Alternative splicing: a new drug target of the post-genome era.

Alternative splicing allows for the creation of multiple distinct mRNA transcripts from a given gene in a multicellular organism. Pre-mRNA splicing is catalyzed by a multi-molecular complex, including serine/arginine-rich (SR) proteins, which are highly phosphorylated in living cells, and thought to play crucial roles in spliceosomal formation and in the regulation of alternative splicing. Recently, reports of low molecular compounds, which alter splicing pattern of genes, have been accumulated. A benzothiazole compound TG003, a kinase inhibitor that targets Clk1 and Clk4, suppressed dissociation of nuclear speckles, altered the splicing patterns, and rescued the embryonic defects induced by excessive Clk activity. The emerging inhibitors of the signal transduction pathways regulating pre-mRNA alternative splicing may open the way to therapies against diseases caused by missplicing.

[1]  J. Bell,et al.  STY, a tyrosine-phosphorylating enzyme with sequence homology to serine/threonine kinases , 1991, Molecular and cellular biology.

[2]  M. Garcia-Blanco,et al.  Both phosphorylation and dephosphorylation of ASF/SF2 are required for pre-mRNA splicing in vitro. , 1997, RNA.

[3]  M. Yanagida,et al.  Fission Yeast Mitotic Regulator Dsk1 Is an SR Protein-specific Kinase* , 1998, The Journal of Biological Chemistry.

[4]  A. Krainer,et al.  A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. , 1998, Genes & development.

[5]  E. Androphy,et al.  Aclarubicin treatment restores SMN levels to cells derived from type I spinal muscular atrophy patients. , 2001, Human molecular genetics.

[6]  Lin Jin,et al.  Aberrant RNA Processing in a Neurodegenerative Disease: the Cause for Absent EAAT2, a Glutamate Transporter, in Amyotrophic Lateral Sclerosis , 1998, Neuron.

[7]  G. Akusjärvi,et al.  Functional inactivation of the SR family of splicing factors during a vaccinia virus infection , 2002, EMBO reports.

[8]  C. Bailly,et al.  Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-506. , 2001, Cancer research.

[9]  T. Pawson,et al.  A mammalian protein kinase with potential for serine/threonine and tyrosine phosphorylation is related to cell cycle regulators. , 1991, The EMBO journal.

[10]  P. Herrlich,et al.  Participation in normal immune responses of a metastasis-inducing splice variant of CD44. , 1992, Science.

[11]  J. Egebjerg,et al.  ASF/SF2 and SC35 regulate the glutamate receptor subunit 2 alternative flip/flop splicing , 2005, FEBS letters.

[12]  S. Riva,et al.  Phosphorylation of human hnRNP protein A1 abrogates in vitro strand annealing activity. , 1993, Nucleic acids research.

[13]  William Arbuthnot Sir Lane,et al.  A serine kinase regulates intracellular localization of splicing factors in the cell cycle , 1994, Nature.

[14]  R. Kole,et al.  Therapeutic potential of antisense oligonucleotides as modulators of alternative splicing. , 2003, The Journal of clinical investigation.

[15]  P. Herrlich,et al.  Regulation of alternative pre‐mRNA splicing by the ERK MAP‐kinase pathway , 2001, The EMBO journal.

[16]  Stefan Stamm,et al.  Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. , 2002, Human molecular genetics.

[17]  M B Roth,et al.  SR proteins: a conserved family of pre-mRNA splicing factors. , 1992, Genes & development.

[18]  J. Valcárcel,et al.  Alternative pre-mRNA splicing: the logic of combinatorial control. , 2000, Trends in biochemical sciences.

[19]  B. Dallapiccola,et al.  Survival motor neuron gene transcript analysis in muscles from spinal muscular atrophy patients. , 1995, Biochemical and biophysical research communications.

[20]  A. Krainer,et al.  Functional analysis of pre‐mRNA splicing factor SF2/ASF structural domains. , 1993, The EMBO journal.

[21]  T. Tsukahara,et al.  Cloning and characterization of two neural‐salient serine/arginine‐rich (NSSR) proteins involved in the regulation of alternative splicing in neurones , 1999, Genes to cells : devoted to molecular & cellular mechanisms.

[22]  R. Sandri-Goldin,et al.  ICP27 interacts with SRPK1 to mediate HSV splicing inhibition by altering SR protein phosphorylation , 2003, The EMBO journal.

[23]  J. Manley,et al.  Phosphorylation of the ASF/SF2 RS domain affects both protein-protein and protein-RNA interactions and is necessary for splicing. , 1997, Genes & development.

[24]  J. Weissenbach,et al.  Identification and characterization of a spinal muscular atrophy-determining gene , 1995, Cell.

