Computational definition of sequence motifs governing constitutive exon splicing.
paper
Cited
Public
Unavailable
- Authors
- Zhang, Xiang H-F; Chasin, Lawrence A
- Year
- 2004
- Journal
- Genes & development
- PMID
- 15145827
- DOI
- 10.1101/gad.1195304
- PMCID
- PMC420350
We have searched for sequence motifs that contribute to the recognition of human pre-mRNA splice sites by comparing the frequency of 8-mers in internal noncoding exons versus unspliced pseudo exons and 5' untranslated regions (5' untranslated regions [UTRs]) of transcripts of intronless genes. This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA.
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External
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| Comparative component analysis of exons with different splicing frequencies. | Song S et al. | β | 2009 | β |
| Computational prediction of splicing regulatory elements shared by Tetrapoda organisms. | Churbanov A et al. | β | 2009 | β |
| Design of phosphorodiamidate morpholino oligomers (PMOs) for the induction of exon skipping of the human DMD gene. | Popplewell LJ et al. | β | 2009 | β |
| Disease-causing mutations improving the branch site and polypyrimidine tract: pseudoexon activation of LINE-2 and antisense Alu lacking the poly(T)-tail. | Meili D et al. | β | 2009 | β |
| Divergence of exonic splicing elements after gene duplication and the impact on gene structures. | Zhang Z et al. | β | 2009 | β |
| Enhanced exon-skipping induced by U7 snRNA carrying a splicing silencer sequence: Promising tool for DMD therapy. | Goyenvalle A et al. | β | 2009 | β |
| Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. | Zou C et al. | β | 2009 | β |
| Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates. | Irimia M et al. | β | 2009 | β |
| Functional analysis of three splicing mutations identified in the PMM2 gene: toward a new therapy for congenital disorder of glycosylation type Ia. | Vega AI et al. | β | 2009 | β |
| Guidelines for antisense oligonucleotide design and insight into splice-modulating mechanisms. | Aartsma-Rus A et al. | β | 2009 | β |
| Human Splicing Finder: an online bioinformatics tool to predict splicing signals. | Desmet FO et al. | β | 2009 | β |
| Intron 7 conserved sequence elements regulate the splicing of the SMN genes. | Gladman JT et al. | β | 2009 | β |
| Mutational spectrum of CDKL5 in early-onset encephalopathies: a study of a large collection of French patients and review of the literature. | Nemos C et al. | β | 2009 | β |
| Predicting potentially functional SNPs in drug-response genes. | Pang GS et al. | β | 2009 | β |
| Regulation of mammalian pre-mRNA splicing. | Hui J | β | 2009 | β |
| RNA analysis of consensus sequence splicing mutations: implications for the diagnosis of Wilson disease. | Lovicu M et al. | β | 2009 | β |
| Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. | Sanford JR et al. | β | 2009 | β |
| Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing. | Zhang XH et al. | β | 2009 | β |
| SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. | Schwartz S et al. | β | 2009 | β |
| The G allele of SNP E1/A118G at the mu-opioid receptor gene locus shows genomic evidence of recent positive selection. | Pang GS et al. | β | 2009 | β |
| The SR protein family of splicing factors: master regulators of gene expression. | Long JC et al. | β | 2009 | β |
| Ab initio identification of functionally interacting pairs of cis-regulatory elements. | Friedman BA et al. | β | 2008 | β |
| Alternative splicing: current perspectives. | Kim E et al. | β | 2008 | β |
| Alternative splicing of Alu exons--two arms are better than one. | Gal-Mark N et al. | β | 2008 | β |
| Antagonistic effects of the SRp30c protein and cryptic 5' splice sites on the alternative splicing of the apoptotic regulator Bcl-x. | Cloutier P et al. | β | 2008 | β |
| A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. | Aznarez I et al. | β | 2008 | β |
| Automatic detection of exonic splicing enhancers (ESEs) using SVMs. | Mersch B et al. | β | 2008 | β |
| Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a natural BRCA1 exon 18 mutant. | Goina E et al. | β | 2008 | β |
| Characterization of regulatory intronic and exonic sequences involved in alternative splicing of scavenger receptor class B gene. | Zhang X et al. | β | 2008 | β |
| Combinatorial control of exon recognition. | Hertel KJ | β | 2008 | β |
| Comparative analysis of sequence features involved in the recognition of tandem splice sites. | Bortfeldt R et al. | β | 2008 | β |
| Computational analysis of splicing errors and mutations in human transcripts. | Kurmangaliyev YZ et al. | β | 2008 | β |
| Dynamic regulation of alternative splicing by silencers that modulate 5' splice site competition. | Yu Y et al. | β | 2008 | β |
| Exon creation and establishment in human genes. | Corvelo A et al. | β | 2008 | β |
