Identification of imprinted genes subject to parent-of-origin specific expression in <it>Arabidopsis thaliana </it>seeds

BMC Plant Biology. 2011;11(1):113 DOI 10.1186/1471-2229-11-113

 

Journal Homepage

Journal Title: BMC Plant Biology

ISSN: 1471-2229 (Online)

Publisher: BMC

LCC Subject Category: Science: Botany

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Wennblom Trevor J
Lao Nga
Comte Aurélie
Duszynska Dorota
Fort Antoine
Donoghue Mark TA
Schmid Marc W
Wolff Philip
Prins Pjotr
Laouielle-Duprat Sylvia
McKeown Peter C
Smant Geert
Köhler Claudia
Grossniklaus Ueli
Spillane Charles

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 19 weeks

 

Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>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 <it>Arabidopsis thaliana</it>. 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.</p> <p>Results</p> <p>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 <it>Arabidopsis thaliana</it>. Expression in seed tissues of the three top-ranked candidate genes, <it>ATCDC48</it>, <it>PDE120 </it>and <it>MS5-like</it>, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in <it>Arabidopsis thaliana </it>F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to <it>ATCDC48 </it>and <it>PDE120</it>, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are <it>MET1</it>-dependent, while their uniparental maternal expression in the seed is not dependent on <it>MET1</it>.</p> <p>Conclusions</p> <p>Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, <it>ATCDC48</it>, <it>PDE120 </it>and <it>MS5-like </it>which represent novel maternally expressed imprinted genes in the <it>Arabidopsis thaliana </it>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.</p>