Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-52805 - Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: BS-seq of Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

Status
Released on 8 July 2014, last updated on 6 August 2014
Organism
Arabidopsis thaliana
Samples (14)
Protocols (3)
Description
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Whole genome bisulfite sequencing of embryo and endosperm (14 samples).
Experiment type
methylation profiling by high throughput sequencing 
Contacts
Daniela Pignatta, George W Bell, Mary Gehring
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-52805.idf.txt
Sample and data relationshipE-GEOD-52805.sdrf.txt
Processed data (2)E-GEOD-52805.processed.1.zip, E-GEOD-52805.processed.2.zip
Links