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Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

ARAN - Access to Research at NUI Galway

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dc.contributor.author McKeown, Peter C.
dc.contributor.author Laouielle-Duprat, Sylvia
dc.contributor.author Donoghue, Mark T.A.
dc.contributor.author Fort, Antoine
dc.contributor.author Duszynska, Dorota
dc.contributor.author Aurélie, Comte
dc.contributor.author Lao, Nga T.
dc.contributor.author Spillane, Charles
dc.date.accessioned 2012-05-03T11:14:26Z
dc.date.available 2012-05-03T11:14:26Z
dc.date.issued 2011
dc.identifier.citation McKeown, PC,Laouielle-Duprat, S,Prins, P,Wolff, P,Schmid, MW,Donoghue, MTA,Fort, A,Duszynska, D,Comte, A,Lao, NT,Wennblom, TJ,Smant, G,Kohler, C,Grossniklaus, U,Spillane, C (2011) 'Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds'. Bmc Plant Biology, 11 . en_US
dc.identifier.uri http://hdl.handle.net/10379/2714
dc.description.abstract Background: Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants.Results: cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to ATCDC48 and PDE120, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are MET1-dependent, while their uniparental maternal expression in the seed is not dependent on MET1.Conclusions: Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, ATCDC48, PDE120 and MS5-like which represent novel maternally expressed imprinted genes in the Arabidopsis thaliana seed. The extent of overlap between our cDNA-AFLP screen for maternally expressed imprinted genes, and other screens for imprinted and endosperm-expressed genes is discussed. en_US
dc.description.sponsorship Irish Department of Agriculture, Fisheries and Food (grant RSF 07-534) and Science Foundation Ireland (SFI) en_US
dc.format application/pdf en_US
dc.language.iso en en_US
dc.relation.ispartof Bmc Plant Biology en
dc.subject DNA METHYLATION en_US
dc.subject TRANSCRIPTOME ANALYSIS en_US
dc.subject MAIZE ENDOSPERM en_US
dc.subject LIFE-CYCLE en_US
dc.subject CELL-CYCLE en_US
dc.subject CDNA-AFLP en_US
dc.subject IN-VIVO en_US
dc.subject PROTEIN en_US
dc.subject GENOME en_US
dc.subject MEDEA en_US
dc.title Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds en_US
dc.type Article en_US
dc.date.updated 2012-05-02T11:32:53Z
dc.local.publishedsource http://www.biomedcentral.com/1471-2229/11/113 en_US
dc.description.peer-reviewed peer-reviewed
dc.contributor.funder |~|SFI|~|
dc.internal.rssid 1051563
dc.local.contact Charles Spillane, Botany, School Of Natural Sciences, Nui Galway. Email: charles.spillane@nuigalway.ie
dc.local.copyrightchecked Yes
dc.local.version ACCEPTED

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