[25]  D. Black Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

[26]  T. Maniatis,et al.  Common themes in the function of transcription and splicing enhancers. , 1997, Current opinion in cell biology.

[27]  P. Herrlich,et al.  Heterogeneous Ribonucleoprotein A1 Is Part of an Exon-specific Splice-silencing Complex Controlled by Oncogenic Signaling Pathways* , 2000, The Journal of Biological Chemistry.

[28]  J. Wyatt,et al.  Insulin Regulates Alternative Splicing of Protein Kinase C βII through a Phosphatidylinositol 3-Kinase-dependent Pathway Involving the Nuclear Serine/Arginine-rich Splicing Factor, SRp40, in Skeletal Muscle Cells* , 2001, The Journal of Biological Chemistry.

[29]  G. Kéri,et al.  Synthesis of selective SRPK-1 inhibitors: novel tricyclic quinoxaline derivatives. , 2005, Bioorganic & medicinal chemistry letters.

[30]  Kristen W. Lynch,et al.  Consequences of regulated pre-mRNA splicing in the immune system , 2004, Nature Reviews Immunology.

[31]  Y. Lazebnik,et al.  Identification of an endogenous dominant-negative short isoform of caspase-9 that can regulate apoptosis. , 1999, Cancer research.

[32]  P. Herrlich,et al.  CD44: From adhesion molecules to signalling regulators , 2003, Nature Reviews Molecular Cell Biology.

[33]  M. Diaz-Meco,et al.  Identification of Heterogeneous Ribonucleoprotein A1 as a Novel Substrate for Protein Kinase C ζ (*) , 1995, The Journal of Biological Chemistry.

[34]  A. Zahler,et al.  Two members of a conserved family of nuclear phosphoproteins are involved in pre-mRNA splicing. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[35]  S. Fox,et al.  Normal human tissues, in addition to some tumors, express multiple different CD44 isoforms. , 1994, Cancer research.

[36]  B. Graveley,et al.  Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs. , 2005, Methods in molecular biology.

[37]  K. Eguchi,et al.  Regulation of alternative splicing of caspase-2 through an intracellular signaling pathway in response to pro-apoptotic stimuli. , 2005, The Journal of laboratory and clinical medicine.

[38]  Jiuyong Xie,et al.  Control of alternative splicing of potassium channels by stress hormones. , 1998, Science.

[39]  A. Krainer,et al.  Regulation of heterogenous nuclear ribonucleoprotein A1 transport by phosphorylation in cells stressed by osmotic shock. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  A. Krainer,et al.  Serine Phosphorylation of SR Proteins Is Required for Their Recruitment to Sites of Transcription In Vivo , 1998, The Journal of cell biology.

[41]  Y. Hannun,et al.  De Novo Ceramide Regulates the Alternative Splicing of Caspase 9 and Bcl-x in A549 Lung Adenocarcinoma Cells , 2002, The Journal of Biological Chemistry.

[42]  A. Das,et al.  Diospyrin, a bisnaphthoquinone: a novel inhibitor of type I DNA topoisomerase of Leishmania donovani. , 1998, Molecular pharmacology.

[43]  P. Herrlich,et al.  Signal-dependent regulation of splicing via phosphorylation of Sam68 , 2002, Nature.

[44]  D. Black,et al.  A CaMK IV responsive RNA element mediates depolarization-induced alternative splicing of ion channels , 2001, Nature.

[45]  T. Cooper,et al.  Pre-mRNA splicing and human disease. , 2003, Genes & development.

[46]  M. Hagiwara,et al.  SPK-1, a C. elegans SR protein kinase homologue, is essential for embryogenesis and required for germline development , 2000, Mechanisms of Development.

[47]  J. Tazi,et al.  Specific phosphorylation of SR proteins by mammalian DNA topoisomerase I , 1996, Nature.

[48]  M. Hagiwara,et al.  Novel SR-protein-specific kinase, SRPK2, disassembles nuclear speckles. , 1998, Biochemical and biophysical research communications.

[49]  M. Hagiwara,et al.  Cloning of Human PRP4 Reveals Interaction with Clk1* , 2001, The Journal of Biological Chemistry.

[50]  A. Krainer,et al.  Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. , 1994, Science.

[51]  D. Price,et al.  Purification of P-TEFb, a Transcription Factor Required for the Transition into Productive Elongation (*) , 1995, The Journal of Biological Chemistry.

[52]  Y. Rao,et al.  Regulation of Ich-1 pre-mRNA alternative splicing and apoptosis by mammalian splicing factors. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[53]  C. Bailly,et al.  Selective Inhibition of Topoisomerase I and Various Steps of Spliceosome Assembly by Diospyrin Derivatives , 2005, Molecular Pharmacology.