| Genes in glucose metabolism and association with spina bifida. | Davidson CM et al. | β | 2008 | β |
| Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF. | Sanford JR et al. | β | 2008 | β |
| Improved identification of conserved cassette exons using Bayesian networks. | Sinha R et al. | β | 2008 | β |
| Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1. | Raponi M et al. | β | 2008 | β |
| Positive selection acting on splicing motifs reflects compensatory evolution. | Ke S et al. | β | 2008 | β |
| Prediction and assessment of splicing alterations: implications for clinical testing. | Spurdle AB et al. | β | 2008 | β |
| Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. | Kechris K et al. | β | 2008 | β |
| RNA landscape of evolution for optimal exon and intron discrimination. | Zhang C et al. | β | 2008 | β |
| Selection against tandem splice sites affecting structured protein regions. | Hiller M et al. | β | 2008 | β |
| Simultaneous assessment of the effects of exonic mutations on RNA splicing and protein functions. | Ho PY et al. | β | 2008 | β |
| Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. | Wang Z et al. | β | 2008 | β |
| Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. | Holste D et al. | β | 2008 | β |
| Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. | Buratti E et al. | β | 2007 | β |
| A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. | Voelker RB et al. | β | 2007 | β |
| A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. | Pertea M et al. | β | 2007 | β |
| ADAM15 gene structure and differential alternative exon use in human tissues. | Kleino I et al. | β | 2007 | β |
| An intronic element contributes to splicing repression in spinal muscular atrophy. | Kashima T et al. | β | 2007 | β |
| An intronic signal for alternative splicing in the human genome. | Havlioglu N et al. | β | 2007 | β |
| Antisense-mediated exon skipping: a versatile tool with therapeutic and research applications. | Aartsma-Rus A et al. | β | 2007 | β |
| Antisense oligonucleotide-induced alternative splicing of the APOB mRNA generates a novel isoform of APOB. | Khoo B et al. | β | 2007 | β |
| Applying genetic programming to the prediction of alternative mRNA splice variants. | Vukusic I et al. | β | 2007 | β |
| Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. | Lee JA et al. | β | 2007 | β |
| Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. | Yeo GW et al. | β | 2007 | β |
| Exon skipping through the creation of a putative exonic splicing silencer as a consequence of the cystic fibrosis mutation R553X. | Aznarez I et al. | β | 2007 | β |
| Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5' splice-site disruption. | Wimmer K et al. | β | 2007 | β |
| Features generated for computational splice-site prediction correspond to functional elements. | Dogan RI et al. | β | 2007 | β |
| Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition. | KrΓ‘lovicovΓ‘ J et al. | β | 2007 | β |
| Identification of common genetic variation that modulates alternative splicing. | Hull J et al. | β | 2007 | β |
| Multiexon skipping leading to an artificial DMD protein lacking amino acids from exons 45 through 55 could rescue up to 63% of patients with Duchenne muscular dystrophy. | BΓ©roud C et al. | β | 2007 | β |
| Multisite and bidirectional exonic splicing enhancer in CD44 alternative exon v3. | Vela E et al. | β | 2007 | β |
| Possible role of nucleotide correlations between human exon junctions. | Piva F et al. | β | 2007 | β |
| Pre-mRNA secondary structures influence exon recognition. | Hiller M et al. | β | 2007 | β |
| Pre-spliceosomal binding of U1 small nuclear ribonucleoprotein (RNP) and heterogenous nuclear RNP E1 is associated with suppression of a growth hormone receptor pseudoexon. | Akker SA et al. | β | 2007 | β |
| Propionic and methylmalonic acidemia: antisense therapeutics for intronic variations causing aberrantly spliced messenger RNA. | RincΓ³n A et al. | β | 2007 | β |
| Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12. | Raponi M et al. | β | 2007 | β |
| RNA 1997-2007: a remarkable decade of discovery. | Nilsen TW | β | 2007 | β |
| RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events. | Buratti E et al. | β | 2007 | β |
| SEAM: a Stochastic EM-type Algorithm for Motif-finding in biopolymer sequences. | Bi C | β | 2007 | β |
| Searching for splicing motifs. | Chasin LA | β | 2007 | β |
| Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. | Nielsen KB et al. | β | 2007 | β |
| Splicing in disease: disruption of the splicing code and the decoding machinery. | Wang GS et al. | β | 2007 | β |
| SR proteins and related factors in alternative splicing. | Lin S et al. | β | 2007 | β |
| The emergence of alternative 3' and 5' splice site exons from constitutive exons. | Koren E et al. | β | 2007 | β |
| A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. | Gooding C et al. | β | 2006 | β |
| Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. | Xing Y et al. | β | 2006 | β |
