title: Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize.
abstract: 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.
authors.affiliation: State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Mei
authors.initials: M
authors.lastname: Zhang
authors.forename: Shaojun
authors.initials: S
authors.lastname: Xie
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Dong
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.forename: Biao
authors.initials: B
authors.lastname: Zeng
authors.forename: Jian
authors.initials: J
authors.lastname: Chen
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Weilong
authors.initials: W
authors.lastname: Yang
authors.forename: Hainan
authors.initials: H
authors.lastname: Zhao
authors.forename: Gaokui
authors.initials: G
authors.lastname: Wang
authors.forename: Zongliang
authors.initials: Z
authors.lastname: Chen
authors.forename: Silong
authors.initials: S
authors.lastname: Sun
authors.forename: Andrew
authors.initials: A
authors.lastname: Hauck
authors.forename: Weiwei
authors.initials: W
authors.lastname: Jin
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Lai
mesh_terms: D000483:Alleles; D018744:DNA, Plant / Q000235:genetics*; D056625:Endosperm / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D018392:Genomic Imprinting; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D008745:Methylation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D006657:Histones; D010940:Plant Proteins