Regulation of Parent-of-Origin Allelic Expression in Arabidopsis thaliana endosperm

Abstract

Genomic imprinting is an epigenetic phenomenon set in the gametes prior to fertilization that causes differential expression of parental alleles mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. In order to achieve high resolution sequencing data we have used sequence capture technology to investigate imprinting. Here, we present a bioinformatics pipeline to assay parent-of-origin allele specific expression and report more than 300 loci with parental expression bias. We find that the level of expression from maternal and paternal alleles in most cases is not binary, instead favouring a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We establish the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of the majority of genes were not affected by these mechanisms. To this end we also demonstrate that the RNA-directed DNA methylation pathway alone does not influence imprinting patterns in a substantial manner, suggesting more complex epigenetic regulation pathways for the majority of identified imprinted genes.\n\nAuthor summaryExpression of gene copies only from the mother or the fathers genome, also termed imprinting, is a specialized epigenetic phenomenon that is found to be enriched at some genes expressed in the mammalian placenta and in the endosperm of the plant seed. Although several studies have reported on imprinted genes in plants, the identified loci are at large non-overlapping between reports. This motivated us to investigate in detail the expression pattern of imprinted genes in the endosperm and to determine how imprinting patterns are established at various imprinted loci. Although several underlying epigenetic regulation mechanisms have been demonstrated to establish imprinting patterns at certain genes, the majority of imprinted genes have not been linked to such mechanisms. In the present study we systematically investigated the mechanisms that are involved in establishing imprinting, by employing mutants of epigenetic regulators and high-throughput sequencing. In our high resolution study, we report more than 300 imprinted genes and demonstrate that the biological phenomenon imprinting involves gradual expression of parental gene copies rather than switching gene copies on or off. Notably, for the majority of imprinted genes, the mechanisms previously believed to be major to establish their imprinting patterns, are not responsible for mediating imprinting.