Systems Biology Analysis of Human Erythropoiesis

描述(申请人提供)：红细胞生成是脊椎动物的一个基本过程，长期以来一直被用作发育调节的分子研究的范例。少数转录因子也被称为主调节因子，在维持细胞特性和/或调节细胞分化过程中发挥着重要作用。然而，它们如何相互结合或与各种辅助因素一起发挥作用，特别是在不同的发育阶段，目前还没有完全阐明。由于哺乳动物中至少有一千种转录调控因子，因此可能的组合数量是天文数字。仅用实验方法来剖析这种复杂性仍然是一项艰巨的任务，因为它需要高得令人望而却步的成本和劳动力。为了克服这一挑战，我们提出了一种由经验丰富的实验和计算生物学家组成的团队实施的系统生物学方法。以人类原代红系前体细胞为模型系统，我们将通过基因组、表观基因组和转录图谱产生大量的实验数据，开发数据整合和预测计算方法，并通过扰乱正常的调节活动来扰乱系统。我们的初步工作已经确定了成人和胎儿红系前体之间重要的调控网络差异，并表明主调控因子和辅助因子之间的合作在通过作用于增强子元件来驱动发育阶段特异性转录变化方面发挥重要作用。我们将把重点放在下列特定目标上：(1)通过整合基因组和表观基因组数据类型来预测和验证人类初级红系前体细胞中发育阶段特异的基因调控网络；(2)利用分子和遗传学实验扰乱基因调控网络，并进一步整合这些信息以完善我们的网络模型；(3)表征影响染色质状态、基因表达和红系特征的遗传变量所扮演的角色。最终，我们的结果将极大地扩展我们目前在建立细胞类型和发育阶段特异性方面对组合控制的机制理解，并为红系特征相关遗传变异提供功能洞察力。

DESCRIPTION (provided by applicant): Erythropoiesis is a fundamental process in vertebrate animals and has long served as a paradigm for molecular investigations of developmental regulation. It has been well established that a small number of transcription factors, also known as master regulators, play an essential role in the maintenance of cell-identity and/or regulate the cell differentiation process. However, it is not fully elucidated how they work in combination with each other or various cofactors, particularly at different developmental stages. Since there are at least a thousand transcriptional regulators in mammals, the number of possible combinations is astronomical. Using experimental methods alone to dissect such complexity remains a daunting task as it demands prohibitively high cost and labor. To overcome this challenge, we propose a systems biology approach to be carried out by a team of experienced experimental and computational biologists. Using human primary erythroid precursor cells as the model system, we will generate extensive experimental data by genomic, epigenomic, and transcriptomic profiling, develop data-integrative and predictive computational methods, and perturb the systems by disrupting the normal regulatory activities. Our preliminary work has identified important regulatory network differences between adult and fetal erythroid precursors and suggested that collaboration between master regulators and cofactors plays an important role in driving developmental stage-specific transcriptional changes through acting upon enhancer elements. This will be extended by focusing on the following specific aims: (1) Predict and validate the developmental stage-specific gene regulatory networks in human primary erythroid precursors by integrating genomic and epigenomic data-types; (2) Perturb the gene regulatory networks using molecular and genetic experiments and further integrate such information to refine our network model; (3) Characterize the role of genetic variants influencing chromatin state, gene expression, and erythroid traits. In the end our results will greatly expand our current mechanistic understanding of combinatorial control in establishing cell-type and developmental stage-specificity and provide functional insights into erythroid trait- associated genetic variants.