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Elife. 2014 Jul 3;3:e03198. doi: 10.7554/eLife.03198.

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

Author information

1
Whitehead Institute for Biomedical Research, Cambridge, United States.
2
Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.
3
Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, United States.

Abstract

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. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

KEYWORDS:

DNA methylation; epialleles; genomic imprinting; natural variation; seeds; transposable elements

PMID:
24994762
PMCID:
PMC4115658
DOI:
10.7554/eLife.03198
[Indexed for MEDLINE]
Free PMC Article

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