Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Extensive imprinted gene expression in Arabidopsis endosperm

ABSTRACT: Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. 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 (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. Epigenetics Examination of genomic imprinting in Arabidopsis endosperm

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Toshiro Nishimura

PROVIDER: E-GEOD-24644 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Regulation of imprinted gene expression in Arabidopsis endosperm.

Hsieh Tzung-Fu TF Shin Juhyun J Uzawa Rie R Silva Pedro P Cohen Stephanie S Bauer Matthew J MJ Hashimoto Meryl M Kirkbride Ryan C RC Harada John J JJ Zilberman Daniel D Fischer Robert L RL

Proceedings of the National Academy of Sciences of the United States of America 20110121 5

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 w ...[more]

PMID: 21257907

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Project description:Seed development is dependent on a well-orchestrated interplay between different transcriptional programs operating in the embryo, the endosperm and the maternally derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, mutation of the cell cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) results in pollen that only successfully fertilizes the egg cell. Seeds generated from crosses with cdka;1 pollen develop endosperm with solely maternal and no paternal contribution. Here we have exploited cdka;1 fertilization as a novel tool for genomic dissection of parental effects during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds. By this approach, we identified 11 differentially expressed AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors. Here, AGL36 was chosen for an in-depth study. We show that AGL36 is imprinted and only expressed from the maternal genome. In addition, we demonstrate that AGL36 imprinting is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2). These findings shed novel light on the interplay between maternal and paternal genomes in the seed and how imprinting is coordinated by different mechanisms. 3 biological replicates, each consisting of 35 siliques from 10 individual plants, were used. Arabidopsis thaliana wild type (ecotype Colombia-0 and Ler-0) and cdka;1 mutant (At3g48750 /SALK_109806) were sown out on soil and grown under the following conditions: 18oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 Î¼mol/m2/sek in light intensity. For each replica, 10 Ler plants were emasculated and pollinated after 48 hours, either with individual WT Col or with individual cdka;1 mutant pollen. Three days after pollination (3 DAP), the siliques of each biological replicate were dissected with hypodermic needles to remove carpel walls, the pistil with pollen attached to it and the pedicel with abcsission zone. The remaining seeds attached to the middle lamella were harvested in bulk in liquid nitrogen at the same time of the day. Biological replicas are dye-swapped between slides.

Dataset Information

Extensive imprinted gene expression in Arabidopsis endosperm

Publications

Regulation of imprinted gene expression in Arabidopsis endosperm.

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