Identification of novel imprinted genes in a genome-wide screen for maternal methylation
Identification of novel imprinted genes in a genome-wide screen for maternal methylation
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DOI：
10.1101/gr.781503
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发表时间：
2003-04-01
期刊：
影响因子：
7
通讯作者：
Kelsey, G
中科院分区：
文献类型：
--
作者：
Smith, RJ;Dean, W;Kelsey, G
印记基因的一个特征是母亲和父亲的等位基因在甲基化方面表现出差异。为了对新的印记基因座进行全基因组筛选，我们将甲基化敏感的代表性差异分析(Me-RDA)应用于孤雌生殖小鼠胚胎，以识别母体等位基因上特异甲基化的差异甲基化区域(DMRS)。我们从已知和新的DMR中分离了26个不同的克隆，并鉴定了三个新的印记基因。Nap115位于近端6号染色体上，编码一种与核小体组装蛋白(NAP)同源的蛋白质；它具有组织特异性印记，表达来自父亲的等位基因。我们在15号染色体上发现了两个DMR，这是一条被认为不包含印记基因的染色体，并证明了每个DMR都与父系表达的转录本相关。Peg13产生一种非编码的RNA，它在大脑中高度表达，并在所有被检查的组织中印迹。在15号染色体SLc38a4基因上也发现了DMR，该基因编码A系统氨基酸转运蛋白；我们发现SLc38a4是以组织特异性的方式印记的。有趣的是，在这张屏幕上发现的三个新基因中，有两个位于其他基因的内含子内；它们的鉴定表明，这种“微印记”结构域可能比之前认为的更常见。
A characteristic of imprinted genes is that the maternal and paternal alleles show differences in methylation. To perform a genome-wide screen for novel imprinted loci, we applied methylation-sensitive representational difference analysis (Me-RDA) to parthenogenetic mouse embryos, to identify differentially methylated regions (DMRs) methylated specifically on the maternal allele. We isolated a total of 26 distinct clones from known and novel DMRs and identified three novel imprinted genes. Nap115 is located on proximal chromosome 6 and encodes a protein with homology with nucleosome assembly proteins (NAPS); it has tissue-specific imprinting with expression from the paternal allele. We identified two DMRs on chromosome 15, a chromosome that was not thought to contain imprinted loci, and demonstrated that each is associated with a paternally expressed transcript. Peg13 gives rise to a noncoding RNA that is highly expressed in the brain and imprinted in all tissues examined. A DMR was also identified at the chromosome 15 Slc38a4 gene, which encodes a system A amino acid transporter; we show that Slc38a4 is imprinted in a tissue-specific manner. Interestingly, two of the three novel genes identified in this screen are located within the introns of other genes; their identification indicates that such "microimprinted" domains may be more common than previously thought.