Genome-wide high resolution parental specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
- Mei Zhang,
- Shaojun Xie,
- Xiaomei Dong,
- Xin Zhao,
- Biao Zeng,
- Jian Chen,
- Hui Li,
- Weilong Yang,
- Hainan Zhao,
- Gaokui Wang,
- Zongliang Chen,
- Silong Sun,
- Andrew Hauck,
- Weiwei Jin and
- Jinsheng Lai1
- ↵* Corresponding author; email: jlai{at}cau.edu.cn
Abstract
Genetic imprinting is a specific epigenetic phenomenon where 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 1,131 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 were associated with maternal specific DNA demethylation, which was primarily located in the upstream and the 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. pDMRs and maternal H3K27me3 peaks associated with PEGs are both enriched in gene body regions. Our results indicate highly complex patterns of regulation on genetic imprinting in maize endosperm.
- Received February 3, 2013.
- Accepted October 8, 2013.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
