Identification of common genetic variation that modulates alternative splicing
Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent i...
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description | Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function. |
doi_str_mv | 10.1371/journal.pgen.0030099 |
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Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.</description><identifier>ISSN: 1553-7404</identifier><identifier>ISSN: 1553-7390</identifier><identifier>EISSN: 1553-7404</identifier><identifier>DOI: 10.1371/journal.pgen.0030099</identifier><identifier>PMID: 17571926</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Alternative Splicing - genetics ; Autoimmune diseases ; Biomedical research ; Cell Line ; Confidence intervals ; Deoxyribonucleic acid ; Disease ; DNA ; Efficiency ; Exons - genetics ; Experiments ; Gene expression ; Genetic engineering ; Genetic Variation ; Genetics ; Genetics and Genomics ; Genomes ; Genomics ; Homo (Human) ; Humans ; Polymorphism, Single Nucleotide - physiology ; Protein Isoforms - genetics ; Protein Isoforms - physiology ; Proteins ; Ratios ; RNA Splice Sites - genetics ; Studies</subject><ispartof>PLoS genetics, 2007-06, Vol.3 (6), p.e99-e99</ispartof><rights>COPYRIGHT 2007 Public Library of Science</rights><rights>2007 Hull et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Hull J, Campino S, Rowlands K, Chan M-S, Copley RR, et al. (2007) Identification of Common Genetic Variation That Modulates Alternative Splicing. PLoS Genet 3(6): e99. doi:10.1371/journal.pgen.0030099</rights><rights>2007 Hull et al. 2007</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c766t-e167328ad301b5f146d9ce0adb7b35551f8aa276f74fab30a0723b4e0d37f70e3</citedby><cites>FETCH-LOGICAL-c766t-e167328ad301b5f146d9ce0adb7b35551f8aa276f74fab30a0723b4e0d37f70e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904363/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904363/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2101,2927,23865,27923,27924,53790,53792,79471,79472</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17571926$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Dermitzakis, Emmanouil T</contributor><creatorcontrib>Hull, Jeremy</creatorcontrib><creatorcontrib>Campino, Susana</creatorcontrib><creatorcontrib>Rowlands, Kate</creatorcontrib><creatorcontrib>Chan, Man-Suen</creatorcontrib><creatorcontrib>Copley, Richard R</creatorcontrib><creatorcontrib>Taylor, Martin S</creatorcontrib><creatorcontrib>Rockett, Kirk</creatorcontrib><creatorcontrib>Elvidge, Gareth</creatorcontrib><creatorcontrib>Keating, Brendan</creatorcontrib><creatorcontrib>Knight, Julian</creatorcontrib><creatorcontrib>Kwiatkowski, Dominic</creatorcontrib><title>Identification of common genetic variation that modulates alternative splicing</title><title>PLoS genetics</title><addtitle>PLoS Genet</addtitle><description>Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.</description><subject>Alternative Splicing - genetics</subject><subject>Autoimmune diseases</subject><subject>Biomedical research</subject><subject>Cell Line</subject><subject>Confidence intervals</subject><subject>Deoxyribonucleic acid</subject><subject>Disease</subject><subject>DNA</subject><subject>Efficiency</subject><subject>Exons - genetics</subject><subject>Experiments</subject><subject>Gene expression</subject><subject>Genetic engineering</subject><subject>Genetic Variation</subject><subject>Genetics</subject><subject>Genetics and Genomics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Homo (Human)</subject><subject>Humans</subject><subject>Polymorphism, Single Nucleotide - physiology</subject><subject>Protein Isoforms - genetics</subject><subject>Protein Isoforms - physiology</subject><subject>Proteins</subject><subject>Ratios</subject><subject>RNA Splice Sites - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hull, Jeremy</au><au>Campino, Susana</au><au>Rowlands, Kate</au><au>Chan, Man-Suen</au><au>Copley, Richard R</au><au>Taylor, Martin S</au><au>Rockett, Kirk</au><au>Elvidge, Gareth</au><au>Keating, Brendan</au><au>Knight, Julian</au><au>Kwiatkowski, Dominic</au><au>Dermitzakis, Emmanouil T</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of common genetic variation that modulates alternative splicing</atitle><jtitle>PLoS genetics</jtitle><addtitle>PLoS Genet</addtitle><date>2007-06-01</date><risdate>2007</risdate><volume>3</volume><issue>6</issue><spage>e99</spage><epage>e99</epage><pages>e99-e99</pages><issn>1553-7404</issn><issn>1553-7390</issn><eissn>1553-7404</eissn><abstract>Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>17571926</pmid><doi>10.1371/journal.pgen.0030099</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Alternative Splicing - genetics Autoimmune diseases Biomedical research Cell Line Confidence intervals Deoxyribonucleic acid Disease DNA Efficiency Exons - genetics Experiments Gene expression Genetic engineering Genetic Variation Genetics Genetics and Genomics Genomes Genomics Homo (Human) Humans Polymorphism, Single Nucleotide - physiology Protein Isoforms - genetics Protein Isoforms - physiology Proteins Ratios RNA Splice Sites - genetics Studies |
title | Identification of common genetic variation that modulates alternative splicing |
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