53BP1 regulates genome biology and cellular physiology through liquid phase separation

53BP1 通过液相分离调节基因组生物学和细胞生理学

• 批准号: 10563657
• 负责人: YOU-WEI ZHANG
• 金额: $ 39.11万
• 依托单位: CASE WESTERN RESERVE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-04 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10563657
• 关键词: 3-Dimensional; Address; Biochemical; Bioinformatics; Biological; Biological Process; Biology; Cell Nucleus; Cell physiology; Cells; Cellular Stress; Cellular biology; Chemicals; Chromatin; Chromatin Structure; Chromosome Segregation; Chromosomes; Co-Immunoprecipitations; Complex; Coupled; Cues; Cytoprotection; DNA; DNA Damage; DNA Double Strand Break; DNA Maintenance; DNA Replication Timing; DNA Structure; DNA biosynthesis; DNA metabolism; DNA replication fork; Dimensions; Double Strand Break Repair; Embryo; Epigenetic Process; Euchromatin; Eukaryota; Fibroblasts; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Genome Stability; Goals; HDAC1 gene; Heterochromatin; Hi-C; Histone Acetylation; Histones; Homeostasis; Human; Human Genome; In Vitro; Knock-out; Knockout Mice; Liquid substance; Location; MCF10A cells; Maintenance; Mass Spectrum Analysis; Mediating; Mediator; Membrane; Molecular; Molecular Sieve Chromatography; Molecular and Cellular Biology; Morphology; Mus; Non-Malignant; Nuclear; Nucleic Acids; Nucleotides; Organelles; Phase; Physiology; Play; Polymers; Process; Proteins; Proteomics; Reporting; Research; Role; Science; Signal Transduction; Structure; Sumoylation Pathway; Testing; chromosome conformation capture; crosslink; domain mapping; epigenetic marker; epigenetic memory; gene repression; information processing; innovation; insight; intermolecular interaction; light scattering; mutant; next generation sequencing; novel; nuclease; p53-binding protein 1; reconstitution; recruit; repair function; repaired; restoration; senescence; stoichiometry; three dimensional structure; transcriptome; transcriptome sequencing; whole genome

The function of nuclear DNA is not only determined by its sequence, but also depends on its three dimensional (3D) structure. A particular type of DNA in eukaryotes is called heterochromatin, which refers to as tightly packed DNA structure in the nucleus. Heterochromatin plays a critical role in genome function including DNA structural maintenance, chromosome segregation, epigenetic inheritance, DNA replication, repair and transcription. Recently, increasing evidence suggests the involvement of a new biological process called liquid- liquid phase separation in the formation and function of heterochromatin. Liquid-liquid phase separation, whose concept was borrowed from polymer sciences, is a unique process that involves the formation of membraneless liquid droplets by proteins and nucleotides when their concentration have reached a threshold. These liquid droplets enable the assembly and disassembly of functional protein-based organelles within a cellular compartment following environmental cues. Hence, liquid-liquid phase separation has facilitated our understanding of fundamental cellular information processing, cellular homeostasis, and cellular physiology. Recently, we unexpectedly identified a new player, human 53BP1, in regulating the heterochromatin integrity through liquid-liquid phase separation. 53BP1 was previously known as a critical player in regulating the DNA double strand break repair. However, we discovered that the protective role of 53BP1 in both the structure and the function of heterochromatin is distinct from its canonical activity in DNA double strand break repair. Hence, our studies opened a new research paradigm for this important protein in signaling, biology and cellular physiology. The goal of this proposal is to establish this new research field by addressing several unanswered important questions regarding this new function of 53BP1. These include the molecular basis by which 53BP1 forms the liquid droplets and its significance in biology, genome biology, and cellular physiology. We have used mass spectrometry to identify components in the liquid droplets formed by 53BP1. We will interrogate their functions in this application. By assembling an interdisciplinary team consisting of experts on molecular and cellular biology, proteomics, computational bioinformatics, and next generation sequencing, we will use a combination of cell biological, molecular, biochemical, genetic, morphological, and chemical approaches to answer these questions. Our studies will illustrate a previously uncharacterized function of 53BP1 and a novel interplay between 53BP1 and heterochromatin and determine their impact on genome stability, facilitating our understanding of fundamental cellular information processing, cellular homeostasis, and cellular physiology.

核DNA的功能不仅取决于其序列，还取决于其三维结构 (3D)结构真核生物中的一种特殊类型的DNA被称为异染色质， 细胞核中的DNA结构异染色质在包括DNA在内的基因组功能中起着关键作用 结构维持、染色体分离、表观遗传、DNA复制、修复和 转录。最近，越来越多的证据表明，一种新的生物过程参与其中，称为液体- 液相分离在异染色质的形成和功能中的作用。液-液相分离， 概念是从聚合物科学借来的，是一个独特的过程，涉及形成 当蛋白质和核苷酸的浓度达到阈值时，无膜液滴被蛋白质和核苷酸吸收。 这些液滴能够在细胞内组装和拆卸功能性蛋白质基细胞器。 细胞隔室跟随环境线索。因此，液-液相分离促进了我们的研究。 了解基本的细胞信息处理，细胞内稳态和细胞生理学。 最近，我们意外地发现了一个新的球员，人53 BP 1，在调节异染色质的完整性， 通过液-液相分离。53 BP 1以前被认为是调节DNA的关键参与者。 双链断裂修复。然而，我们发现53 BP 1在结构和功能上的保护作用均不明显。 异染色质的功能不同于其在DNA双链断裂修复中的典型活性。因此，我们认为， 我们的研究为这种重要的蛋白质在信号传导、生物学和细胞生物学中开辟了一个新的研究范式。 physiology.该提案的目标是通过解决几个悬而未决的问题来建立这个新的研究领域 关于53 BP 1的新功能的重要问题。这些包括53 BP 1的分子基础， 形成液滴及其在生物学、基因组生物学和细胞生理学中的意义。我们已经使用 质谱法以鉴定由53 BP 1形成的液滴中的组分。我们会审问他们 功能在此应用中。通过组建一个由分子和生物学专家组成的跨学科团队， 细胞生物学、蛋白质组学、计算生物信息学和下一代测序，我们将使用 细胞生物学、分子学、生物化学、遗传学、形态学和化学方法的组合， 回答这些问题我们的研究将阐明53 BP 1的一个以前未表征的功能和一个新的 53 BP 1和异染色质之间的相互作用，并确定其对基因组稳定性的影响，促进我们的研究。 了解基本的细胞信息处理，细胞内稳态和细胞生理学。