Data from: Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice and Arabidopsis and at least 10 examples of conserved imprinting between maize and each of the other species were identified.

基因组印记（Imprinting）指的是等位基因依据其亲本来源而呈现差异表达的现象。本研究对授粉后14天的玉米胚乳与胚胎组织的RNA进行深度测序，在B73与Mo17基因型间存在序列多态性且已表达的约12000个基因集合中，鉴定基因组印记基因。通过分析表达的亲本起源模式，本研究在玉米胚乳中鉴定出100个潜在基因组印记基因，其中包含54个母本表达基因（maternally expressed genes, MEGs）与46个父本表达基因（paternally expressed genes, PEGs）。其中3个基因此前已被证实为印记基因，剩余97个均为全新的玉米基因组印记基因。全基因组DNA甲基化分析显示，在100个印记基因中的19个基因内部或其邻近区域，存在胚乳DNA甲基化水平降低的现象。在所有受检测的样本中，胚乳的DNA甲基化水平降低均由母本等位基因的低甲基化引发，且该现象同时存在于母本表达基因与父本表达基因两类基因中。诸多携带DNA甲基化水平降低特征的印记基因，同时呈现胚乳特异性表达模式。本研究将玉米基因组印记基因与通过全基因组筛选鉴定得到的水稻、拟南芥印记基因进行比对，最终在玉米与各物种间分别鉴定出至少10组保守的基因组印记现象。