Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus

• Published in: Nature plants Vol. 2; no. 10; p. 16145
• Main Authors: Klosinska, Maja, Picard, Colette L., Gehring, Mary
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.09.2016; Nature Publishing Group
• Subjects: 38; 38/23; 38/39; 38/90; 38/91; 631/208/176/1968; 631/208/176/1988; 631/208/177; 631/449/2491; Alleles; Arabidopsis - genetics; Arabidopsis lyrata; Biomedical and Life Sciences; Deoxyribonucleic acid; DNA; DNA Methylation; Endosperm; Epigenesis, Genetic; Epigenetics; Evolution, Molecular; Evolutionary conservation; Gene expression; Gene Expression Regulation, Plant; Gene silencing; Genes; Genomes; Genomic Imprinting; Inbreeding; letter; Life Sciences; Plant Sciences; Self-fertilization; Species
• ISSN: 2055-0278; 2055-0278
• DOI: 10.1038/nplants.2016.145

In plants, imprinted gene expression occurs in endosperm seed tissue and is sometimes associated with differential DNA methylation between maternal and paternal alleles 1 . Imprinting is theorized to have been selected for because of conflict between parental genomes in offspring 2 , but most studies of imprinting have been conducted in Arabidopsis thaliana , an inbred primarily self-fertilizing species that should have limited parental conflict. We examined embryo and endosperm allele-specific expression and DNA methylation genome-wide in the wild outcrossing species Arabidopsis lyrata . Here we show that the majority of A. lyrata imprinted genes also exhibit parentally biased expression in A. thaliana , suggesting that there is evolutionary conservation in gene imprinting. Surprisingly, we discovered substantial interspecies differences in methylation features associated with paternally expressed imprinted genes (PEGs). Unlike in A. thaliana , the maternal allele of many A. lyrata PEGs was hypermethylated in the CHG context. Increased maternal allele CHG methylation was associated with increased expression bias in favour of the paternal allele. We propose that CHG methylation maintains or reinforces repression of maternal alleles of PEGs. These data suggest that the genes subject to imprinting are largely conserved, but there is flexibility in the epigenetic mechanisms employed between closely related species to maintain monoallelic expression. This supports the idea that imprinting of specific genes is a functional phenomenon, and not simply a byproduct of seed epigenomic reprogramming. By examining imprinted gene expression and methylomes in Arabidopsis lyrata and A. thaliana , a study found that while imprinted genes are largely conserved between the species, different epigenetic mechanisms were employed to maintain the imprinted gene expression.