel regulation system based on alternative splicing. Alternative splicing is the inclusion or skipping of an alternative exon in between two exons that are ..
- MECHANISM OF PRE-MRNA SPLICINGMAGDA KONARSKA; Fiscal Year: 2009..By contrast, splice site signals in Saccharomyces cerevisiae fit well to the consensus and alternative splicing is thought not to occur in yeast...
- Regulation of Ovarian Cancer Multidrug Resistance by MAP KinasesScott T Eblen; Fiscal Year: 2010..Most importantly, phosphorylation of SPF45 on Ser222 by MAP kinases increases its alternative splicing activity...
- The Mammalian Cellular Splicing Machine - Structure and FunctionRuth Sperling; Fiscal Year: 2010..Health Relevance: Defects in alternative splicing were correlated with human pathologies and malignancy...
- Nuclear Function of Abl in DNA Damage ResponseJean Y J Wang; Fiscal Year: 2010..b>Alternative splicing has been shown to generate pro-death and anti-death protein isoforms from a single gene, underscoring the ..
- Nuclear Function of Abl in DNA Damage ResponseJean Wang; Fiscal Year: 2009..b>Alternative splicing has been shown to generate pro-death and anti-death protein isoforms from a single gene, underscoring the ..
- MECHANISMS OF ENHANCER DEPENDENT SPLICE SITE ACTIVATIONKlemens J Hertel; Fiscal Year: 2010..Current estimates indicate that over 90% of human genes undergo alternative splicing, thus greatly increasing the coding potential of our genome...
- Mechanisms Regulating Alternative pre-mRNA SplicingJames Patton; Fiscal Year: 2005..Further, 60% or more of human genes are subject to alternative splicing requiring that cells not only be able to accurately recognize the difference between introns and exons, but ..
- TROPONIN T ALTERNATIVE SPLICING IN EMBRYONIC HEARTThomas Cooper; Fiscal Year: 1999..The long term goal of this proposal is to understand the m o lecular basis for the regulation of pre-mRNA alternative splicing. Alternative splicing is a common and key regulatory step for the expression of diverse protein isoforms ..
- EXON LIGATION--THE SPLICEOSOME AND GROUP 11 INTRONSMelissa Moore; Fiscal Year: 1999..Many nascent transcripts are subject to alternative splicing, which provides a means for making more than one protein from a single gene...
- MECHANISM OF MIS-SPLICING IN MYOTONIC DYSTROPHY 1MUGE KUYUMCU MARTINEZ; Fiscal Year: 2007..The pathogenesis of DM1 involves misregulation of alternative splicing resulting in expression of inappropriate protein isoforms causing specific symptoms...
- RNA Binding Proteins & Alternative SplicingPaula Grabowski; Fiscal Year: 2007..b>Alternative splicing is a major driving force generating proteomic diversity in mammals, yet its mechanisms, regulatory networks,..
- Differential regulation of multiple transgenes for treatment of eye diseaseRICHARD J contact SAMULSKI; Fiscal Year: 2010..a new type of regulation system without such drawbacks, we are exploring a novel regulation system based on alternative splicing. To date, we have developed minimal alternative splicing introns capable of regulating transgene expression...
- Alternative processing and antisense regulation of thyroid hormone receptor mRNASTEPHEN MUNROE; Fiscal Year: 2007..The first specific aim is to characterize both cis-acting elements and trans-acting proteins that regulate alternative splicing specific to TRa2 mRNA...
- MECHANISMS OF PREMRNA SPLICINGTHOMAS MANIATIS; Fiscal Year: 2001..Experiments are proposed to address three aspects of RNA processing: 1. The regulation of alternative splicing. 2. The recognition and pairing of splice sites in constitutively spliced pre- mRNA. 3...
- GENERATION OF A NOVEL RECOMBINANT MOUSE MODEL EXPRESSING ONLY ONE COL2A1 ISOFORMAudrey McAlinden; Fiscal Year: 2007..in this post-genome sequencing era where we now know that the majority of protein diversity results from alternative splicing of pre-mRNA...
- REGULATION OF C-SRC PREMRNA SPLICINGDouglas Black; Fiscal Year: 2001b>Alternative splicing is an important means of genetic control in eucaryotic cells. By altering the splicing pattern of the primary transcript, a variety of proteins can be created from a single gene...