| Alternative splicing: new insights from global analyses. | Blencowe BJ | β | 2006 | β |
| An apparent pseudo-exon acts both as an alternative exon that leads to nonsense-mediated decay and as a zero-length exon. | Grellscheid SN et al. | β | 2006 | β |
| An exonic splicing silencer is involved in the regulated splicing of glucose 6-phosphate dehydrogenase mRNA. | Szeszel-Fedorowicz W et al. | β | 2006 | β |
| An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. | Smith PJ et al. | β | 2006 | β |
| Bioinformatics of alternative splicing and its regulation. | Florea L | β | 2006 | β |
| Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. | Goren A et al. | β | 2006 | β |
| Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. | Dewey CN et al. | β | 2006 | β |
| Defective splicing, disease and therapy: searching for master checkpoints in exon definition. | Buratti E et al. | β | 2006 | β |
| Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. | Cartegni L et al. | β | 2006 | β |
| Differentiated evolutionary rates in alternative exons and the implications for splicing regulation. | Plass M et al. | β | 2006 | β |
| Functional single nucleotide polymorphism-based association studies. | Carlton VE et al. | β | 2006 | β |
| Identification of a splicing enhancer in MLH1 using COMPARE, a new assay for determination of relative RNA splicing efficiencies. | Xu DQ et al. | β | 2006 | β |
| Identification of hnRNPs K, L and A2/B1 as candidate proteins involved in the nutritional regulation of mRNA splicing. | Griffith BN et al. | β | 2006 | β |
| Inference of splicing regulatory activities by sequence neighborhood analysis. | Stadler MB et al. | β | 2006 | β |
| In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects. | Lastella P et al. | β | 2006 | β |
| Phenotypic consequences of branch point substitutions. | KrΓ‘lovicovΓ‘ J et al. | β | 2006 | β |
| Phylogenetically widespread alternative splicing at unusual GYNGYN donors. | Hiller M et al. | β | 2006 | β |
| Regions of extreme synonymous codon selection in mammalian genes. | Schattner P et al. | β | 2006 | β |
| Splicing of a critical exon of human Survival Motor Neuron is regulated by a unique silencer element located in the last intron. | Singh NK et al. | β | 2006 | β |
| The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test. | Chen FC et al. | β | 2006 | β |
| Unweaving the meanings of messenger RNA sequences. | GuigΓ³ R et al. | β | 2006 | β |
| A combinatorial code for splicing silencing: UAGG and GGGG motifs. | Han K et al. | β | 2005 | β |
| An exonic splicing silencer downstream of the 3' splice site A2 is required for efficient human immunodeficiency virus type 1 replication. | Madsen JM et al. | β | 2005 | β |
| A simple answer for a splicing conundrum. | Black DL | β | 2005 | β |
| Biased exon/intron distribution of cryptic and de novo 3' splice sites. | KrΓ‘lovicovΓ‘ J et al. | β | 2005 | β |
| Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. | Zheng CL et al. | β | 2005 | β |
| Characterization of the intronic splicing silencers flanking FGFR2 exon IIIb. | Wagner EJ et al. | β | 2005 | β |
| Dephosphorylation-dependent sorting of SR splicing factors during mRNP maturation. | Lin S et al. | β | 2005 | β |
| Dichotomous splicing signals in exon flanks. | Zhang XH et al. | β | 2005 | β |
| Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. | Wang J et al. | β | 2005 | β |
| Exonic splicing enhancers in fission yeast: functional conservation demonstrates an early evolutionary origin. | Webb CJ et al. | β | 2005 | β |
| Exon inclusion is dependent on predictable exonic splicing enhancers. | Zhang XH et al. | β | 2005 | β |
| Exonization of AluYa5 in the human ACE gene requires mutations in both 3' and 5' splice sites and is facilitated by a conserved splicing enhancer. | Lei H et al. | β | 2005 | β |
| HnRNP L represses exon splicing via a regulated exonic splicing silencer. | Rothrock CR et al. | β | 2005 | β |
| Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression. | Lei H et al. | β | 2005 | β |
| Regulatory elements of the melanocortin 1 receptor. | Rouzaud F et al. | β | 2005 | β |
| Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. | Pagani F et al. | β | 2005 | β |
| The spliceosome: a novel multi-faceted target for therapy. | Tazi J et al. | β | 2005 | β |
| The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. | Minovitsky S et al. | β | 2005 | β |
| U2AF binding selects for the high conservation of the C. elegans 3' splice site. | Hollins C et al. | β | 2005 | β |
| Understanding alternative splicing: towards a cellular code. | Matlin AJ et al. | β | 2005 | β |
| Branch site haplotypes that control alternative splicing. | KrΓ‘lovicovΓ‘ J et al. | β | 2004 | β |
| Systematic identification and analysis of exonic splicing silencers. | Wang Z et al. | β | 2004 | β |
| Towards a splicing code. | Fu XD | β | 2004 | β |