Cellular Systems Genetic Approaches to Understanding Regulatory Variation

项目摘要/摘要 我的实验室的首要目标是确定自然遗传变异如何影响 染色质生物学，以及最终的表型多样性。大多数与疾病相关的变异在 人类的研究发生在调节元件而不是基因的编码区，突出了 了解调节变异在正常健康和疾病中的作用的重要性。基因转录是 受顺式作用的调控元件和约束它们的反式作用因子之间的相互作用所控制。 调控元件内的变异可以通过破坏DNA结合位点来影响局部功能 在该位置被反式作用因子靶向，而反式作用因子的序列或表达的变化 因子可导致许多调控元件远端的功能变异。确定了监管要素 由各种染色质编写者催化的表观遗传特征。虽然我们有大量关于 写入和擦除表观遗传修饰的酶，对其反式作用机制知之甚少 规范这些修改的位置和程度，这仍然是该领域的一个决定性挑战。至 推动这一领域向前发展，我们已经开发出一种新的细胞系统遗传学方法，它将 统计遗传学中的定量实验技术和计算方法 全面了解监管差异并发现广泛适用的控制机制 表观遗传景观。我们将利用一组独特的小鼠身上固有的自然遗传变异 胚胎干细胞将使我们能够利用遗传多样性来识别关键的染色质调节因子，定义 它们在多种表型上的分子功能，并描绘了在 发育时间。这个哺乳动物基因参考小组将极大地提高统计能力，以有效地 绘制与人类直接相关的功能基因座，而细胞平台将使其能够识别其 相关基因和控制机制。利用这个系统，我们已经发现了多个基因组 远端控制数百个调控元件并改变基因表达的位置。我们下一步的目标 五年的时间将回答以下问题：反式转录的分子和机制是什么 染色质景观的调控？遗传变异如何影响染色质的结构和功能？ 染色质景观的早期建立对发展有何影响？这个项目的成功将会 描绘了调控元素、控制它们的系统和表观遗传学之间的相互作用 定义了它们的风景。这些努力预计将在我们的基础上产生广泛影响 了解染色质和表观遗传调控在早期发育以及我们的能力 直接根据遗传背景定制体外细胞分化，最终影响发育生物学， 再生生物学和个性化医学。

PROJECT SUMMARY/ABSTRACT The overarching goal of my laboratory is to determine how natural genetic variation influences chromatin biology, and, ultimately, phenotypic diversity. Most disease-associated variants identified in human studies occur in regulatory elements rather than in the coding region of genes, highlighting the importance of understanding the role of regulatory variation in normal health and disease. Gene transcription is controlled by the interplay between cis-acting regulatory elements and the trans-acting factors that bind them. Variation within a regulatory element can influence function locally through disruption of a DNA-binding site targeted by a trans-acting factor at that site, whereas variation in sequence or expression of a trans-acting factor can result in functional variation distally at many regulatory elements. Regulatory elements are identified by epigenetic features catalyzed by a variety of chromatin writers. While we have substantial information on the enzymes that write and erase epigenetic modifications, less is known about the trans-acting mechanisms that regulate the locations and levels of these modifications, remaining a defining challenge within the field. To move the field forward, we have developed a novel cellular systems genetics approach that integrates quantitative experimental techniques and computational methods in statistical genetics to create a comprehensive understanding of regulatory variation and uncover broadly applicable mechanisms that control the epigenetic landscape. We will utilize the natural genetic variation intrinsic in a unique panel of mouse embryonic stem cells that will enable us to harness genetic diversity to identify key chromatin regulators, define their molecular functionality across multiple phenotypes, and delineate changes in regulatory variation over developmental time. This mammalian genetic reference panel will greatly improve statistical power to efficiently map functional loci directly relatable to humans, whereas a cellular platform will enable the identification of their associated genes and mechanisms of control. Using this system we have discovered multiple genomic locations that distally control hundreds of regulatory elements and alter gene expression. Our goals in the next five years are to answer the following questions: What are the molecules and mechanisms underlying trans regulation of the chromatin landscape? How does genetic variation influence chromatin structure and function? How does the early establishment of the chromatin landscape impact development? Success of this project will delineate the interplay between regulatory elements, the systems that control them, and the epigenetic landscape that defines them. These efforts are expected to have broad implications in both our basic understanding of chromatin and epigenetic regulation during early development as well as on our ability to directly tailor in vitro cellular differentiation to genetic background, ultimately impacting developmental biology, regenerative biology and personalized medicine.