Searching for splicing motifs.

Intron removal during pre-mRNA splicing in higher eukaryotes requires the accurate identification of the two splice sites at the ends of the exons, or exon definition. The sequences constituting the splice sites provide insufficient information to distinguish true splice sites from the greater number of false splice sites that populate transcripts. Additional information used for exon recognition resides in a large number of positively or negatively acting elements that lie both within exons and in the adjacent introns. The identification of such sequence motifs has progressed rapidly in recent years, such that extensive lists are now available for exonic splicing enhancers and exonic splicing silencers. These motifs have been identified both by empirical experiments and by computational predictions, the validity of the latter being confirmed by experimental verification. Molecular searches have been carried out either by the selection of sequences that bind to splicing factors, or enhance or silence splicing in vitro or in vivo. Computational methods have focused on sequences of 6 or 8 nucleotides that are over- or under-represented in exons, compared to introns or transcripts that do not undergo splicing. These various methods have sought to provide global definitions of motifs, yet the motifs are distinctive to the method used for identification and display little overlap. Astonishingly, at least three-quarters of a typical mRNA would be comprised of these motifs. A present challenge lies in understanding how the cell integrates this surfeit of information to generate what is usually a binary splicing decision.

[1]  E. Buratti,et al.  Influence of RNA Secondary Structure on the Pre-mRNA Splicing Process , 2004, Molecular and Cellular Biology.

[2]  A. Krainer,et al.  Evidence for the function of an exonic splicing enhancer after the first catalytic step of pre-mRNA splicing. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Michael Q. Zhang,et al.  Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes , 2005, Nucleic acids research.

[4]  Yongqing Zhang,et al.  Distribution of exonic splicing enhancer elements in human genes. , 2005, Genomics.

[5]  G. Dreyfuss,et al.  Differential binding of heterogeneous nuclear ribonucleoproteins to mRNA precursors prior to spliceosome assembly in vitro. , 1992, Molecular and cellular biology.

[6]  Xiang-Dong Fu,et al.  Towards a Splicing Code , 2004, Cell.

[7]  N L Harris,et al.  Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project. , 1990, Methods in enzymology.

[8]  K. Heller,et al.  Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. , 2003, Genome research.

[9]  M. Streuli,et al.  Regulation of tissue‐specific alternative splicing: exon‐specific cis‐elements govern the splicing of leukocyte common antigen pre‐mRNA. , 1989, The EMBO journal.

[10]  J. Alwine,et al.  Utilization of Splicing Elements and Polyadenylation Signal Elements in the Coupling of Polyadenylation and Last-Intron Removal , 1999, Molecular and Cellular Biology.

[11]  E. Buratti,et al.  Exon Enhancer Elements in the Fibronectin EDA Proteins by Mouse and Human Polypurinic RNA Folding Affects the Recruitment of SR , 2004 .

[12]  C. Leslie,et al.  Dichotomous splicing signals in exon flanks. , 2005, Genome research.

[13]  Michael Q. Zhang,et al.  Exonic Splicing Enhancer Motif Recognized by Human SC35 under Splicing Conditions , 2000, Molecular and Cellular Biology.

[14]  L. Chasin,et al.  Human Genomic Sequences That Inhibit Splicing , 2000, Molecular and Cellular Biology.

[15]  S. TD.,et al.  Information Content of Individual Genetic Sequences , 1998 .

[16]  Jurg Ott,et al.  Nucleotide frequency variation across human genes. , 2003, Genome research.

[17]  J. G. Patton,et al.  Functional crosstalk between exon enhancers, polypyrimidine tracts and branchpoint sequences , 1997, The EMBO journal.

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

[19]  Jørgen Kjems,et al.  Defining a 5' splice site by functional selection in the presence and absence of U1 snRNA 5' end. , 2002, RNA.

[20]  T A Thanaraj,et al.  Prediction and statistical analysis of alternatively spliced exons. , 2003, Progress in molecular and subcellular biology.

[21]  Ravi Sachidanandam,et al.  Intrinsic differences between authentic and cryptic 5' splice sites. , 2003, Nucleic acids research.

[22]  Michael R Green,et al.  Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. , 2006, Molecular cell.

[23]  Michael R Green,et al.  A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. , 2004, Molecular cell.

[24]  Tom Maniatis,et al.  Selection and Characterization of Pre-mRNA Splicing Enhancers: Identification of Novel SR Protein-Specific Enhancer Sequences , 1999, Molecular and Cellular Biology.

