Inter-individual epigenetic variation in hematopoietic progenitor cells

描述（由申请人提供）：人类的特征和疾病受到遗传和非遗传因素的严重影响。不是直接改变个体的遗传蓝图，而是非遗传或“表观遗传”因素改变细胞读取和解释这一蓝图的方式。虽然细胞的表观遗传景观通常由发育程序精确控制，但个体之间的差异可能来自环境和随机影响，如营养状况（Barker 1989）。这些外部影响利用广泛的非遗传细胞机制来留下它们的表观遗传标记，包括：DNA甲基化（Busslinger 1983）；转录因子网络改变（Iliopoulos 2009）；和组蛋白修饰（Jenuwein 2001）。总的来说，这些可变的表观遗传标记形成了影响未来细胞行为的表观遗传记忆（Feinberg 2010）。组织的表观遗传景观受个体特异性表观遗传记忆事件影响的程度尚不清楚。因此，本提案旨在确定个体之间表观遗传变异的原因和后果，目标是确定表观遗传记忆的位点。我们将特别关注初级人类造血祖细胞的表观遗传变异，因为它们在形成多种组织类型和疾病中的核心作用，以及已经存在的用于在体外分离和分化它们的丰富工具。利用高通量技术表征11个人类初级造血祖细胞样本的活性染色质景观，我们已经确定3-5%的活性染色质位点在个体之间表现出显著的可变性。根据这一建议，我们将确定其中哪些地点；(1)是由表观遗传记忆事件引起的，而不是遗传变异；(2)由电池稳定维持；(3)引起邻近基因调控的改变。该提案将利用许多已建立的和新颖的基因组和蛋白质组学技术，包括靶向捕获重测序，高通量dna -seq和靶向蛋白质组学。总的来说，这项研究将提供一个全面的图景表观遗传记忆及其对转录调控的影响。此外，该研究将为临床医生和研究人员提供基线，以便使用全基因组活性染色质数据来阐明病理或生理过程。

DESCRIPTION (provided by applicant): Human traits and diseases are heavily influenced by genetic and non-genetic factors. Rather than directly altering an individual's genetic blueprint, non-genetic or "epigenetic" factors change how cells read and interpret this blueprint. While the epigenetic landscape of a cell is typically precisely controlled by developmental programs, variability between individuals can result from environmental and stochastic influences such as nutritional status (Barker 1989). These external influences utilize a wide array of non- genetic cellular mechanisms to leave their epigenetic marks, including: DNA methylation (Busslinger 1983); altered transcription factor networks (Iliopoulos 2009); and histone modifications (Jenuwein 2001). Collectively, these variable epigenetic marks form an epigenetic memory that influences future cellular behavior (Feinberg 2010). The extent to which the epigenetic landscape of a tissue is influenced by individual-specific epigenetic memory events is unknown. Consequently, this proposal aims to identify the causes and consequences of epigenetic variation between individuals with the goal of identifying sites of epigenetic memory. We will specifically focus on epigenetic variation in primary human hematopoietic progenitor cells due to their central role in forming a diverse array of tissue types and diseases and the wealth of tools that already exist for isolating them and differentiating them in vitro. Using high-throughput technologies to characterize the active chromatin landscape of 11 human primary hematopoietic progenitor cell samples we have already established that 3-5% of all active chromatin sites show a significant amount of variability between individuals. With this proposal we will identify which of these sites; (1) are caused by epigenetic memory events, as opposed to genetic variation; (2) are stably maintained by the cell; and (3) cause changes in the regulation of neighboring genes. This proposal will utilize a number of established and novel genomic and proteomic technologies including targeted capture resequencing, high-throughput DNaseI-seq and targeted proteomics. Overall, this research will provide a comprehensive picture of epigenetic memory and its effects on transcriptional regulation. Additionally, this study will provide a baseline for clinicians and researchers intending to use genome-wide active chromatin data to elucidate pathological or physiological processes. PUBLIC HEALTH RELEVANCE: This proposal aims to expand our knowledge of how the epigenetic landscape of human blood cells varies between individuals and is expected to yield fundamental insights into the nature and prevalence of inter-individual epigenetic variation in human blood cells. The specific focus of the proposal will be on hematopoietic progenitor cells, which are of major therapeutic and biological importance. The project combines multiple cutting-edge technologies including genome-scale mapping of chromatin remodeling, targeted analysis of genetic variation and DNA methylation by massively parallel sequencing, and targeted quantitative proteomics.