Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds
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- 作者：Peter C McKeown (1)
Sylvia Laouielle-Duprat (1)
Pjotr Prins (2)
Philip Wolff (3) (4)
Marc W Schmid (5)
Mark TA Donoghue (1)
Antoine Fort (1)
Dorota Duszynska (1)
Aurélie Comte (1)
Nga Thi Lao (1)
Trevor J Wennblom (6)
Geert Smant (2)
Claudia K?hler (3) (4)
Ueli Grossniklaus (5)
Charles Spillane (1) - 刊名：BMC Plant Biology
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：11
- 期：1
- 全文大小：1183KB
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72. Raissig M, Baroux C, Grossniklaus U: Regulation and flexibility of genomic imprinting during seed development. / Plant Cell 2011, in press. - 作者单位：Peter C McKeown (1)
Sylvia Laouielle-Duprat (1)
Pjotr Prins (2)
Philip Wolff (3) (4)
Marc W Schmid (5)
Mark TA Donoghue (1)
Antoine Fort (1)
Dorota Duszynska (1)
Aurélie Comte (1)
Nga Thi Lao (1)
Trevor J Wennblom (6)
Geert Smant (2)
Claudia K?hler (3) (4)
Ueli Grossniklaus (5)
Charles Spillane (1)
1. Genetics and Biotechnology Lab, Botany and Plant Science, National University of Ireland Galway (NUIG), C306 Aras de Brun, University Road, Galway, Ireland
2. Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands
3. Department of Biology and Zürich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092, Zürich, Switzerland
4. Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE, 75007, Uppsala, Sweden
5. Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
6. Silicon Life Sciences, Minneapolis, MN, USA
文摘
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.