Transcriptomics

Dataset Information

417

Transcription profiling by high throughput sequencing of Arabidopsis polymorphic F1 seeds to identify imprented genes


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: Daniel Zilberman   John J Harad  Juhyun Shin  Tzung-Fu Hsieh  Matthew J Bauer  Pedro Silva  Stephanie Cohen  Toshiro Nishimura  Rie Uzawa  Robert L Fischer  Meryl Hashimoto 

PROVIDER: E-GEOD-24644 | ArrayExpress | 2011-03-10

SECONDARY ACCESSION(S): SRP003799GSE24644PRJNA132535

REPOSITORIES: GEO, ArrayExpress, ENA

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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]

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