[25]  T. Cooper,et al.  Identification of Putative New Splicing Targets for ETR-3 Using Sequences Identified by Systematic Evolution of Ligands by Exponential Enrichment , 2005, Molecular and Cellular Biology.

[26]  Christopher W. J. Smith,et al.  Mutually exclusive splicing of α-tropomyosin exons enforced by an unusual lariat branch point location: Implications for constitutive splicing , 1989, Cell.

[27]  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.

[28]  S. Furuyama,et al.  Ser/Arg-rich Protein-mediated Communication between U1 and U2 Small Nuclear Ribonucleoprotein Particles* , 2004, Journal of Biological Chemistry.

[29]  Hua-Lin Zhou,et al.  Role for Fox-1/Fox-2 in Mediating the Neuronal Pathway of Calcitonin/Calcitonin Gene-Related Peptide Alternative RNA Processing , 2006, Molecular and Cellular Biology.

[30]  A. Zahler,et al.  SC35 and Heterogeneous Nuclear Ribonucleoprotein A/B Proteins Bind to a Juxtaposed Exonic Splicing Enhancer/Exonic Splicing Silencer Element to Regulate HIV-1 tat Exon 2 Splicing* , 2004, Journal of Biological Chemistry.

[31]  Elisa de Stanchina,et al.  Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. , 2006, American journal of human genetics.

[32]  B. Blencowe,et al.  An RNA map predicting Nova-dependent splicing regulation , 2006, Nature.

[33]  S. Grellscheid,et al.  An Apparent Pseudo-Exon Acts both as an Alternative Exon That Leads to Nonsense-Mediated Decay and as a Zero-Length Exon , 2006, Molecular and Cellular Biology.

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

[35]  E. Androphy,et al.  In vivo selection reveals combinatorial controls that define a critical exon in the spinal muscular atrophy genes. , 2004, RNA.

[36]  G. Ast,et al.  Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. , 2006, Molecular cell.

[37]  Y. Shimura,et al.  The role of exon sequences in splice site selection. , 1993, Genes & development.

[38]  E. Wagner,et al.  Polypyrimidine Tract Binding Protein Antagonizes Exon Definition , 2001, Molecular and Cellular Biology.

[39]  R. Kole,et al.  Strong RNA Splicing Enhancers Identified by a Modified Method of Cycled Selection Interact with SR Protein* , 2001, The Journal of Biological Chemistry.

[40]  I. Eperon,et al.  Hierarchy for 5' splice site preference determined in vivo. , 1990, Journal of molecular biology.

[41]  Dirk Holste,et al.  Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers , 2004, PLoS biology.

[42]  Christina S Leslie,et al.  Computational searches for splicing signals. , 2005, Methods.

[43]  J. Manley,et al.  Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[44]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[45]  Oliver Mühlemann,et al.  Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA , 1996, Nature.

[46]  L. Chasin,et al.  Splicing mutants and their second-site suppressors at the dihydrofolate reductase locus in Chinese hamster ovary cells , 1993, Molecular and cellular biology.

[47]  Michael Q. Zhang,et al.  An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. , 2006, Human molecular genetics.

[48]  Monika Heiner,et al.  Intronic CA‐repeat and CA‐rich elements: a new class of regulators of mammalian alternative splicing , 2005, The EMBO journal.

[49]  J. Conboy,et al.  The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons , 2005, Nucleic acids research.

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

[51]  S. D. Fraser,et al.  The RNA binding protein YB‐1 binds A/C‐rich exon enhancers and stimulates splicing of the CD44 alternative exon v4 , 2001, The EMBO journal.

[52]  R Kole,et al.  Selection of novel exon recognition elements from a pool of random sequences , 1995, Molecular and cellular biology.

[53]  R. Darnell,et al.  Nova Regulates GABAA Receptor γ2 Alternative Splicing via a Distal Downstream UCAU-Rich Intronic Splicing Enhancer , 2003, Molecular and Cellular Biology.

[54]  Dan Graur,et al.  Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. , 2004, Molecular cell.

[55]  S. Sugano,et al.  A vertebrate RNA‐binding protein Fox‐1 regulates tissue‐specific splicing via the pentanucleotide GCAUG , 2003, The EMBO journal.

[56]  S. Brenner,et al.  Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. , 2005, Genes & development.

[57]  Christina L. Zheng,et al.  Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. , 2005, RNA.

[58]  S. K. Purushothaman,et al.  Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. , 2004, Molecular cell.

[59]  Jinhua Wang,et al.  ESEfinder: a web resource to identify exonic splicing enhancers , 2003, Nucleic Acids Res..

