Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events

Table 4. Selection of actively maintained AS databases. Most databases have been constructed from automated large-scale comparisons of transcript sequences to genomic DNA of known genes, following ENSEMBL, UNIGENE, SWISS-PROT annotation and nomenclature, whereas “hybrid-like” approaches attempt to curate AS data by searches of published research. Databases are purposefully different and serve different users needs: they do so in the scope of interrogated genomes and sequence data, splicing conservation, annotation of functional elements, data download, and several other features (last column). They show further differences in their inference of AS events, for reasons such as different primary data, rules to detect splice patterns, and filter criteria.

[1]  C. Gooding,et al.  Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. , 2004, Molecular cell.

[2]  Christopher J. Lee,et al.  Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes , 2006, Nature Reviews Genetics.

[3]  Christopher B. Burge,et al.  Hollywood: a comparative relational database of alternative splicing , 2005, Nucleic Acids Res..

[4]  Brenton R Graveley,et al.  Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary Structures , 2005, Cell.

[5]  Simon Cawley,et al.  HMM sampling and applications to gene finding and alternative splicing , 2003, ECCB.

[6]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[7]  Huanming Yang,et al.  Origin and evolution of new exons in rodents. , 2005, Genome research.

[8]  B. Frey,et al.  Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. , 2006, Genes & development.

[9]  W. Reinhold,et al.  Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles. , 2002, Genomics.

[10]  P. Sharp,et al.  Splicing of precursors to mRNAs by the spliceosomes , 1993 .

[11]  Christopher B. Burge,et al.  Recognition of Unknown Conserved Alternatively Spliced Exons , 2005, PLoS Comput. Biol..

[12]  Melissa S Jurica,et al.  Pre-mRNA splicing: awash in a sea of proteins. , 2003, Molecular cell.

[13]  David States,et al.  Selecting for functional alternative splices in ESTs. , 2002, Genome research.

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

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

[16]  B. Ganem.  RNA world , 1987, Nature.

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

[18]  T. Cooper,et al.  Finding signals that regulate alternative splicing in the post-genomic era , 2002, Genome Biology.

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

[20]  S. Brenner,et al.  The evolving roles of alternative splicing. , 2004, Current opinion in structural biology.

[21]  Nicholas J. McGlincy,et al.  Regulation of alternative splicing by PTB and associated factors. , 2005, Biochemical Society transactions.

[22]  Peer Bork,et al.  Extraction of Transcript Diversity from Scientific Literature , 2005, PLoS Comput. Biol..

[23]  P. Grabowski.  Genetic Evidence for a Nova Regulator of Alternative Splicing in the Brain , 2000, Neuron.

[24]  Gil Ast,et al.  How did alternative splicing evolve? , 2004, Nature Reviews Genetics.

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

[26]  Brenton R Graveley,et al.  A computational and experimental approach toward a priori identification of alternatively spliced exons. , 2004, RNA.

[27]  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 .

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

[29]  G. Ast,et al.  Different levels of alternative splicing among eukaryotes , 2006, Nucleic acids research.

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

[31]  Hiram Clawson,et al.  Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes , 2006, PLoS Comput. Biol..

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

[33]  Michael Ruogu Zhang,et al.  An alternative-exon database and its statistical analysis. , 2000, DNA and cell biology.

[34]  Gunnar Rätsch,et al.  Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning , 2006, PLoS Comput. Biol..

[35]  Jan-Fang Cheng,et al.  Primate-specific evolution of an LDLR enhancer , 2006, Genome Biology.

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

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

[38]  Gunnar Rätsch,et al.  RASE: recognition of alternatively spliced exons in C.elegans , 2005, ISMB.

[39]  S. Brenner,et al.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  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.

[41]  Roded Sharan,et al.  A motif-based framework for recognizing sequence families , 2005, ISMB.

[42]  Gene W. Yeo,et al.  Variation in alternative splicing across human tissues , 2004, Genome Biology.

[43]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[44]  Ron Shamir,et al.  Accurate identification of alternatively spliced exons using support vector machine , 2005, Bioinform..

[45]  Douglas G Scofield,et al.  Intron size, abundance, and distribution within untranslated regions of genes. , 2006, Molecular biology and evolution.

[46]  Steven Salzberg,et al.  A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons , 2006, Algorithms for Molecular Biology.

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

[48]  M. Brent,et al.  Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts , 2006, Genome Biology.

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

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

[51]  R. Shamir,et al.  Assessing the number of ancestral alternatively spliced exons in the human genome , 2006, BMC Genomics.

[52]  Christopher B. Burge,et al.  Identification and analysis of alternative splicing events conserved in human and mouse Gene , 2005 .

[53]  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.

[54]  L. Maquat,et al.  Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. , 2005, Current opinion in cell biology.

[55]  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.

[56]  K. Huse,et al.  Non-EST based prediction of exon skipping and intron retention events using Pfam information , 2005, Nucleic acids research.

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

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

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

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

[61]  Qi Wang,et al.  Bioinformatics analysis of alternative splicing , 2005, Briefings Bioinform..

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

[63]  Juha Muilu,et al.  Conservation of human alternative splice events in mouse. , 2003, Nucleic acids research.

[64]  P. Green,et al.  Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[65]  M. Gelfand,et al.  Low conservation of alternative splicing patterns in the human and mouse genomes. , 2003, Human molecular genetics.

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

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

[68]  David Penny,et al.  Coevolution of genomic intron number and splice sites. , 2007, Trends in genetics : TIG.

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

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

[71]  Robi David Mitra,et al.  Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human , 2007, Nucleic acids research.

[72]  Peer Bork,et al.  Common exon duplication in animals and its role in alternative splicing. , 2002, Human molecular genetics.

[73]  T. Nilsen.  The spliceosome: the most complex macromolecular machine in the cell? , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

[75]  Ron Shamir,et al.  A non-EST-based method for exon-skipping prediction. , 2004, Genome research.