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

Genetic imprinting is a specific epigenetic phenomenon in which a subset of genes is expressed depending on their parent-of-origin. Two types of chromatin modifications, DNA methylation and histone modification, are generally believed to be involved in the regulation of imprinting. However, the genome-wide correlation between allele-specific chromatin modifications and imprinted gene expression in maize remains elusive. Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. For DNA methylation, thousands of parent-of-origin dependent differentially methylated regions (pDMRs) were identified. All pDMRs were uniformly paternally hypermethylated and maternally hypomethylated. We also identified 1131 allele-specific H3K27me3 peaks that are preferentially present in the maternal alleles. Maternally expressed imprinted genes (MEGs) and paternally expressed imprinted genes (PEGs) had different patterns of allele-specific DNA methylation and H3K27me3. Allele-specific expression of MEGs was not directly related to allele-specific H3K27me3, and only a subset of MEGs was associated with maternal-specific DNA demethylation, which was primarily located in the upstream and 5′ portion of gene body regions. In contrast, allele-specific expression of a majority of PEGs was related to maternal-specific H3K27me3, with a subgroup of PEGs also associated with maternal-specific DNA demethylation. Both pDMRs and maternal H3K27me3 peaks associated with PEGs are enriched in gene body regions. Our results indicate highly complex patterns of regulation on genetic imprinting in maize endosperm.Genetic imprinting is an epigenetic phenomenon, where genes are expressed in a parent-of-origin dependent manner in many plant species and mammals. Although first discovered in plants (Kermicle and Alleman 1990), research on genetic imprinting is much more advanced in mammals in terms of the number of imprinted genes identified and the understanding of their regulatory mechanisms (Koerner and Barlow 2010; Barlow 2011; Bartolomei and Ferguson-Smith 2011). Only a small number of imprinted genes were observed in plants for a long time since the phenomenon is highly specific to the triploid endosperm (Raissig et al. 2011). However, recent studies have indicated that genetic imprinting in plants is much more prevalent than previously thought, with hundreds of genes shown to be imprinted in several plant species (Gehring et al. 2011; Hsieh et al. 2011; Luo et al. 2011; Waters et al. 2011; Zhang et al. 2011). In contrast to mammals, where the regulation of genetic imprinting has been extensively studied (Koerner and Barlow 2010; Barlow 2011; Abramowitz and Bartolomei 2012), the understanding of regulation of parental imprinting in plants is highly limited.DNA methylation is one of the primary modifications reported to be associated with genetic imprinting. In Arabidopsis, DNA methylation around several maternally expressed imprinted protein-coding genes (MEG) including FWA, FIS2, and MPC was shown to be important for their maternally preferred expression, as all these genes exhibited biallelic expression in endosperm fertilized with met1 pollen (Kinoshita et al. 2004; Jullien et al. 2006; Tiwari et al. 2008). Two studies using RNA-seq in Arabidopsis also showed that a number of MEGs exhibited biallelic expression in paternal met1 endosperm, and the maternal alleles of dozens of paternally expressed imprinted genes (PEGs) were reactivated in maternal dme endosperm (Hsieh et al. 2011; Wolff et al. 2011). In maize, five confirmed endosperm MEGs (Fie1, Fie2, Mez1, Meg1, and Mee1) contain differentially methylated regions (DMRs) (Gutierrez-Marcos et al. 2004; Gutierrez-Marcos et al. 2006; Haun et al. 2007), and activation of the Fie1 maternal allele in the endosperm requires DNA demethylation of the maternal allele (Hermon et al. 2007).Another modification associated with genetic imprinting involves histone methylation. Polycomb repressive complex 2 (PRC2) is known to mediate the trimethylation of histone H3 lysine 27 (H3K27me3) (Schuettengruber and Cavalli 2009). Results on PHE1, the only well-studied PEG in plants, indicated that silencing of its maternal allele depends on a functional PRC2 complex in addition to DNA demethylation (Kohler et al. 2003, 2005; Makarevich et al. 2008). Recently, a number of MEGs and PEGs were shown to be biallelically expressed in maternal fie or fis2 endosperm (Hsieh et al. 2011; Wolff et al. 2011).Although the studies above suggest that DNA methylation and the PRC2 complex could be responsible for monoallelic expression of imprinted genes, there is not yet any general rule for the function of DNA and histone methylation on the regulation of genetic imprinting in plants. 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 (Zhang et al. 2011; 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).Here we report a genome-wide analysis of allele-specific DMRs, H3K27me3, and imprinted gene expression in maize endosperm. Thousands of pDMRs and allele-specific H3K27me3 peaks were identified. Correlation of pDMRs, allele-specific H3K27me3 profile, and the expression of imprinted genes showed that MEGs and PEGs have different patterns of DNA methylation and H3K27me3. This study reveals complex patterns of genetic imprinting regulation in maize endosperm.