Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
Identifieur interne : 001653 ( Main/Exploration ); précédent : 001652; suivant : 001654Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
Auteurs : Raphae L Kiekens ; Annelies Vercauteren ; Beatrijs Moerkerke [Belgique] ; Els Goetghebeur [Belgique] ; Hilde Van Den Daele ; Roel Sterken ; Martin Kuiper ; Fred Van Eeuwijk [Pays-Bas] ; Marnik VuylstekeSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2006.
Abstract
Large-scale screening studies carried out to date for genetic variants that affect gene regulation are generally limited to descriptions of differences in allele-specific expression (ASE) detected in vivo. Allele-specific differences in gene expression provide evidence for a model whereby cis-acting genetic variation results in differential expression between alleles. Such gene surveys for regulatory variation are a first step in identifying the specific nucleotide changes that govern gene expression differences, but they leave the underlying mechanisms unexplored. Here, we propose a quantitative genetics approach to perform a genome-wide analysis of ASE differences (GASED). The GASED approach is based on a diallel design that is often used in plant breeding programs to estimate general combining abilities (GCA) of specific inbred lines and to identify high-yielding hybrid combinations of parents based on their specific combining abilities (SCAs). In a context of gene expression, the values of GCA and SCA parameters allow cis- and trans-regulatory changes to be distinguished and imbalances in gene expression to be ascribed to cis-regulatory variation. With this approach, a total of 715 genes could be identified that are likely to carry allelic polymorphisms responsible for at least a 1.5-fold allelic expression difference in a total of 10 diploid Arabidopsis thaliana hybrids. The major strength of the GASED approach, compared to other ASE detection methods, is that it is not restricted to genes with allelic transcript variants. Although a false-positive rate of 9/41 was observed, the GASED approach is a valuable pre-screening method that can accelerate systematic surveys of naturally occurring cis-regulatory variation among inbred lines for laboratory species, such as Arabidopsis, mouse, rat and fruitfly, and economically important crop species, such as corn.
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DOI: 10.1093/nar/gkl510
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Acids Res.</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2006">2006</date><biblScope unit="volume">34</biblScope><biblScope unit="issue">13</biblScope><biblScope unit="page" from="3677">3677</biblScope><biblScope unit="page" to="3686">3686</biblScope></imprint><idno type="ISSN">0305-1048</idno></series><idno type="istex">B1E328B33A676102B90A8EE60CCD65F2AB2F89BC</idno><idno type="DOI">10.1093/nar/gkl510</idno><idno type="local">gkl510</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Large-scale screening studies carried out to date for genetic variants that affect gene regulation are generally limited to descriptions of differences in allele-specific expression (ASE) detected in vivo. Allele-specific differences in gene expression provide evidence for a model whereby cis-acting genetic variation results in differential expression between alleles. Such gene surveys for regulatory variation are a first step in identifying the specific nucleotide changes that govern gene expression differences, but they leave the underlying mechanisms unexplored. Here, we propose a quantitative genetics approach to perform a genome-wide analysis of ASE differences (GASED). The GASED approach is based on a diallel design that is often used in plant breeding programs to estimate general combining abilities (GCA) of specific inbred lines and to identify high-yielding hybrid combinations of parents based on their specific combining abilities (SCAs). In a context of gene expression, the values of GCA and SCA parameters allow cis- and trans-regulatory changes to be distinguished and imbalances in gene expression to be ascribed to cis-regulatory variation. With this approach, a total of 715 genes could be identified that are likely to carry allelic polymorphisms responsible for at least a 1.5-fold allelic expression difference in a total of 10 diploid Arabidopsis thaliana hybrids. The major strength of the GASED approach, compared to other ASE detection methods, is that it is not restricted to genes with allelic transcript variants. Although a false-positive rate of 9/41 was observed, the GASED approach is a valuable pre-screening method that can accelerate systematic surveys of naturally occurring cis-regulatory variation among inbred lines for laboratory species, such as Arabidopsis, mouse, rat and fruitfly, and economically important crop species, such as corn.</div></front></TEI><affiliations><list><country><li>Belgique</li><li>Pays-Bas</li></country></list><tree><noCountry><name sortKey="Kiekens, Raphae L" sort="Kiekens, Raphae L" uniqKey="Kiekens R" first="Raphae L" last="Kiekens">Raphae L Kiekens</name><name sortKey="Kuiper, Martin" sort="Kuiper, Martin" uniqKey="Kuiper M" first="Martin" last="Kuiper">Martin Kuiper</name><name sortKey="Sterken, Roel" sort="Sterken, Roel" uniqKey="Sterken R" first="Roel" last="Sterken">Roel Sterken</name><name sortKey="Van Den Daele, Hilde" sort="Van Den Daele, Hilde" uniqKey="Van Den Daele H" first="Hilde" last="Van Den Daele">Hilde Van Den Daele</name><name sortKey="Vercauteren, Annelies" sort="Vercauteren, Annelies" uniqKey="Vercauteren A" first="Annelies" last="Vercauteren">Annelies Vercauteren</name><name sortKey="Vuylsteke, Marnik" sort="Vuylsteke, Marnik" uniqKey="Vuylsteke M" first="Marnik" last="Vuylsteke">Marnik Vuylsteke</name></noCountry><country name="Belgique"><noRegion><name sortKey="Moerkerke, Beatrijs" sort="Moerkerke, Beatrijs" uniqKey="Moerkerke B" first="Beatrijs" last="Moerkerke">Beatrijs Moerkerke</name></noRegion><name sortKey="Goetghebeur, Els" sort="Goetghebeur, Els" uniqKey="Goetghebeur E" first="Els" last="Goetghebeur">Els Goetghebeur</name></country><country name="Pays-Bas"><noRegion><name sortKey="Van Eeuwijk, Fred" sort="Van Eeuwijk, Fred" uniqKey="Van Eeuwijk F" first="Fred" last="Van Eeuwijk">Fred Van Eeuwijk</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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