Principals of Chromatin Organization

项目摘要 基因表达是由转录因子控制的，这些转录因子通常与染色质结合， 距离这种基因表达的远程控制是通过染色质相互作用来完成的，这是基因表达调控的一部分。 基因组的3D组织。染色质相互作用的全基因组研究（Hi-C）已经确定了几个 染色质组织的模式，包括区室，拓扑相关结构域（TADs），和高 强度点对点循环。导致这些结构形成的基本原理不是 明白例如，人类细胞形成与CTCF相关的高强度环， 取决于其主题的方向。提出了一个环形挤压模型来解释这种特征， 哺乳动物CTCF基序取向，但这种现象背后的机制原理是未知的。我发现 在果蝇中，CTCF不形成高强度环，并且基序方向与 任何交互偏好。相反，非CTCF环出现在早期发展，但在后期消失， 出现隔室和TAD的阶段。In C. elegans，完全缺乏CTCF，高强度 环对应于剂量补偿复合物募集位点。我在分析C. elegans的数据表明，这些环的网络跨越X染色体。这个项目的一个主要目标 是发现环路形成的基本原理。本项目的目标1将A）利用差异 为了确定人类CTCF环是如何形成的，B）探索了人类CTCF环与果蝇CTCF环之间的关系。 在整个开发过程中，循环与TAD和隔室的关系，以及C）测试循环是否 创造一个相互作用的网络，有助于整个X染色体结构和基因表达 控制在C.优雅我以前的工作表明转录在隔室中起着重要的作用 以及蛋白质的形成，这是一个可能被建筑蛋白质的突出作用所掩盖的特征， 比如CTCF本项目的aim 2将证实转录延伸在染色质组织中的作用， 将破译的建筑蛋白质和转录活性的个别作用，在区室和细胞内， 阵这些发现将有助于改进一种可以模拟染色质的初步算法 高分辨率的组织，使研究人员能够预测突变或染色质的影响 晶体结构的畸变。这些目标范围内的实验将在2000年的K99阶段开始。 将包括关于遗传方法的培训以及与 果蝇和C.优雅这次培训将为我提供必要的工具和指导， 在R 00阶段成功过渡到独立研究。

Project Summary Gene expression is controlled by transcription factors that are often bound to chromatin hundreds of kilobases away. This long-range control of gene expression is accomplished through chromatin interactions as part of the 3D organization of the genome. Genome-wide studies of chromatin interactions (Hi-C) have identified several patterns of chromatin organization including compartments, topologically associated domains (TADs), and high intensity point-to-point loops. Fundamental principles causing the formation of these structures are not understood. For example, human cells form high intensity loops that are associated with CTCF and are dependent on its motif’s orientation. A loop extrusion model has been proposed to explain this feature of mammalian CTCF motif orientation, but the mechanistic principle behind this phenomenon is unknown. I found that in Drosophila, CTCF does not form high intensity loops and the motif orientation does not correlate with any interaction preferences. Instead, non-CTCF loops occur in early development, but disappear in later stages when compartments and TADs appear. In C. elegans, which lacks CTCF altogether, high intensity loops correspond to dosage compensation complex recruitment sites. My preliminary work in analyzing C. elegans data indicates that a network of these loops spans the X chromosome. One major goal of this project is to discover fundamental principles of loop formation. Aim1 of this project will A) exploit the differences between CTCF looping in humans and Drosophila to determine how human CTCF loops form, B) explore the relationship of loops to TADs and compartments throughout development, and C) test whether or not loops create a network of interactions that contributes to the overall X chromosome structure and gene expression control in C. elegans. My previous work has indicated that transcription plays an important role in compartment and TAD formation, a feature that can be somewhat obscured by the prominent role of architectural proteins, like CTCF. Aim2 of this project will confirm the role of transcriptional elongation in chromatin organization and will decipher the individual roles of architectural proteins and transcriptional activity in compartment and TAD formation. These findings will contribute to refining a preliminary algorithm that can simulate chromatin organization at high resolution, giving researchers the ability to predict the effects of mutations or chromatin aberrations on TAD structure. The experiments within these aims will be initiated during the K99 phase of the award and will include training on genetic methods and the considerations necessary for working with Drosophila and C. elegans. This training will provide me with the tools and mentorship necessary for a successful transition to independent research during the R00 phase.