Mapping the short-range chromatin architecture of the repressive epigenome

绘制抑制性表观基因组的短程染色质结构图

基本信息

批准号：
10543052
负责人：
Andres Mansisidor
金额：
$ 7.18万
依托单位：
ROCKEFELLER UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-01-01 至 2023-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10543052
关键词：
3-Dimensional Address Affect Architecture Cell Differentiation process Cell physiology Cells Centromere Chromatin Chromatin Fiber Chromatin Modeling Chromatin Structure Chromosome Mapping Chromosome Segregation Chromosomes Complex DNA DNA Folding DNA Structure DNA sequencing Data Disease Epigenetic Process Fiber Fission Yeast Foundations Functional disorder Gene Expression Profile Gene Silencing Genetic Transcription Genome Genome Stability Genomic Instability Genomic Segment Genomics Heterochromatin Higher Order Chromatin Structure Histone Deacetylation Histone H3 Human Genome In Vitro Length Linker DNA Lysine Maintenance Malignant Neoplasms Maps Measurement Measures Methodology Methods Methylation Modeling Modification Molecular Conformation Mutagenesis Nuclear Envelope Nucleosomes Pathway interactions Pattern Phase Physical condensation Process Protein Isoforms Radiation Refractory Regulation Repetitive Sequence Repression Research Resolution Role Structure Technology Testing Transcriptional Regulation Work cell type embryo cell epigenome experimental study gene repression genetic approach genetic manipulation genome integrity genome-wide genomic locus heterochromatin-specific nonhistone chromosomal protein HP-1 histone methylation histone modification human disease in silico in vivo insight model organism nanopore nanoscale prevent technological innovation telomere tumorigenesis

项目摘要

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.

项目摘要基因组结构与从转录调控到染色体分离。最新的技术创新已实现了长期的详细表征范围染色体构象。远程染色体压实出现在压抑区域统称称为异染色质。这些基因组区域对于适当的细胞类型依赖性至关重要基因表达模式及其结构也有助于通过控制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。尽管在理解远程染色质压实方面取得了进步，但很少存在测量在亚核体分辨率下DNA的空间组织的方法，这是长度比例与转录和其他关键DNA过程相关。此外，许多杂色结构包含DNA重复序列，由于无法将其映射到单个基因组基因座，因此很难研究。我试图使用最近开发的方法来确定异染色质的短距离压实状态， 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- 使用纳米孔长读测序的基于方法来测量DNA重复序列。我也会基因操纵组蛋白修饰途径，调节异染色质以确定其作用在短距离染色质结构上。组蛋白脱乙酰化和甲基化是两个主要的表观遗传途径该动态调节异染色质。除了这些修改之外，多种同工型保守的异染色质蛋白1（HP1）有助于调节异染色质结构。我将确定这些表观遗传因素对染色质压实和转录的各自的体内贡献沉默。除了定义有关异染色质组织和功能的基本规则外，我还建议研究相分离的冷凝物的压实态。相位被认为是但是，调节异染色质动力学和转录，它如何影响短范围染色质组织尚未解决。我将确定体外相的3D DNA折叠构象分离的染色质，连接在体外观察到的现象，并测量染色质压实细胞。这项拟议的工作将取消基因组组织的基本原理并为理解异染色质调节以及可能的影响提供了结构性基础它在疾病状态下的破坏。