Regulation of alternative pre-mRNA splicing.

The first wave of bioinformatic studies that followed genome and complementary DNA sequencing projects revealed that alternative splicing of messenger RNA precursors (pre-mRNAs) contributes substantially to transcriptome complexity in higher eukaryotes. Together with the realisation of the impact of the process on cell differentiation, development and disease, these studies portray alternative splicing as a fundamental component of gene regulation. Both detailed mechanistic studies and genome-wide analyses will be necessary to unravel the molecular basis for cell type-specific splice site selection. This paper will highlight some recent progress and future challenges for functional genomics and bioinformatics in this rapidly developing area.

[1]  A. Simpson,et al.  Alternative Spliced Transcripts as Cancer Markers , 2002, Disease markers.

[2]  G. C. Roberts,et al.  Alternative splicing: combinatorial output from the genome. , 2002, Current opinion in chemical biology.

[3]  Tyson A. Clark,et al.  Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays , 2002, Science.

[4]  Christine Guthrie,et al.  Spliceosomal snRNAs Mg2+-Dependent Chemistry at the Catalytic Core? , 2002, Cell.

[5]  T. Maniatis,et al.  An extensive network of coupling among gene expression machines , 2002, Nature.

[6]  A. Krainer,et al.  Listening to silence and understanding nonsense: exonic mutations that affect splicing , 2002, Nature Reviews Genetics.

[7]  A. Kornblihtt,et al.  Alternative splicing: multiple control mechanisms and involvement in human disease. , 2002, Trends in genetics : TIG.

[8]  Malgorzata Kisielow,et al.  Isoform-specific knockdown and expression of adaptor protein ShcA using small interfering RNA. , 2002, The Biochemical journal.

[9]  Xiang-Dong Fu,et al.  Profiling alternative splicing on fiber-optic arrays , 2002, Nature Biotechnology.

[10]  T. Dörk,et al.  A new type of mutation causes a splicing defect in ATM , 2002, Nature Genetics.

[11]  A. Krainer,et al.  Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1 , 2002, Nature Genetics.

[12]  B. Kerem,et al.  Splicing regulation as a potential genetic modifier. , 2002, Trends in genetics : TIG.

[13]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[14]  Donald J. Patterson,et al.  Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction , 2001, Pacific Symposium on Biocomputing.

[15]  A. Krainer,et al.  Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. , 2001, Molecular cell.

[16]  Anton J. Enright,et al.  A genome-wide survey of RS domain proteins. , 2001, RNA.

[17]  A. Kornblihtt,et al.  Antagonistic effects of T‐Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing , 2001, The EMBO journal.

[18]  B. Graveley,et al.  Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. , 2001, Genetics.

[19]  D. Black,et al.  Alternative RNA splicing in the nervous system , 2001, Progress in Neurobiology.

[20]  T. Cooper,et al.  Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophy , 2001, Nature Genetics.

[21]  N. Hastie,et al.  Life, Sex, and WT1 Isoforms— Three Amino Acids Can Make All the Difference , 2001, Cell.

[22]  A. Schedl,et al.  Two Splice Variants of the Wilms' Tumor 1 Gene Have Distinct Functions during Sex Determination and Nephron Formation , 2001, Cell.

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

[24]  I. Hope.  RNAi surges on: application to cultured mammalian cells. , 2001, Trends in genetics : TIG.

[25]  T. Jatkoe,et al.  Predicting splice variant from DNA chip expression data. , 2001, Genome research.

[26]  T A Thanaraj,et al.  Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. , 2001, Nucleic acids research.

[27]  A. Krainer,et al.  Pre-mRNA splicing in the new millennium. , 2001, Current opinion in cell biology.

[28]  C. Will,et al.  Spliceosomal UsnRNP biogenesis, structure and function. , 2001, Current opinion in cell biology.

[29]  I-Min A. Dubchak,et al.  Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. , 2001, Nucleic acids research.

[30]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[31]  C. Bortner,et al.  Modification of Alternative Splicing of Bcl-x Pre-mRNA in Prostate and Breast Cancer Cells , 2001, The Journal of Biological Chemistry.

[32]  W. Gish,et al.  Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. , 2001, Genome research.

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

[34]  T J Gibson,et al.  Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries. , 2001, Nucleic acids research.

[35]  R. Stoughton,et al.  Experimental annotation of the human genome using microarray technology , 2001, Nature.

[36]  B. Graveley.  Alternative splicing: increasing diversity in the proteomic world. , 2001, Trends in genetics : TIG.

