Epigenetic Control of DNA Replication in Arabidopsis

拟南芥 DNA 复制的表观遗传控制

• 批准号: 1121245
• 负责人: Steven Jacobsen
• 金额: $ 70.5万
• 依托单位: University of California-Los Angeles
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2015-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1121245&HistoricalAwards=false
• 关键词: Epigenetic; Control; DNA; Replication; Arabidopsis

Intellectual merit: The faithful replication of DNA is the basis of inheritance in all organisms. DNA replication is a carefully regulated process, but it is still incompletely understood. For example, little is known about the relationship between DNA replication, and processes such as the chemical modification of histone proteins that package the DNA in the cell. Many different modifications of histones are known, but their function is unclear. The long-term objective of this project is to understand the relationship between DNA replication and such histone modifications in the genome of the model plant, Arabidopsis thaliana. This will be approached through detailed exploration of a recently observed link between DNA replication and a particular histone modification whose function is to prevent gene expression within certain regions of the Arabidopsis thaliana genome. Two proteins named ATXR5 and ATXR6 (ATXR5/6) act redundantly to maintain repression of gene expression of genes located within repetitive elements in the Arabidopsis genome. It has been recently discovered that in atxr5/6 mutants, such silenced regions of the genome replicate more than once per cell cycle in a form of aberrant DNA replication termed "re-replication". Re-replicating regions of the genome have been mapped using next-generation sequencing approaches, and found to closely correspond to regions that are characterized by histone modifications associated with repression of gene expression. This research project aims to use the genetic and genomic resources for Arabidopsis to investigate the interplay between the fundamental biological processes of histone modifications and DNA replication. Novel genome sequencing techniques will be used to explore the ways in which DNA replication and repair pathways interact with local chromatin environments. Furthermore, multiple biochemical and genetics approaches will be used to expand the understanding of ATXR5 and ATXR6 pathway mechanisms. Broader impacts: This project will generate a significant number of genomic datasets, which provides a unique opportunity to involve undergraduate students in state-of-the-art genomic techniques and data analysis. Initially, three undergraduates will be involved in the research. Each will be extensively trained in standard molecular biology techniques required for the project. In addition, these students will be trained in data analysis techniques, from the initial processing and mapping of high throughput sequencing reads to downstream higher-level analysis. This will facilitate the training of a new class of students with skills that lie at the interface of molecular biology and computational biology. A goal will be to expand such cross disciplinary training to a larger pool of UCLA undergraduate students as part of the new Biomedical Research minor program which is being spearheaded by the Principal Investigator's department of Molecular Cell and Developmental Biology, together with the MIMG department. A course will be developed that will be taught through the new interdepartmental instructional laboratory curriculum, in which larger groups of students can use real world data sets from this project to learn computational biology techniques and apply them to hypothesis testing. An understanding of the relationship between histone modifications and DNA replication will have a broad impact not only on plant research, but also on DNA replication research in other eukaryotes. In addition, the data from this project will be widely disseminated through public browsers and web sites, and will be of wide utility to a broad set of plant biologists interested in development, stress responses, gene expression, and plant genomics.

智力优点：DNA的忠实复制是所有生物体遗传的基础。 DNA复制是一个被仔细调控的过程，但它仍然没有完全被理解。 例如，我们对DNA复制与细胞中包装DNA的组蛋白的化学修饰等过程之间的关系知之甚少。 已知组蛋白的许多不同修饰，但其功能尚不清楚。 该项目的长期目标是了解模式植物拟南芥基因组中DNA复制与此类组蛋白修饰之间的关系。这将通过最近观察到的DNA复制和一个特定的组蛋白修饰，其功能是防止基因表达在拟南芥基因组的某些区域之间的联系进行详细的探索。两种名为ATXR 5和ATXR 6（ATXR 5/6）的蛋白质冗余地起作用以维持位于拟南芥基因组中重复元件内的基因的基因表达的抑制。最近已经发现，在atxr 5/6突变体中，基因组的这种沉默区域以称为“再复制”的异常DNA复制的形式在每个细胞周期复制一次以上。已经使用下一代测序方法绘制了基因组的再复制区域，并且发现其与以与基因表达抑制相关的组蛋白修饰为特征的区域密切对应。 本研究计划旨在利用拟南芥的遗传和基因组资源，研究组蛋白修饰和DNA复制的基本生物学过程之间的相互作用。新的基因组测序技术将用于探索DNA复制和修复途径与局部染色质环境相互作用的方式。此外，多种生物化学和遗传学方法将用于扩展对ATXR 5和ATXR 6通路机制的理解。更广泛的影响：该项目将产生大量的基因组数据集，这为本科生参与最先进的基因组技术和数据分析提供了一个独特的机会。 最初，三名本科生将参与这项研究。 每个人都将接受该项目所需的标准分子生物学技术的广泛培训。 此外，这些学生将接受数据分析技术的培训，从高通量测序读数的初始处理和映射到下游更高级别的分析。 这将有助于培养一批具有分子生物学和计算生物学界面技能的新学生。 一个目标是将这种跨学科的培训扩大到更大的UCLA本科生群体，作为新的生物医学研究未成年人计划的一部分，该计划由主要研究者的分子细胞和发育生物学部门与MIMG部门共同领导。 将开发一门课程，通过新的跨部门教学实验室课程进行教学，其中较大的学生群体可以使用该项目的真实的世界数据集来学习计算生物学技术，并将其应用于假设检验。 了解组蛋白修饰和DNA复制之间的关系不仅对植物研究，而且对其他真核生物中的DNA复制研究具有广泛的影响。 此外，该项目的数据将通过公共浏览器和网站广泛传播，并将广泛适用于对发育，胁迫反应，基因表达和植物基因组学感兴趣的广泛植物生物学家。