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. 2011 Feb 1;108(5):1755-62.
doi: 10.1073/pnas.1019273108. Epub 2011 Jan 21.

Regulation of Imprinted Gene Expression in Arabidopsis Endosperm

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Free PMC article

Regulation of Imprinted Gene Expression in Arabidopsis Endosperm

Tzung-Fu Hsieh et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Drawing of an A. thaliana seed with a linear cotyledon stage embryo showing the major seed compartments.
Fig. 2.
Fig. 2.
Maternally expressed imprinted genes. (A) RT-PCR sequencing chromatographs at selected SNP regions measuring allele-specific expression in reciprocal crosses between Ler and Col ecotypes and in female Ler crossed to male met1-6 Col-gl. (B) CG methylation profiles in WT embryo, endosperm, aerial tissues, and dme endosperm for genes shown in A are displayed. Genes and transposable elements oriented 5′ to 3′ and 3′ to 5′ are shown above and below the line, respectively. Gene models indicated in yellow represent the imprinted genes as shown in A. Arrows indicate the 5′ end of imprinted genes where CG demethylation is seen in WT endosperm.
Fig. 3.
Fig. 3.
Paternally expressed imprinted genes. (A) RT-PCR sequencing chromatographs at selected SNP regions measuring allele-specific expression in reciprocal crosses between Ler and Col ecotypes, in female fie Ler crossed to male Col for all genes, and in female Ler crossed to male met1-6 Col-gl. (B) CG methylation profiles of genes shown in A and PHE1 are displayed. Genes and transposable elements oriented 5′ to 3′ and 3′ to 5′ are shown above and below the line, respectively. Gene models indicated in yellow color represent the imprinted genes shown in A. Arrows indicate 5′ and 3′ ends of imprinted genes where CG demethylation is detected in WT endosperm. (C) Expression analysis by semiquantitative RT-PCR in WT reciprocal crosses between Ler and Col ecotypes and in female WT Ler crossed to male met1-6 Col-gl. (D) Allele-specific expression of At1g48910 (YUC10) and At1g57800 (VIM5). RT-PCR analysis using F1 endosperm RNA isolated from Col females crossed to Ler males, Ler females crossed to Col males, and Ler females crossed to Col-gl met1-6 males. For YUC10 RT-PCR products, HpaII enzyme cuts the Ler allele into a 212- and 77-bp band, whereas the Col allele is cut into 212-, 53-, and 24-bp bands. For VIM5 RT-PCR products, enzyme BsmI cuts the Col allele but not the Ler allele.

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