Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

Abstract

Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin-specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants.D NA methylation is a covalent modification of cytosine observed across the tree of life (1). In plants, methylation is mediated by distinct enzymatic systems in the CG, CHG, and CHH contexts (where H is A, C, or T), and regulates gene expression and transposon repression (2). The establishment of plant DNA methylation in all sequence contexts and the maintenance of CHH methylation is mediated by a specialized branch of the RNA interference pathway that generates nuclear-targeted 24-nt small RNA (sRNA) molecules (3, 4). Plants also possess DEMETER (DME) family DNA glycosylases that actively demethylate DNA by excising 5-methylcytosine in all sequence contexts (5, 6), with a preference for relatively euchromatic transposable elements (TEs) (7).Homologs of DME are expressed in various tissues of the model dicot Arabidopsis thaliana throughout development (8), but DME expression is most prominent in the so-called gamete companion cells: the central and vegetative cells (9, 10). The vegetative cell forms the pollen tube that delivers two sperm cells, one of which fuses with the haploid egg cell to form the embryo, whereas the other fuses with the adjacent diploid centra...

DNA demethylation is initiated in the central cells of Arabidopsis and rice

“…As in Arabidopsis (Fig. 3 A and B), analysis of the loci that show demethylation of maternal chromosomes in the endosperm (12) demonstrates that almost all of these are hypomethylated in the central cell (red trace in Fig. 5A).…”

“…In the vegetative cell, DME catalyzes demethylation of thousands of discrete loci, most of which are relatively euchromatic TEs (10,11). The maternal endosperm chromosomes inherited from the central cell are also extensively demethylated at similar sequences in Arabidopsis (10) as well as in the distantly related monocots rice (12) and maize (13). As in the vegetative cell, demethylation of maternal endosperm chromosomes requires DME in Arabidopsis (10), and loss of DME function disrupts endosperm gene expression, gene imprinting, and causes seeds to abort (8,14).…”

“…As in the vegetative cell, demethylation of maternal endosperm chromosomes requires DME in Arabidopsis (10), and loss of DME function disrupts endosperm gene expression, gene imprinting, and causes seeds to abort (8,14). Several lines of evidence strongly argue that the demethylation observed in the endosperm is inherited from the central cell: Only the central cell-derived chromosomes are demethylated (10,12,13), DME is rapidly down-regulated following sperm fusion (8), and genes activated by demethylation are expressed in the central cell (15,16). Down-regulation of MET1 in the central cell has also been proposed to contribute to demethylation (2,17).…”

Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize

“…A high resolution genome-wide map of allele-specific DNA methylation and allele-specific histone modification will be crucial to gain better understanding of the regulation of genetic imprinting. Recently, several genome-wide studies have provided evidence that allele-specific patterns of DNA methylation or parent-of-origin dependent differentially methylated regions (pDMRs) are associated with some imprinted genes in mice and plants Ibarra et al 2012;Xie et al 2012;Rodrigues et al 2013). Several studies in mammals also suggest a mutually exclusive relationship between allele-specific DNA methylation and histone modification or among different histone modifications (Xin et al 2001;Fournier et al 2002;Carr et al 2007;Lindroth et al 2008;Singh et al 2010;Hon et al 2012).…”

DNA sequence properties that predict susceptibility to epiallelic switching

“…Although in rice the influence of gene body methylation on transcription seems to be significant (Rodrigues et al, 2013), in Arabidopsis changes in body methylation of genes do not significantly alter their transcriptional activities (Saze & Kakutani, 2011). Nevertheless, it is intriguing that body methylated genes are able to form and transgenerationally maintain two alternative epiallelic states.…”