[60]  Gene W. Yeo,et al.  Systematic Identification and Analysis of Exonic Splicing Silencers , 2004, Cell.

[61]  R. Sorek,et al.  Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. , 2003, Genome research.

[62]  A. Krainer,et al.  Identification of Functional Exonic Splicing Enhancer Motifs Recognized by Individual Sr Proteins Using an in Vitro Randomization and Functional Selection Procedure, We Have Identified Three Novel Classes of Exonic Splicing Enhancers (eses) Recognized by Human Sf2/asf, Srp40, and Srp55, Respectively , 2022 .

[63]  B. Graveley Sorting out the complexity of SR protein functions. , 2000, RNA.

[64]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[65]  David I. K. Martin,et al.  Transcriptional Interference by Independently Regulated Genes Occurs in Any Relative Arrangement of the Genes and Is Influenced by Chromosomal Integration Position , 2002, Molecular and Cellular Biology.

[66]  J. Valcárcel,et al.  Post-transcriptional regulation: The dawn of PTB , 1997, Current Biology.

[67]  Susan M. Berget,et al.  An Intronic Splicing Enhancer Binds U1 snRNPs To Enhance Splicing and Select 5′ Splice Sites , 2000, Molecular and Cellular Biology.

[68]  J. Manley,et al.  A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy , 2003, Nature Genetics.

[69]  J. Kjems,et al.  Characterization of human RNA splice signals by iterative functional selection of splice sites. , 2000, RNA.

[70]  Michael R Green,et al.  A single polypyrimidine tract binding protein (PTB) binding site mediates splicing inhibition at mouse IgM exons M1 and M2. , 2004, RNA.

[71]  L. Chasin,et al.  Computational definition of sequence motifs governing constitutive exon splicing. , 2004, Genes & development.

[72]  M. Garcia-Blanco,et al.  Protein–protein interactions and 5'-splice-site recognition in mammalian mRNA precursors , 1994, Nature.

[73]  S. Kawamoto,et al.  Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities , 2005, Nucleic acids research.

[74]  M. Adams,et al.  An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element. , 2001, RNA.

[75]  M. Green,et al.  Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. , 1991, Annual review of cell biology.

[76]  J. Manley,et al.  The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. , 1995, The EMBO journal.

[77]  L. Chasin,et al.  Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons , 2006, Proceedings of the National Academy of Sciences.

[78]  F. Clark,et al.  Understanding alternative splicing: towards a cellular code , 2005, Nature Reviews Molecular Cell Biology.

[79]  J. Ellis,et al.  Multiple roles of arginine/serine-rich splicing factors in RNA processing. , 2005, Biochemical Society transactions.

[80]  T. Cooper,et al.  Identification of a new class of exonic splicing enhancers by in vivo selection , 1997, Molecular and cellular biology.

[81]  Zhi-Ming Zheng,et al.  Regulation of Alternative RNA Splicing by Exon Definition and Exon Sequences in Viral and Mammalian Gene Expression , 2004, Journal of Biomedical Science.

[82]  S. Berget,et al.  G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection , 1997, Molecular and cellular biology.

[83]  J. Stévenin,et al.  The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers. , 1999, RNA.

[84]  D. Black,et al.  Molecular basis of RNA recognition by the human alternative splicing factor Fox‐1 , 2006, The EMBO journal.

[85]  R Nussinov,et al.  Conserved signals around the 5' splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5' and 3' splice sites. , 1989, Journal of biomolecular structure & dynamics.

[86]  A. Bindereif,et al.  In vitro selection of exonic splicing enhancer sequences: identification of novel CD44 enhancers. , 2001, Nucleic acids research.

[87]  Thaned Kangsamaksin,et al.  Exon Inclusion Is Dependent on Predictable Exonic Splicing Enhancers , 2005, Molecular and Cellular Biology.

[88]  Jane Y. Wu,et al.  SRp54 (SFRS11), a Regulator for tau Exon 10 Alternative Splicing Identified by an Expression Cloning Strategy , 2006, Molecular and Cellular Biology.

[89]  T. Cooper,et al.  Nucleotide substitutions within the cardiac troponin T alternative exon disrupt pre-mRNA alternative splicing. , 1989, Nucleic acids research.

[90]  Jurg Ott,et al.  Distribution and characterization of regulatory elements in the human genome. , 2002, Genome research.

[91]  L. Bell,et al.  Sex-lethal Interactions with Protein and RNA , 1997, The Journal of Biological Chemistry.

[92]  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.