- Regulation of CD45 alternative splicing by HNRPLLAnjana Rao; Fiscal Year: 2009The long-term goal of this project is to understand the mechanisms underlying CD45 alternative splicing and the role of CD45 splicing in lymphocyte and haematopoietic cell biology...
- Regulation of CD45 alternative splicing by HNRPLLAnjana Rao; Fiscal Year: 2010The long-term goal of this project is to understand the mechanisms underlying CD45 alternative splicing and the role of CD45 splicing in lymphocyte and haematopoietic cell biology...
- Regulation of alternative pre-mRNA processing by small nucleolar RNAsStefan Stamm; Fiscal Year: 2010..Our long-term goal is to elucidate the regulation of alternative splicing by small RNAs that are estimated to comprise more than 40% of human gene expression...
- Regulation of alternative pre-mRNA processing by small nucleolar RNAsStefan Stamm; Fiscal Year: 2009..Our long-term goal is to elucidate the regulation of alternative splicing by small RNAs that are estimated to comprise more than 40% of human gene expression...
- Neural Calcium Channels-Regulation and FunctionDiane Lipscombe; Fiscal Year: 2006..We transition from a general description of splice isoforms to determine the importance of alternative splicing in identified neuronal populations...
- TROPONIN T ALTERNATIVE SPLICING IN EMBRYONIC HEARTTHOMAS ALEXANDER COOPER; Fiscal Year: 2010Our long term goal in this project is to understand the mechanisms that regulate pre-mRNA alternative splicing. The majority of human genes express multiple mRNAs resulting in the expression of functionally diverse isoforms or the on-..
- EXON-SPECIFIC FIBRONECTIN ISOFORMS AND CHONDROGENESISNOREEN HICKOK; Fiscal Year: 2003..Fibronectin isoform-changes result from mRNA alternative splicing events involving at least three exons in the fibronectin gene (IIIB, IIIA, and V)...
- REGULATION OF MRNA PROCESSINGPhillip A Sharp; Fiscal Year: 2010..These latter activities are dependent upon alternative splicing of CD44 which produces isoforms containing v6 and other exons...
- REGULATION OF MRNA PROCESSINGPHILLIP SHARP; Fiscal Year: 2009..These latter activities are dependent upon alternative splicing of CD44 which produces isoforms containing v6 and other exons...
- Mechanisms of Bronchial MyogenesisLucia Schuger; Fiscal Year: 2005..studies we found that heterogeneous ribonucleoprotein-H (hnRNP-H), an RNA-binding protein involved in alternative splicing, inhibits SM differentiation and bronchial myogenesis...
- FUNCTIONAL ANALYSIS OF NUCLEAR RECEPTOR VARIANTSCurtis J Omiecinski; Fiscal Year: 2011..program included the discovery of novel forms of CAR, CAR2 and CAR3;receptors generated through the use of alternative splicing mechanisms that result in the insertion of 4- and 5- amino acids, respectively, within the receptors'..
- FUNCTIONAL ANALYSIS OF NUCLEAR RECEPTOR VARIANTSCurtis J Omiecinski; Fiscal Year: 2010..program included the discovery of novel forms of CAR, CAR2 and CAR3;receptors generated through the use of alternative splicing mechanisms that result in the insertion of 4- and 5- amino acids, respectively, within the receptors'..
- Regulation of Alternative Splicing of FGF-R2 pre-mRNAMARIANO GARCIA BLANCO; Fiscal Year: 2004..from the applicant's abstract): The broad long-term goal of the proposed work is to understand regulated alternative splicing in mammals...
- RED CELL BAND 4.1 - CHANGES IN RNA SPLICINGJOHN CONBOY; Fiscal Year: 2003..In the red cell, key mechanical and morphological properties of the membrane skeleton are influenced by alternative splicing choices that occur in progenitor cells...
- Pathogenesis of Myopathy in Models of Myotonic DystrophyCharles Thornton; Fiscal Year: 2009..foci -> sequestration of muscleblind [Mbnl] proteins in nuclear foci -> abnormal regulation of alternative splicing -> expression of inappropriate splice isoforms -> symptoms of DM...