Epigenetic regulation of stem cell fate choice

描述（申请人提供）：基因调控的表观遗传机制在正常发育和疾病发病中起着重要作用。我们的长期目标是了解参与干细胞命运选择的表观遗传机制，以胚胎干细胞（ESCs）发育成造血干细胞（hsc）作为我们的模型。由于造血干细胞可以通过胚胎干细胞（ESCs）的定向分化在体外获得，这一过程对血液系统疾病的细胞治疗具有很大的希望。然而，与产生各种血细胞谱系的造血干细胞分化的后期阶段相比，控制造血干细胞命运规范的表观遗传机制尚不清楚，这阻碍了开发有效的体外造血干细胞衍生方案的努力。我们的初步数据表明，动态和组合染色质修饰对这一过程至关重要。本应用程序旨在通过将湿实验室实验与计算模型相结合，获得对HSC命运的表观遗传调控的系统级理解。具体来说，我们建议了解表观遗传调控的动态和基因网络方面。为此，我们假设染色质修饰的动态组合调节了HSC发育的关键调控因子的表达。首先，我们将绘制esc向hsc过渡的不同阶段的全基因组染色质修饰图谱。其次，使用我们实验室开发的计算工具和染色质状态图，我们将预测和实验验证在发育过程的不同阶段起作用的调控DNA元件。最后，我们将开发一种新的计算工具，用于整合染色质状态图和其他基因组学数据，以揭示控制HSC命运选择的基因途径。我们相信这些系统水平的研究将揭示发育中表观遗传调控的基本原理。此外，HSC表观遗传调控的具体知识将填补HSC命运规范的关键知识空白。

DESCRIPTION (provided by applicant): Epigenetic mechanisms of gene regulation contribute significantly to normal development and disease pathogenesis. Our long-term goal is to understand the epigenetic mechanisms involved in stem cell fate choice, using the development of hematopoietic stem cells (HSCs) from embryonic stem cells (ESCs) as our model. Since HSCs can be derived in vitro by directed differentiation of embryonic stem cells (ESCs), this procedure holds great promise for cell-based therapy of hematological disorders. However, compared to later stages of HSC differentiation that give rise to various blood cell lineages, epigenetic mechanisms controlling HSC fate specification from ESCs are poorly understood, impeding efforts to develop an efficient protocol for in vitro derivation of HSCs. Our preliminary data suggest that dynamic and combinatorial chromatin modifications are critical to this process. This application seeks to obtain a systems-level understanding of epigenetic regulation of HSC fate by coupling wet-lab experiments with computational modeling. Specifically, we propose to understand the dynamic and gene network aspects of epigenetic regulation. To this end, we hypothesize that dynamic combination of chromatin modifications modulates the expression of key regulators of HSC development. First, we will map genome-wide chromatin modifications at different stages of the ESC-to-HSC transition. Second, using computational tools developed in our lab and chromatin state maps, we will predict and experimentally validate regulatory DNA elements acting at different stages of the developmental process. Finally, we will develop a novel computational tool for integrating chromatin state maps with other genomics data to uncover gene pathways controlling HSC fate choice. We believe that these systems-level studies will reveal the basic principles of epigenetic regulation in development. Further, the specific knowledge of epigenetic regulation in HSCs will fill a critical knowledge gap in HSC fate specification.