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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE52814 | GEO | 2014/07/08

SECONDARY ACCESSION(S): PRJNA230120

REPOSITORIES: GEO

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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-07-08 | E-GEOD-52814 | biostudies-arrayexpress

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.

Project description: Not available

| S-EPMC4115658 | biostudies-literature

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

Project 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.

2014-07-08 | GSE52805 | GEO

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds

2014-07-08 | GSE52807 | GEO

2014-07-08 | E-GEOD-52807 | biostudies-arrayexpress

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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

Project description:Imprinted gene expression occurs during seed development in plants and is closely tied to differential DNA methylation of maternal and paternal alleles, particularly at proximal transposable elements (TEs). Since the epigenetic modification of TEs can vary within species, we investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three strains of Arabidopsis that display diverse seed size phenotypes. Unexpectedly we found that one strain, Cvi, is globally CG hypomethylated. We discovered three examples of strain-specific imprinting caused by epigenetic variation at a TE. Our data allowed us to predict and experimentally validate an instances of allele-specific imprinting in additional strains based only on methylation patterns. We conclude that numerous differences in imprinting can evolve in highly similar, recently diverged genotypes due to epiallelic variation present within the species. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

2014-07-08 | GSE52806 | GEO

2014-07-08 | E-GEOD-52806 | biostudies-arrayexpress

Epigenetic natural variation in Arabidopsis thaliana.

Project description: Not available

| S-EPMC1892575 | biostudies-literature

Selection of epigenetic variation in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-09-01 | GSE36846 | GEO