Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.
Bottom Line: Imprinting variability could contribute to observed parent-of-origin effects on seed development.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.
Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.Show MeSH
Related in: MedlinePlus
Mentions: (A) HDG3 is a PEG except when Cvi is the paternal parent. Blue bars, % paternal allele expression; red bars, % maternal allele expression from combined mRNA-seq data; vertical line, expected percent paternal allele expression for a non-imprinted gene. (B) Methylation of HDG3 5′ flanking region in Col embryo, Ler embryo and endosperm, and Cvi embryo (additional analysis in Figure 6—figure supplement 1). Red track, CG; green track, CHH. (C) Methylation profile of maternal and paternal HDG3 alleles in Col x Cvi and Cvi x Col endosperm as determined by locus-specific bisulfite PCR. Red circles, CG; blue circles, CHG; green circle, CHH. Filled circles indicate methylation, whereas unmethylated positions are unfilled. (D) Methylation profile of HDG3 in Col, Ler, Cvi, Kz_9 and An_1 in leaves (http://neomorph.salk.edu/1001_epigenomes.html). (E) HDG3 is not imprinted in 6 DAP endosperm when another hypomethylated strain (Kz_9) is the pollen parent, but is a PEG in a cross with another methylated strain (An_1), as determined by sequencing RT-PCR products that span informative SNPs. Blue bars, % paternal allele expression; red bars, % maternal allele expression; vertical line, expected paternal allele expression for a non-imprinted gene. The number of RT-PCR clones sequenced is indicated. p value represents a binomial test of whether the observed maternal:total ratio is less than the expected 2:3 ratio. (F) Cartoon representation of results. Expression and methylation results for AT3G14205 and AT2G34890 are in Figure 6—figure supplement 2. Examples of genetic differences causing methylation differences are in Figure 6—figure supplement 3.
Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.