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Regulation of Chromosomal DNA Replication Dynamics in S cerevisiae

酿酒酵母染色体 DNA 复制动力学的调控

基本信息

批准号：
10458597
负责人：
OSCAR M APARICIO
金额：
$ 46.93万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
依托单位国家：
美国
项目类别：
财政年份：
2003
资助国家：
美国
起止时间：
2003-02-01 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10458597
关键词：
Address Architecture Base Sequence Binding Biology Cell Cycle Cell Nucleus Cell division Chromatin Chromosomes Cyclin-Dependent Kinases DNA DNA Repair DNA biosynthesis DNA replication origin DNA-Protein Interaction Defect Development Dimerization Elements Ensure Environment Epigenetic Process Event Foxes G1 Phase Gene Expression Genetic Transcription Genome Genome Stability Genomic Segment Goals Heart Homeostasis Human Biology Licensing Link Maintenance Malignant Neoplasms Medicine Modeling Molecular Movement Nuclear Phosphotransferases Positioning Attribute Process Protein Analysis Proteins Regulation Replication Initiation Replication Origin Reporting Role S phase Saccharomyces cerevisiae Saccharomycetales Structure System Testing Transcriptional Regulation Work Yeasts epigenetic regulation experimental study genetic approach genetic element insight novel programs recruit tool transcription factor yeast genome

项目摘要

PROJECT SUMMARY The extremely long DNA molecules that comprise eukaryotic genomes are wrapped, folded, and looped to compact and organize the DNA for its essential activities, including gene expression, DNA replication, and DNA repair. Exactly how the spatial architecture of chromosomes regulates DNA processes is still poorly understood, and relatively few involved factors have been identified. DNA replication origins are subject to epigenetic regulation of their activity resulting in differential replication timings and origin efficiencies during S phase. This level of control over replication origins helps ensure an appropriate level of origin activity for genome stability, however, the molecular mechanism(s) responsible for this regulation have remained obscure. We discovered the budding yeast Fox proteins, Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as key regulators of replication origin initiation timing, required for most early origin firing across the yeast genome. Fkh1 and/or Fkh2 (Fkh1/2) bind to specific sequences at some origins (called Fkh-activated origins). Recent studies indicate that a key function of Fkh1/2 is to recruit Dbf4-dependent kinase (DDK), which is required for replication origin initiation. This project is geared toward fully understanding the cell cycle-regulated binding of Fkh1/2 with origins and Fkh1/2 interactions with DDK. We have identified a potential dimerization motif in Fkh1/2 that is required for its function in origin regulation but not in other functions like transcriptional regulation. We will determine the function of this motif in origin regulation. Fkh1 establishes the origin-timing program in G1 phase and this correlates with re-localization of Fkh1-activated origins from the late-replicating nuclear periphery to an early-replicating interior environment of the nucleus. The exact significance of these movements is unclear but likely represent the assembly of origin clusters that will transform into replication factories. Therefore, this system provides a novel and powerful opportunity to elucidate fundamental mechanisms of chromosomal dynamics, which is a major goal of this proposal. We will use genetic approaches to eliminate function of candidate regulator proteins to dissect the molecular events associated with origin dynamics and replication initiation. We will also develop new tools for better analysis of protein- DNA interactions. Finally, we will perform experiments to strip away epigenetic layers of origin regulation to reveal the underlying sequence-based determinants of origin firing. We will determine the impact on genome stability of these layers of regulation. These studies have strong potential to reveal novel molecular events at the DNA level governing the dynamics of chromosomes and their essential genetic elements, such as replication origins.

项目摘要组成真核生物基因组的极长DNA分子被包裹、折叠和成环，压缩和组织DNA的基本活动，包括基因表达，DNA复制， DNA修复染色体的空间结构究竟是如何调节DNA过程的，这一点已经得到了理解，并且已经确定了相对较少的相关因素。DNA复制起点受表观遗传调节它们的活动，导致不同的复制时间和起源效率在S 相位对复制起点的这种控制水平有助于确保适当水平的起点活动，然而，基因组稳定性，负责这种调节的分子机制仍然不清楚。我们发现了芽殖酵母Fox蛋白，Forkhead 1（Fkh 1）和Forkhead 2（Fkh 2），它们是复制起点起始时间，这是酵母基因组中大多数早期起点激发所需的。Fkh 1和/或 Fkh 2（Fkh 1/2）在某些起点（称为Fkh-activated origins）与特定序列结合。最近的研究表明Fkh 1/2关键功能是募集Dbf 4依赖性激酶（DDK），这是复制起点起始。该项目旨在充分了解细胞周期调节的结合， Fkh 1/2与起源和Fkh 1/2与DDK的相互作用。我们已经确定了一个潜在的二聚化基序， Fkh 1/2是其在起源调节中的功能所必需的，但在其他功能如转录调节中不需要。我们将确定这个基序在起源调节中的功能。fkh 1建立了原点计时程序， G1期，这与Fkh 1激活的起源从晚期复制的核中重新定位相关早期复制的核心内部环境的外围。这些的确切意义运动尚不清楚，但可能代表了将转化为复制的起源簇的组装工厂因此，该系统提供了一个新颖而有力的机会来阐明基本的染色体动力学的机制，这是本提案的主要目标。我们将使用基因消除候选调节蛋白的功能以剖析相关分子事件的方法与起源动力学和复制起始有关。我们还将开发新的工具来更好地分析蛋白质- DNA相互作用最后，我们将进行实验，剥离起源调节的表观遗传层，揭示了起源放电的潜在序列决定因素。我们将确定对基因组的影响这些监管层的稳定性。这些研究有很强的潜力揭示新的分子事件，控制染色体动态及其基本遗传元素的DNA水平，例如复制起点

项目成果

期刊论文数量（30）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.

DOI：
10.1016/j.cell.2011.12.012
发表时间：
2012-01-20
期刊：
Cell
影响因子：
64.5
作者：
Knott SR;Peace JM;Ostrow AZ;Gan Y;Rex AE;Viggiani CJ;Tavaré S;Aparicio OM
通讯作者：
Aparicio OM

SnapShot: Replication timing.

快照：复制计时。

DOI：
10.1016/j.cell.2013.02.038
发表时间：
2013
期刊：
Cell
影响因子：
64.5
作者：
Pope,BenjaminD;Aparicio,OscarM;Gilbert,DavidM
通讯作者：
Gilbert,DavidM

Genome-wide analysis of DNA synthesis by BrdU immunoprecipitation on tiling microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae.

DOI：
10.1101/pdb.prot5385
发表时间：
2010-02
期刊：
Cold Spring Harbor protocols
影响因子：
0
作者：
C. Viggiani;S. Knott;O. Aparicio
通讯作者：
C. Viggiani;S. Knott;O. Aparicio

Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data.

DOI：
10.3390/ijms24119271
发表时间：
2023-05-25
期刊：
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
影响因子：
5.6
作者：
Petrie, Meghan V.;He, Yiwei;Gan, Yan;Ostrow, Andrew Zachary;Aparicio, Oscar M.
通讯作者：
Aparicio, Oscar M.

Strategies for analyzing highly enriched IP-chip datasets.