State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China.
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China; Department of Biology, Stanford University, Stanford, CA 94305, USA.
Mol Plant. 2017 Mar 6;10(3):442-455. doi: 10.1016/j.molp.2016.10.007. Epub 2016 Oct 25.
Genomic imprinting is often associated with allele-specific epigenetic modifications. Although many reports suggested potential roles of DNA methylation and H3K27me3 in regulating genomic imprinting, the contributions of allele-specific active histone modifications to imprinting remain still unclear in plants. Here, we report the identification of 337 high-stringency allele-specific H3K4me3 and H3K36me3 peaks in maize endosperm. Paternally preferred H3K4me3 and H3K36me3 peaks mostly co-localized with paternally expressed genes (PEGs), while endosperm-specific maternally expressed genes (endo-MEGs) were associated with maternally preferred H3K4me3 and H3K36me3 peaks. A unique signature for PEGs was observed, where the active H3K4me4 and H3K36me3 as well as repressive H3K27me3 appeared together. At the gene body of con-PEGs (constitutively expressed PEG), H3K27me3 and H3K36me3 were specifically deposited on hypomethylated maternal alleles and hypermethylated paternal alleles, respectively. Around the transcription start sites of endo-MEGs, DNA methylation and H3K4me3 specifically marked paternal and maternal alleles, respectively. In addition, 35 maternally expressed non-coding RNAs exhibited the same allele-specific epigenetic features as endo-MEGs, indicating similar mechanisms for the regulation of imprinted genes and non-coding RNAs. Taken together, our results uncover the complex patterns of mutually exclusive epigenetic modifications deposited at different alleles of imprinted genes that are required for genomic imprinting in maize endosperm.
基因组印迹通常与等位基因特异性的表观遗传修饰有关。尽管许多报道表明 DNA 甲基化和 H3K27me3 在调控基因组印迹中可能发挥作用，但在植物中，等位基因特异性活性组蛋白修饰对印迹的贡献仍不清楚。在这里，我们报告了在玉米胚乳中鉴定出 337 个高严格性等位基因特异性 H3K4me3 和 H3K36me3 峰。父本偏好的 H3K4me3 和 H3K36me3 峰大多与父本表达基因（PEGs）共定位，而胚乳特异性母本表达基因（endo-MEGs）与母本偏好的 H3K4me3 和 H3K36me3 峰相关。观察到 PEGs 的独特特征，其中活性 H3K4me4 和 H3K36me3 以及抑制性 H3K27me3 一起出现。在 con-PEGs（组成型表达的 PEG）的基因体中，H3K27me3 和 H3K36me3 分别特异性地沉积在低甲基化的母本等位基因和高甲基化的父本等位基因上。在 endo-MEGs 的转录起始位点周围，DNA 甲基化和 H3K4me3 分别特异性地标记父本和母本等位基因。此外，35 个母本表达的非编码 RNA 表现出与 endo-MEGs 相同的等位基因特异性表观遗传特征，表明印迹基因和非编码 RNA 的调控存在相似的机制。总之，我们的研究结果揭示了在玉米胚乳中，印迹基因不同等位基因上需要相互排斥的表观遗传修饰的复杂模式，这些修饰是基因组印迹所必需的。
