title: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.
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.
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.
authors.forename: Daniela
authors.initials: D
authors.lastname: Pignatta
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.|Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Erdmann
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.
authors.forename: Elias
authors.initials: E
authors.lastname: Scheer
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.|Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, United States.
authors.forename: Colette L
authors.initials: CL
authors.lastname: Picard
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.
authors.forename: George W
authors.initials: GW
authors.lastname: Bell
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.|Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.|Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, United States.
authors.forename: Mary
authors.initials: M
authors.lastname: Gehring
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D018392:Genomic Imprinting; D005838:Genotype; D010641:Phenotype; D012639:Seeds / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements
keywords: DNA methylation; epialleles; genomic imprinting; natural variation; seeds; transposable elements