[93]  James Stévenin,et al.  Broad specificity of SR (serine/arginine) proteins in the regulation of alternative splicing of pre-messenger RNA. , 2004, Progress in nucleic acid research and molecular biology.

[94]  Mark Groudine,et al.  Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells , 2004, Nature Structural &Molecular Biology.

[95]  K. Neugebauer,et al.  Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells , 2006, Nature Structural &Molecular Biology.

[96]  A. Prats,et al.  Heterogeneous Nuclear Ribonucleoprotein A1 Is a Novel Internal Ribosome Entry Site trans-Acting Factor That Modulates Alternative Initiation of Translation of the Fibroblast Growth Factor 2 mRNA* , 2005, Journal of Biological Chemistry.

[97]  U. Pozzoli,et al.  Silencers regulate both constitutive and alternative splicing events in mammals , 2005, Cellular and Molecular Life Sciences CMLS.

[98]  C. Burge,et al.  A computational analysis of sequence features involved in recognition of short introns , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[99]  Nikolaus Grigorieff,et al.  Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. , 2002, RNA.

[100]  P. Sharp,et al.  A minimal spliceosomal complex A recognizes the branch site and polypyrimidine tract , 1997, Molecular and cellular biology.

[101]  Michael R. Green,et al.  Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. , 2004, Molecular cell.

[102]  N. Bresolin,et al.  Silencer elements as possible inhibitors of pseudoexon splicing. , 2004, Nucleic acids research.

[103]  Zefeng Wang,et al.  General and specific functions of exonic splicing silencers in splicing control. , 2006, Molecular cell.

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

[105]  C. McGuigan,et al.  A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site. , 1996, Genes & development.

[106]  S. Berget Exon Recognition in Vertebrate Splicing (*) , 1995, The Journal of Biological Chemistry.

[107]  J. Manley,et al.  Determinants of SR protein specificity. , 1999, Current opinion in cell biology.

[108]  E. Buratti,et al.  Defective splicing, disease and therapy: searching for master checkpoints in exon definition , 2006, Nucleic acids research.

[109]  K. Williams,et al.  hnRNP A1 binds promiscuously to oligoribonucleotides: utilization of random and homo-oligonucleotides to discriminate sequence from base-specific binding. , 1996, Nucleic acids research.

[110]  Gene W. Yeo,et al.  A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs , 2005, PLoS biology.

[111]  J. Lis,et al.  Specific SR protein-dependent splicing substrates identified through genomic SELEX. , 2003, Nucleic acids research.

[112]  Michael R. Green,et al.  RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans. , 2006, Genes & development.

[113]  S. Berget,et al.  Exon definition may facilitate splice site selection in RNAs with multiple exons. , 1990, Molecular and cellular biology.

[114]  Gene W. Yeo,et al.  Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis , 2006, PLoS genetics.

[115]  D. Brutlag,et al.  A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[116]  M. Tomita,et al.  Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. , 2004, RNA.

[117]  S. Saxonov,et al.  Comparison of intron-containing and intron-lacking human genes elucidates putative exonic splicing enhancers. , 2001, Nucleic acids research.

[118]  P. Sharp,et al.  SC35-mediated reconstitution of splicing in U2AF-depleted nuclear extract. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[119]  T. Maniatis,et al.  A systematic analysis of the factors that determine the strength of pre‐mRNA splicing enhancers , 1998, The EMBO journal.

[120]  G. Varani,et al.  RNA recognition by RNP proteins during RNA processing. , 1998, Annual review of biophysics and biomolecular structure.

[121]  L. Chasin,et al.  Large exon size does not limit splicing in vivo , 1994, Molecular and cellular biology.

[122]  S. Berget,et al.  Participation of the C-Terminal Domain of RNA Polymerase II in Exon Definition during Pre-mRNA Splicing , 2000, Molecular and Cellular Biology.

[123]  T. Maniatis,et al.  Multiple Distinct Splicing Enhancers in the Protein-Coding Sequences of a Constitutively Spliced Pre-mRNA , 1999, Molecular and Cellular Biology.

[124]  Michael Ruogu Zhang,et al.  Statistical features of human exons and their flanking regions. , 1998, Human molecular genetics.

[125]  R. Darnell,et al.  The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo , 1997, Molecular and cellular biology.

[126]  Jernej Ule,et al.  CLIP Identifies Nova-Regulated RNA Networks in the Brain , 2003, Science.

[127]  L. Chasin,et al.  Multiple Splicing Defects in an Intronic False Exon , 2000, Molecular and Cellular Biology.