Epigenetic gene regulation in Arabidopsis

拟南芥表观遗传基因调控

• 批准号: 10551231
• 负责人: STEVEN E JACOBSEN
• 金额: $ 31.2万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-02-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10551231
• 关键词: Arabidopsis; Binding; Biological Models; Biology; Cancer Etiology; Cells; Chemicals; Cytosine; DNA; DNA Damage; DNA Methylation; DNA Modification Methylases; DNA-Directed RNA Polymerase; Defect; Epigenetic Process; Five-Year Plans; Gene Expression; Gene Expression Regulation; Gene Silencing; Genes; Genetic; Genome; Genome Stability; Genomics; Heterochromatin; Histones; Laboratories; Laboratory Finding; Lead; Maintenance; Mass Spectrum Analysis; Methods; Methylation; Modification; Mouse-ear Cress; Nature; Pathway interactions; Pattern; Play; Post-Translational Protein Processing; Proteins; Proteomics; RNA; Repression; Research; Tissues; Untranslated RNA; derepression; gene function; histone methylation; histone modification; methylation pattern; mutant; prevent; protein complex; response; structural biology

Project Summary/Abstract Our laboratory focuses on the biology and mechanisms of gene silencing by DNA methylation and histone modifications, primarily using Arabidopsis thaliana as a model system. Recent efforts have focused on the mechanisms by which DNA methylation is properly patterned in the genome. The main findings are that four distinct DNA methylation pathways, driven by four different DNA methyltransferases act in self- reinforcing mechanisms to maintain cytosine methylation in three different sequence contexts, CG, CHG and CHH (where H = A, T, or C). The establishment of DNA methylation is controlled by the RNA-directed DNA methylation pathway, and studying this pathway has been a major recent focus of the lab. Most recently, the laboratory has used genetics, genomics, proteomics, and structural biology approaches to characterize the mechanisms by which two RNA polymerases, Pol IV and Pol V, act to produce non- coding RNAs that act to target RNA-directed DNA methylation to specific loci. The newest findings from the laboratory are also taking us into new directions aimed at understanding factors that act downstream of DNA methylation, to both control gene expression and to maintain genome stability. In the next five years, we plan to utilize all available approaches to understand the proteins that recognize methylated DNA and certain modified histones, and to decipher their functions in gene expression and in the maintenance of genome stability. These approaches will include mass spectrometry to directly identify proteins and protein complexes able to bind to methylated DNA and methylated histones. The laboratory will also use Arabidopsis mutant screens to identify factors that act downstream of DNA methylation and various histone marks. A post translational modification of histones called H3K27 monomethylation is critical for repression of heterochromatin. In the absence of this mark, cells undergo both inappropriate gene expression and a massive DNA damage response resulting in amplification of heterochromatic DNA. A key part of the five-year plan will be to understand the mechanisms at play, and to understand the precise nature of the relationship between gene derepression and DNA damage.

项目总结/摘要 本实验室主要研究DNA甲基化和组蛋白介导的基因沉默的生物学和机制 修饰，主要使用拟南芥作为模型系统。最近的努力集中在 DNA甲基化在基因组中正确模式化的机制。研究发现 四种不同的DNA甲基化途径，由四种不同的DNA甲基转移酶驱动， 在三种不同的序列背景下，CG，CHG， 和CHH（其中H = A、T或C）。DNA甲基化的建立是由RNA指导的甲基化过程控制的。 DNA甲基化途径，研究这一途径一直是实验室最近的一个主要重点。最 最近，该实验室利用遗传学、基因组学、蛋白质组学和结构生物学方法， 描述了两种RNA聚合酶Pol IV和Pol V产生非- 编码RNA，其作用是将RNA指导的DNA甲基化靶向特定基因座。最新发现来自 这些实验室也将我们带入了新的方向，旨在了解作用于下游的因素 DNA甲基化，以控制基因表达和维持基因组稳定性。未来五 在接下来的几年里，我们计划利用所有可用的方法来了解识别甲基化的蛋白质。 DNA和某些修饰的组蛋白，并破译它们在基因表达和基因表达中的功能。 保持基因组的稳定性。这些方法将包括质谱法，以直接识别 能够与甲基化DNA和甲基化组蛋白结合的蛋白质和蛋白质复合物。实验室 还将使用拟南芥突变体筛选来鉴定作用于DNA甲基化下游的因子， 各种组蛋白标记组蛋白的翻译后修饰称为H3 K27单甲基化， 对抑制异染色质至关重要。在没有这种标记的情况下，细胞经历了不适当的 基因表达和大量的DNA损伤反应，导致异染色质DNA的扩增。 五年计划的一个关键部分将是了解正在发挥作用的机制，并了解 基因去阻遏和DNA损伤之间关系的精确性质。

项目成果

DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis.

• DOI: 10.1186/s13059-020-02190-1
• 发表时间: 2020-11-25
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Bourguet P;López-González L;Gómez-Zambrano Á;Pélissier T;Hesketh A;Potok ME;Pouch-Pélissier MN;Perez M;Da Ines O;Latrasse D;White CI;Jacobsen SE;Benhamed M;Mathieu O
• 通讯作者: Mathieu O

Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis.

组蛋白伴侣 ASF1 介导拟南芥中 H3.3-H4 沉积

• DOI: 10.1038/s41467-022-34648-0
• 发表时间: 2022-11-15
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Zhong, Zhenhui;Wang, Yafei;Wang, Ming;Yang, Fan;Thomas, Quentin Angelo;Xue, Yan;Zhang, Yaxin;Liu, Wanlu;Jami-Alahmadi, Yasaman;Xu, Linhao;Feng, Suhua;Marquardt, Sebastian;Wohlschlegel, James A.;Ausin, Israel;Jacobsen, Steven E.
• 通讯作者: Jacobsen, Steven E.

A SYBR Gold-based Label-free in vitro Dicing Assay.

基于 SYBR Gold 的无标记体外切割测定。

• DOI: 10.21769/bioprotoc.4382
• 发表时间: 2022
• 期刊: Bio-protocol
• 影响因子: 0.8
• 作者: Wang,Qian;Xue,Yan;Zhang,Laixing;Zhong,Zhenhui;Feng,Suhua;Wang,Changshi;Xiao,Lifan;Yang,Zhenlin;Harris,JakeC;Wu,Zhe;Zhai,Jixian;Yang,Maojun;Li,Sisi;Jacobsen,StevenE;Du,Jiamu
• 通讯作者: Du,Jiamu

MBD2 couples DNA methylation to transposable element silencing during male gametogenesis.

• DOI: 10.1038/s41477-023-01599-3
• 发表时间: 2024-01
• 期刊: NATURE PLANTS
• 影响因子: 18
• 作者: Wang, Shuya;Wang, Ming;Ichino, Lucia;Boone, Brandon A.;Zhong, Zhenhui;Papareddy, Ranjith K.;Lin, Evan K.;Yun, Jaewon;Feng, Suhua;Jacobsen, Steven E.
• 通讯作者: Jacobsen, Steven E.

Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen.

• DOI: 10.1016/j.celrep.2022.111699
• 发表时间: 2022-11-22
• 期刊: Cell reports
• 影响因子: 8.8