[37]  T. Hughes,et al.  DNA microarrays for expression profiling. , 2001, Current opinion in chemical biology.

[38]  Jiyeon Lee,et al.  Two isoforms of sarco/endoplasmic reticulum calcium ATPase (SERCA) are essential in Caenorhabditis elegans. , 2000, Gene.

[39]  Sebastian A. Leidel,et al.  Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III , 2000, Nature.

[40]  J. Valcárcel,et al.  The apoptosis-promoting factor TIA-1 is a regulator of alternative pre-mRNA splicing. , 2000, Molecular cell.

[41]  D. Black.  Protein Diversity from Alternative Splicing A Challenge for Bioinformatics and Post-Genome Biology , 2000, Cell.

[42]  D. Black,et al.  Cooperative Assembly of an hnRNP Complex Induced by a Tissue-Specific Homolog of Polypyrimidine Tract Binding Protein , 2000, Molecular and Cellular Biology.

[43]  R Kole,et al.  Restoration of hemoglobin A synthesis in erythroid cells from peripheral blood of thalassemic patients. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[44]  P. Puigserver,et al.  Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. , 2000, Molecular cell.

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

[46]  J. Manley,et al.  RNA polymerase II and the integration of nuclear events. , 2000, Genes & development.

[47]  J. C. Clemens,et al.  Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity , 2000, Cell.

[48]  N D Hastie,et al.  Did nucleotides or amino acids drive evolutionary conservation of the WT1 +/-KTS alternative splice? , 2000, Human molecular genetics.

[49]  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.

[50]  Kevin Burrage,et al.  ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome , 2000, Nature Genetics.

[51]  R Kole,et al.  Modification of alternative splicing pathways as a potential approach to chemotherapy. , 2000, Pharmacology & therapeutics.

[52]  C. Schütt,et al.  Structure, function and evolution of sex-determining systems in Dipteran insects. , 2000, Development.

[53]  Robert B Darnell,et al.  Nova-1 Regulates Neuron-Specific Alternative Splicing and Is Essential for Neuronal Viability , 2000, Neuron.

[54]  X. Estivill,et al.  Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. , 2000, Human molecular genetics.

[55]  M. Gelfand,et al.  Frequent alternative splicing of human genes. , 1999, Genome research.

[56]  A. Wolffe,et al.  A novel transcriptional coactivator, p52, functionally interacts with the essential splicing factor ASF/SF2. , 1998, Molecular cell.

[57]  G. C. Roberts,et al.  Co-transcriptional commitment to alternative splice site selection. , 1998, Nucleic acids research.

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

[59]  T. Cooper,et al.  Disruption of splicing regulated by a CUG-binding protein in myotonic dystrophy. , 1998, Science.

[60]  D L Black,et al.  Splicing in the Inner Ear: a Familiar Tune, but What Are the Instruments? , 1998, Neuron.

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

[62]  A. Krainer,et al.  Splicing of a divergent subclass of AT-AC introns requires the major spliceosomal snRNAs. , 1997, RNA.

[63]  J. Manley,et al.  Regulation of pre-mRNA splicing in metazoa. , 1997, Current opinion in genetics & development.

[64]  Phillip A. Sharp,et al.  Split genes and RNA splicing , 1994, Cell.

[65]  E. Birney,et al.  Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. , 1993, Nucleic acids research.

[66]  D. Libri,et al.  Pre‐mRNA secondary structure and the regulation of splicing , 1993, BioEssays : news and reviews in molecular, cellular and developmental biology.

[67]  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.

[68]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[69]  Y.-H. Huang,et al.  PALS db: Putative Alternative Splicing database , 2002, Nucleic Acids Res..

[70]  Christopher J. Lee,et al.  A genomic view of alternative splicing , 2002, Nature Genetics.

[71]  P. Bork,et al.  Alternative splicing and genome complexity , 2002, Nature Genetics.

[72]  Martin Vingron,et al.  SpliceNest: visualizing gene structure and alternative splicing based on EST clusters , 2002 .

[73]  Michael Q. Zhang,et al.  A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes , 2001, Nature Genetics.

[74]  Alexandros D. Polydorides,et al.  The splice of life: Alternative splicing and neurological disease , 2001, Nature Reviews Neuroscience.

[75]  M. Mataa,et al.  Coordination between transcription and pre-mRNA processing , 2001 .

[76]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[77]  A. J. Lopez,et al.  Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. , 1998, Annual review of genetics.

[78]  R. Amann,et al.  Predictive Identification of Exonic Splicing Enhancers in Human Genes , 2022 .