[54]  J. Castle,et al.  Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays , 2003, Science.

[55]  Y. Jong,et al.  Treatment of spinal muscular atrophy by sodium butyrate , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Robert V Farese,et al.  Regulation of Alternative Splicing of Protein Kinase Cβ by Insulin (*) , 1995, The Journal of Biological Chemistry.

[57]  D. Cooper,et al.  The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: Causes and consequences , 1992, Human Genetics.

[58]  S. Nishimura,et al.  Novel antitumor indolocarbazole compound 6-N-formylamino-12,13-dihydro-1,11- dihydroxy-13-(beta-D-glucopyranosyl)-5H-indolo[2,3-a]pyrrolo[3,4- c]carbazole-5,7(6H)-dione (NB-506): induction of topoisomerase I-mediated DNA cleavage and mechanisms of cell line-selective cytotoxicity. , 1995, Cancer research.

[59]  Adrian R. Krainer,et al.  Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2 , 1992, Cell.

[60]  J. Bell,et al.  In vivo regulation of alternative pre-mRNA splicing by the Clk1 protein kinase , 1997, Molecular and cellular biology.

[61]  A. Ullrich,et al.  Identification of SRPK1 and SRPK2 as the Major Cellular Protein Kinases Phosphorylating Hepatitis B Virus Core Protein , 2002, Journal of Virology.

[62]  L. Cantley,et al.  SRPK2: A Differentially Expressed SR Protein-specific Kinase Involved in Mediating the Interaction and Localization of Pre-mRNA Splicing Factors in Mammalian Cells , 1998, The Journal of cell biology.

[63]  A. Krainer,et al.  Correction of disease-associated exon skipping by synthetic exon-specific activators , 2003, Nature Structural Biology.

[64]  T Pawson,et al.  The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. , 1996, The EMBO journal.

[65]  C. Guthrie,et al.  Conservation in budding yeast of a kinase specific for SR splicing factors. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[66]  A. Kornblihtt,et al.  Trypanosoma cruzi TcSRPK, the first protozoan member of the SRPK family, is biochemically and functionally conserved with metazoan SR protein-specific kinases. , 2003, Molecular and biochemical parasitology.

[67]  J. Gui,et al.  Purification and characterization of a kinase specific for the serine- and arginine-rich pre-mRNA splicing factors. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[68]  L. Corcos,et al.  Topoisomerase I and II inhibitors control caspase-2 pre-messenger RNA splicing in human cells. , 2004, Molecular cancer research : MCR.

[69]  C. Thompson,et al.  bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death , 1993, Cell.

[70]  B. Sakmann,et al.  Flip and flop: a cell-specific functional switch in glutamate-operated channels of the CNS. , 1990, Science.

[71]  M. Hagiwara,et al.  cdc2 kinase-mediated phosphorylation of splicing factor SF2/ASF. , 1998, Biochemical and biophysical research communications.

[72]  P. Herrlich,et al.  Coupling of signal transduction to alternative pre‐mRNA splicing by a composite splice regulator , 1998, The EMBO journal.

[73]  P. Leder,et al.  FBP WW domains and the Abl SH3 domain bind to a specific class of proline‐rich ligands , 1997, The EMBO journal.

[74]  Hiroshi Kimura,et al.  Manipulation of Alternative Splicing by a Newly Developed Inhibitor of Clks* , 2004, Journal of Biological Chemistry.

[75]  S. Stamm,et al.  The Cellular Localization of the Murine Serine/Arginine-rich Protein Kinase CLK2 Is Regulated by Serine 141 Autophosphorylation* , 1998, The Journal of Biological Chemistry.

[76]  R. Weinmann,et al.  Casein kinase type II is involved in the inhibition by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole of specific RNA polymerase II transcription. , 1986, The Journal of biological chemistry.

[77]  S. Stamm,et al.  Characterization and comparison of four serine- and arginine-rich (SR) protein kinases. , 1997, The Biochemical journal.

[78]  C. Lorson,et al.  A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[79]  A. Krainer,et al.  The Mkk3/6-p38–Signaling Cascade Alters the Subcellular Distribution of Hnrnp A1 and Modulates Alternative Splicing Regulation , 2000, The Journal of cell biology.

[80]  Christopher J. Lee,et al.  Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss , 2003, Nature Genetics.

[81]  S. Stamm,et al.  Ischemia Induces a Translocation of the Splicing Factor tra2-β1 and Changes Alternative Splicing Patterns in the Brain , 2002, The Journal of Neuroscience.

[82]  J. McPherson,et al.  A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2. , 1999, Human molecular genetics.