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，它以依赖的方式修饰基因表达， 关于父母的起源一些估计表明，多达3%的基因显示出印记的证据。然而 哺乳动物体内印记的真实程度仍不清楚。许多印记基因在 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，识别印迹对于 正确理解与疾病相关的基因组功能。我提出了一个研究计划， 各种互补策略，以确定在DNA和RNA水平上的起源亲本效应， 人类和老鼠的研究。我们的三个具体目标是： i）在113名患有单亲二体性的患者的队列中进行比较DNA甲基化谱分析 （民主联盟）。UPD患者提供了一个独特的系统，允许对来自单个细胞的DNA进行分离研究。 亲本，代表用于检测差异甲基化区域的强大系统。这些数据将 提供了显示人类中亲本来源特异性甲基化的基因座的全基因组图谱。 ii）利用新的全基因组关联研究方法，其利用SNP基因型和基因 以鉴定印迹调控元件。我们将对150名患者进行RNAseq研究， 来自HapMap trios的后代，其全基因组SNP数据可用。这些研究将使基因组- 广泛检测显示基因表达上的亲本来源偏差的调节元件。 iii）在三个不同的成人和哺乳动物中进行深度RNA测序和全基因组亚硫酸氢盐测序， 从C57/B16和Mus castaneus相互交配产生的F1杂交小鼠中分离的胎儿组织类型。 这些F1杂种代表了一种体内模型，其中在整个基因组中存在高杂合性率， 每个变体都具有确定的亲本来源，因此代表了检测印记的强大系统。 这些数据将使印迹基因表达和差异表达的全面评估成为可能。 在多种组织类型中的甲基化标记。 这些研究将产生一个哺乳动物基因组中亲本起源效应的综合图谱， 为今后研究印记在许多人类疾病中的作用提供了强有力的基础。

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.