A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements

BackgroundPolymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We have developed a new tool (SpliceScan II) for predicting the effects of genetic variants on splicing and cis-regulatory elements. The novel Bayesian non-canonical 5'GC splice site (SS) sensor used in our tool allows inference on non-canonical exons.ResultsOur tool performed favorably when compared with the existing methods in the context of genes linked to the Autism Spectrum Disorder (ASD). SpliceScan II was able to predict more aberrant splicing isoforms triggered by the mutations, as documented in DBASS5 and DBASS3 aberrant splicing databases, than other existing methods. Detrimental effects behind some of the polymorphic variations previously associated with Alzheimer's and breast cancer could be explained by changes in predicted splicing patterns.ConclusionsWe have developed SpliceScan II, an effective and sensitive tool for predicting the detrimental effects of genomic variants on splicing leading to Mendelian and complex hereditary disorders. The method could potentially be used to screen resequenced patient DNA to identify de novo mutations and polymorphic variants that could contribute to a genetic disorder.

[1]  D. Gudbjartsson,et al.  Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor–positive breast cancer , 2007, Nature Genetics.

[2]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[3]  J. Deogun,et al.  Method of predicting Splice Sites based on signal interactions , 2006, Biology Direct.

[4]  Y. Hua,et al.  Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. , 2008, American journal of human genetics.

[5]  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.

[6]  Christopher B. Burge,et al.  RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons , 2004, Nucleic Acids Res..

[7]  Volker Brendel,et al.  Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants , 2005, Bioinform..

[8]  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.

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

[10]  Peter G. Korning,et al.  Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. , 1996, Nucleic acids research.

[11]  I. Vořechovský,et al.  Computational prediction of splicing regulatory elements shared by Tetrapoda organisms , 2009, BMC Genomics.

[12]  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.

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

[14]  Gene W. Yeo,et al.  Variation in sequence and organization of splicing regulatory elements in vertebrate genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Stephen Neidle,et al.  Quadruplex nucleic acids. , 2006 .

[16]  Luciano Milanesi,et al.  Analysis of donor splice sites in different eukaryotic organisms , 1997, Journal of Molecular Evolution.

[17]  Michael Q. Zhang,et al.  RNA landscape of evolution for optimal exon and intron discrimination , 2008, Proceedings of the National Academy of Sciences.

[18]  J. Královičová,et al.  Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition , 2007, Nucleic acids research.

[19]  M. Garcia-Blanco,et al.  Alternative splicing in disease and therapy , 2004, Nature Biotechnology.

[20]  C. Baker,et al.  Selection of the bovine papillomavirus type 1 nucleotide 3225 3' splice site is regulated through an exonic splicing enhancer and its juxtaposed exonic splicing suppressor , 1996, Journal of virology.

[21]  J. Fickett,et al.  Assessment of protein coding measures. , 1992, Nucleic acids research.

[22]  R. Guigó,et al.  Are splicing mutations the most frequent cause of hereditary disease? , 2005, FEBS letters.

[23]  E. Koonin,et al.  Accumulation of GC donor splice signals in mammals , 2008, Biology Direct.

[24]  Martin J. Bishop,et al.  Guide to Human Genome Computing , 1994 .

[25]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[26]  W. Willett,et al.  A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer , 2007, Nature Genetics.

[27]  S Brunak,et al.  Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA. , 2004, Nucleic acids research.

[28]  D. Hwang,et al.  U1 small nuclear RNA-promoted exon selection requires a minimal distance between the position of U1 binding and the 3' splice site across the exon , 1997, Molecular and cellular biology.

[29]  C. Burge,et al.  Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. , 2008, RNA.

[30]  J. Cogan,et al.  High frequency of BMPR2 exonic deletions/duplications in familial pulmonary arterial hypertension. , 2006, American journal of respiratory and critical care medicine.

[31]  Thilo Dörk,et al.  Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: Maximum entropy estimates of splice junction strengths , 2004, Human mutation.

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

[33]  Christopher B. Burge,et al.  Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals , 2003, RECOMB '03.

[34]  Christine B Ambrosone,et al.  SNPs, haplotypes, and cancer: applications in molecular epidemiology. , 2004, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[35]  Igor Vorechovsky,et al.  Position-Dependent Repression and Promotion of DQB1 Intron 3 Splicing by GGGG Motifs1 , 2006, The Journal of Immunology.

[36]  Petr Divina,et al.  Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping , 2009, European Journal of Human Genetics.

[37]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

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

[39]  V. Solovyev,et al.  Analysis of canonical and non-canonical splice sites in mammalian genomes. , 2000, Nucleic acids research.

[40]  Adrian R. Krainer,et al.  Aberrant 5′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization , 2007, Nucleic acids research.

[41]  J. Listgarten,et al.  Predictive Models for Breast Cancer Susceptibility from Multiple Single Nucleotide Polymorphisms , 2004, Clinical Cancer Research.

[42]  R. Sachidanandam,et al.  Comprehensive splice-site analysis using comparative genomics , 2006, Nucleic acids research.

[43]  I. Vořechovský,et al.  Aberrant 3′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization , 2006, Nucleic acids research.

[44]  P. Stenson,et al.  Human Gene Mutation Database: towards a comprehensive central mutation database , 2007, Journal of Medical Genetics.

[45]  A. Krogh.  11 – Gene Finding: Putting the Parts Together , 1998 .

[46]  BMC Bioinformatics , 2005 .

[47]  Genica,et al.  Commonly studied single-nucleotide polymorphisms and breast cancer: Results from the Breast Cancer Association Consortium , 2006 .

[48]  Anders Krogh,et al.  Two Methods for Improving Performance of a HMM and their Application for Gene Finding , 1997, ISMB.

[49]  B. Shankar,et al.  Fundamentals of Quadruplex Structures , 2006 .

[50]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[51]  A. Churbanov.  Contemporary Progress in Gene Structure Prediction , 2006 .

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

[53]  Alison M Dunning,et al.  Common ERBB2 polymorphisms and risk of breast cancer in a white British population: a case–control study , 2005, Breast Cancer Research.

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

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

[56]  Paul D.P. Pharoah,et al.  Commonly studied single-nucleotide polymorphisms and breast cancer: results from the Breast Cancer Association Consortium. , 2007, Journal of the National Cancer Institute.

[57]  Lester L. Peters,et al.  Genome-wide association study identifies novel breast cancer susceptibility loci , 2007, Nature.

[58]  D. Penny.  Inferring Phylogenies.—Joseph Felsenstein. 2003. Sinauer Associates, Sunderland, Massachusetts. , 2004 .

[59]  R. Guigó,et al.  Comparison of splice sites in mammals and chicken. , 2005, Genome research.

[60]  Stephen M. Mount,et al.  Genomic sequence, splicing, and gene annotation. , 2000, American journal of human genetics.