Characterization of topological machines that control chromosome conformation

项目摘要/摘要 本研究的目的是研究染色体的分子机制。 构象。染色体结构对控制基因组过程很重要，例如转录， 复制、染色体分离和这种结构的破坏在遗传性疾病和 癌细胞。染色体的组织主要有三个层次：染色体区域、染色体 间隔和拓扑关联结构域(TADS)。目前的模型是TAD的形成 由于染色质纤维的动态环状挤出，这在方向性上被CTCF结合到 泰德的界限。然而，提出的拓扑机的组成和分子机制 这些染色质环是由什么形成的目前尚不清楚。先前的研究表明，拓扑异构酶和 组蛋白变异体可能在调节染色体构象和拓扑机活性方面发挥作用。在……里面 此外，最近的分子建模研究已经涉及到环挤出，例如动态挤出的DNA 环，作为染色体结构的一个重要特征，但这还没有得到检验 试验性的。本研究将结合使用Hi-C、ChIP-seq和TMP-seq等基因组学方法 用细胞生物学和功能遗传学的方法来研究细胞的分子组成和动力学 拓扑机。将执行三个相辅相成的目标来解决这个问题：1)评估角色 最近发现的拓扑异构酶是位于TAD边界的CTCF复合体的一部分。2) 研究修饰TAD生物学中的关键元件的组蛋白变体的作用。3)开发新的 确定TADS内染色质动力学的方法，以检验最近提出的TAD形成模型 动态环路形成。总而言之，完成这些目标将导致对功能和 染色体构象的调控。

PROJECT SUMMARY/ABSTRACT The goal of this research is to investigate the molecular mechanisms responsible for chromosome conformation. Chromosome structure is important for controlling genomic processes such as transcription, replication, and chromosome segregation, and disruptions to this structure are found in genetic diseases and cancer cells. There are three main levels of chromosome organization: chromosome territories, chromosome compartments, and topologically associating domains (TADs). The current model is that TAD formation occurs due to dynamic loop extrusion of chromatin fibers, which is blocked in a directional manner by CTCF bound to TAD boundaries. However, the components and molecular mechanism of this proposed topological machine which forms these chromatin loops are currently unknown. Previous studies suggest that topoisomerases and histone variants may have a role in regulating chromosome conformation and topological machine activity. In addition, recent molecular modeling research has implicated loop extrusion e.g. dynamically extruded DNA loops, as an important characteristic of chromosome structure, however this has not yet been tested experimentally. This study will use genomic methods such as Hi-C, ChIP-seq, and TMP-seq in combination with cell biological and functional genetic approaches to study the molecular components and dynamics of the topological machine. Three complementary aims will be performed to address this question: 1) Assess the role of topoisomerases that have recently been identified as a part of the CTCF complex at TAD boundaries. 2) Investigate the role of histone variants that decorate key elements involved in TAD biology. 3) Develop new methods to determine chromatin dynamics inside TADs to test recently proposed models of TAD formation by dynamic loop formation. Together, completion of these aims will lead to new insights about the function and regulation of chromosome conformation.