Mapping the short-range chromatin architecture of the repressive epigenome

项目摘要 基因组结构与从转录调控到 染色体分离最近的技术创新使详细的特点，长期- 范围染色体构象。长距离染色体紧密化出现在抑制区域 统称为异染色质。这些基因组区域对于适当的细胞类型依赖性 基因表达模式，以及它们的结构也有助于防止基因组的不稳定性， 寄生转座子的表达和通过调节着丝粒附近的染色质结构， 端粒和其他DNA重复序列。尽管在理解长距离染色质致密化方面取得了进展， 存在以亚核小体分辨率测量DNA的空间组织的方法，所述亚核小体分辨率是长度 与转录和其他关键DNA过程相关的规模。此外，许多异色结构 含有DNA重复序列，由于它们不能映射到单个基因组位点而难以研究。 我试图确定短程压缩状态的异染色质，使用最近开发的方法， RICC-seq，可以在亚核小体分辨率下测量3D DNA接触。我将创建新的RICC-seq- 基于Nanopore长读测序的方法，以实现DNA重复序列的测量。我也会 基因操纵组蛋白修饰途径，调节异染色质，以确定其影响 短距离染色质结构。组蛋白脱乙酰化和甲基化是两种主要的表观遗传途径 动态调节异染色质。除了这些修饰之外，多个异构体的表达也是如此。 保守的异染色质蛋白1（HP 1）帮助调节异染色质结构。我将决定 这些表观遗传因子对染色质致密化和转录的各自体内贡献 沉默除了定义异染色质组织和功能的基本规则外， 建议研究相分离冷凝物的压实状态。相分离被认为是 调节异染色质动力学和转录，然而，它如何影响短程染色质 组织有待解决。我将确定体外阶段的三维DNA折叠构象- 分离的染色质，连接在体外观察到的现象与染色质压实的测量， 细胞这项拟议中的工作将梳理出纳米级分辨率的基因组组织的基本原则 并为理解异染色质调节和 它在疾病状态下的破坏。

Project Summary Genome architecture is associated with many essential cellular processes from transcriptional regulation to chromosome segregation. Recent technological innovations have enabled detailed characterization of long- range chromosome conformations. Long-range chromosome compaction appears at repressive regions collectively referred to as heterochromatin. These genomic regions are vital for proper cell type-dependent gene expression patterns, and their architecture also helps to protect against genomic instability by controlling the expression of parasitic transposons and by regulating the chromatin structure near centromeres, telomeres, and other DNA repeats. Despite advances in understanding long-range chromatin compaction, few methods exist that measure the spatial organization of DNA at sub-nucleosome resolution, which is the length scale relevant to transcription and other critical DNA processes. Furthermore, many heterochromatic structures contain DNA repeats, which are difficult to study due to their inability to be mapped to a single genomic locus. I seek to determine the short-range compaction states of heterochromatin, using a recently developed method, RICC-seq, which can measure 3D DNA contacts at sub-nucleosome resolution. I will create new RICC-seq- based methods using Nanopore long-read sequencing to enable measurements of DNA repeats. I will also genetically manipulate histone modification pathways that regulate heterochromatin to determine their effects on short-range chromatin structure. Histone deacetylation and methylation are two major epigenetic pathways that dynamically regulate heterochromatin. In addition to these modifications, multiple isoforms of the conserved heterochromatin protein 1 (HP1) help regulate heterochromatin structures. I will determine the respective in vivo contributions that these epigenetic factors have on chromatin compaction and transcriptional silencing. In addition to defining the basic rules governing heterochromatin organization and function, I also propose to investigate the compaction states of phase-separated condensates. Phase separation is thought to regulate heterochromatin dynamics and transcription, however, how it affects short-range chromatin organization has yet to be addressed. I will determine the 3D DNA folding conformations of in vitro phase- separated chromatin, connecting phenomena observed in vitro with measurements of chromatin compaction in cells. This proposed work will tease out fundamental principles of genomic organization at nanoscale resolution and provide a structural foundation for understanding heterochromatin regulation and the possible impacts of its disruption in disease states.