Comprehensive identification of parent of origin effects in human and mouse

基因组印记是一种表观遗传机制，它以一种依赖的方式改变基因的表达 关于父母出身的问题。一些估计表明，多达3%的基因显示出印记的证据。然而， 哺乳动物身上印记的真实程度尚不清楚。许多印记基因在人类基因组中起着重要作用 发展，现在有很好的证据表明，印记也有助于常见疾病 如癌症、糖尿病和代谢综合征。因此，印迹的识别对于 对与疾病相关的基因组功能的正确理解。我提出了一个研究计划，利用一个 使用多种互补策略在DNA和RNA水平上识别亲本效应 对人和老鼠的研究。我们的三个具体目标是： I)在113名单亲二体患者队列中进行比较DNA甲基化分析 (UPD)。UPD患者提供了一种独特的系统，允许对来自单个 亲本，代表了一个强大的系统，用于检测差异甲基化区域。这些数据将 提供一张全基因组的基因座图谱，显示人类中父母来源的特定甲基化。 二)利用一种新的全基因组关联研究方法，利用SNP基因型和基因 三元组中的表达数据，以识别印记的调控元件。我们将执行150个RNAseq研究 可获得全基因组SNP数据的HapMap三元组的后代。这些研究将允许基因组- 广泛检测显示亲本来源在基因表达上存在偏见的调控元件。 三)对三个不同的成人和 C57/BL6与卡氏小鼠交配产生的F1杂交小鼠分离的胎儿组织类型。 这些F1杂交种代表了一种体内模型，在该模型中，整个基因组的杂合率很高， 具有确定的亲本来源的每个变体，因此代表了用于检测印记的强大系统。 这些数据将使印记基因表达和差异的全面评估成为可能 多种组织类型的甲基化标记。 这些研究将产生哺乳动物基因组中亲本起源效应的全面图谱， 为未来研究印记在许多人类疾病中的作用提供了坚实的基础。

Genomic imprinting is an epigenetic mechanism that modifies gene expression in a manner that is dependent on parental origin. Some estimates suggest that as many as 3% of genes show evidence of imprinting. however the true extent of imprinting in mammals remains unknown. Many imprinted genes play important roles in development, and there is now good evidence that imprinting also contributes towards the common diseases such as cancer, diabetes and metabolic syndrome. The identification of imprinting is therefore important for the proper understanding of genome function in relation to disease. I propose a research plan that utilizes a variety of complementary strategies to identify parent of origin effects at both the DNA and RNA level using studies of human and mouse. Our three specific aims are: i) Perform comparative DNA methylation profiling in a cohort of 113 patients with uniparental disomy (UPD). Patients with UPD provide a unique system that allows the isolated study of DNA derived from a single parent, representing a powerful system for the detection of differentially methylated regions. These data will provide a genome-wide map of loci that show parent-of origin specific methylation in human. ii) Utilize a novel genome-wide association study approach that utilizes SNP genotype and gene expression data in trios to identify imprinted regulatory elements. We will perform RNAseq studies of 150 offspring from HapMap trios for which genome-wide SNP data are available. These studies will allow genome- wide detection of regulatory elements that show parent of origin biases on gene expression. iii) Perform deep RNA sequencing and whole-genome bisulfite sequencing in three different adult and fetal tissues types isolated from F1 hybrid mice produced by reciprocal C57/Bl6 and Mus castaneus matings. These F1 hybrids represent an in vivo model in which there is a high heterozygosity rate across the genome, with each variant of defined parental origin, therefore representing a powerful system for detecting imprinting. These data will enable the comprehensive assessment of both imprinted gene expression and differential methylation marks in multiple tissue types. These studies will produce a comprehensive map of parent of origin effects in the mammalian genome, providing a strong basis for future studies of the effects of imprinting in many human diseases.