Mechanisms of epigenetic gene regulation by the Drosophila COMPASS-like complex

果蝇COMPASS样复合体的表观遗传基因调控机制

• 批准号: 1716431
• 负责人: Andrew Dingwall
• 金额: $ 83.88万
• 依托单位: Loyola University Stritch School of Medicine
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1716431&HistoricalAwards=false
• 关键词: Mechanisms; epigenetic; gene; regulation; Drosophila

Developmental processes in eukaryotic cells are controlled by DNA elements called enhancers. The molecular nature of enhancers is not well understood, although current evidence suggests they differ from other DNA elements by having a distinct structure within the chromosomes. Structural differences can arise from enzymatic modification of the histone proteins responsible for packaging the DNA in the nucleus. This project focuses on studying the enzymes that modify enhancer elements and how their action helps turn on critical genes at the right time and location during development. The work will be carried out using a multi-disciplinary approach that combines genetic, biochemical and high-throughput bioinformatics tools in the fruit fly, Drosophila melanogaster, as the model organism. Because the mechanisms governing how, when and where genes are turned on and off during development are conserved across evolution, the results should have far-reaching impact, from yeast to humans. The project will have broad educational impact by providing students with training in multiple areas, including protein structure modeling, biochemistry, bioinformatics, genetics and advanced microscopy imaging. Students also learn how to develop scientific hypotheses, independently carry out experiments and interpret results, prepare oral and written summaries and publish their work, skills that provide a strong technical knowledge base for diverse scientific careers.The metazoan COMPASS related coactivator complexes catalyze the methylation of histone H3 on Lysine 4 (H3K4), epigenetic marks associated with controlling eukaryotic gene transcription. The Cmi/Trr COMPASS-like complex in Drosophila is responsible for monomethylating H3K4 and regulates enhancer activity in cooperation with transcription factors important for normal development. Trr provides histone methyltransferase activity, while Cmi contains plant homeodomain Zn fingers in two conserved clusters that co-evolved over 1.5 billion years with chromosome compaction in nucleosomes. Despite the conservation and importance in transcription control, it is not well understood how the COMPASS-like complexes are able to prime and maintain enhancer activities during development. This project focuses on the role of the conserved PHD finger domains in chromatin recognition and key cellular signaling pathways that depend on precise enhancer control. Taking advantage of the versatile Drosophila genetic model system, this project tests broad hypotheses (1) that the clustered PHD domains found in Cmi and homologous vertebrate proteins contribute essential epigenetic histone reader functions that drive the proper priming and regulation of gene enhancers and (2) the Drosophila COMPASS-like coactivator complex regulates the timing of enhancer utilization to integrate key developmental signals. One aim of this project explores the combined functions of the finger domains in the conserved PHD cluster that are essential for proper enhancer regulation. Structural modeling studies of the PHD finger domains and targeted mutagenesis, combined with in vitro and in vivo measurements of chromatin association, will define the histone recognition and binding properties of Cmi and mammalian PHD finger domains and further elucidate the mechanisms of enhancer control by the COMPASS-like complexes. A second aim incorporating developmental, genetic and molecular analyses (ChIP-seq, RNA-seq, chromatin capture) will expand our understanding of target gene regulation in vivo, help correlate specific enhancer epigenetic marks with COMPASS-like complex functions, and provide significant new insights regarding conserved mechanisms of chromatin regulation.

真核细胞中的发育过程由称为增强子的DNA元素控制。 增强子的分子性质尚不清楚，尽管目前的证据表明它们与其他DNA元素不同，通过在染色体内具有独特的结构而有所不同。结构差异可能是由负责包装核中DNA包装的组蛋白蛋白的酶促修饰引起的。 该项目的重点是研究修改增强子元素的酶，以及它们的作用如何有助于在开发过程中正确的时间和位置打开关键基因。这项工作将使用多学科的方法进行，该方法结合了果蝇中的遗传，生化和高通量生物信息学工具，即果蝇Melanogaster，作为模型有机体。 因为在发育过程中如何，何时何地打开基因的何时何地的机制在整个进化过程中都保存下来，因此结果应具有深远的影响，从酵母到人类。 该项目将通过为学生提供多个领域的培训，包括蛋白质结构建模，生物化学，生物信息学，遗传学和高级显微镜成像，从而产生广泛的教育影响。 学生还学习如何发展科学假设，独立进行实验并解释结果，准备口头和书面摘要并发布其工作，为多种科学职业提供了强大的技术知识基础的技能。相关的相关共激活器催化了与赖氨酸4（H3K4）上组蛋白H3的甲基化相关的sepentic Marks contecentic contecentic euks contening Euk，催化了组蛋白H3的甲基化。果蝇中的CMI/TRR指南针样复合物负责单甲基化H3K4，并根据对正常发育重要的转录因子的合作调节增强剂活性。 TRR提供组蛋白甲基转移酶活性，而CMI在两个保守的簇中含有植物同源域的Zn手指，这些簇在核小体中与染色体压实合作的15亿年合作。尽管在转录控制方面具有保护和重要性，但尚未充分了解指南针样复合物如何能够在开发过程中启动和维持增强剂活动。该项目的重点是保守的PhD指域在染色质识别和取决于精确增强子控制的钥匙细胞信号通路中的作用。 Taking advantage of the versatile Drosophila genetic model system, this project tests broad hypotheses (1) that the clustered PHD domains found in Cmi and homologous vertebrate proteins contribute essential epigenetic histone reader functions that drive the proper priming and regulation of gene enhancers and (2) the Drosophila COMPASS-like coactivator complex regulates the timing of enhancer utilization to integrate key发展信号。该项目的一个目的探讨了保守的PHD群集中手指域的组合功能，这对于适当的增强子调节至关重要。博士手指结构域和靶向诱变的结构建模研究，结合染色质缔合的体外和体内测量，将定义CMI和哺乳动物PhD手指的组蛋白识别和结合特性，并进一步阐明通过Compass类似的复合物来增强器控制的机制。结合发育，遗传和分子分析的第二个目的（CHIP-SEQ，RNA-SEQ，染色质捕获）将扩大我们对体内靶基因调控的理解，有助于将特定的增强子表观遗传学标记与指南针样的复杂功能相关联，并提供有关染色质调节的保守机制的重要新见解。

项目成果

The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development

果蝇 MLR COMPASS 复合体对于顺式调控信息编程和发育过程中维持表观遗传记忆至关重要

• DOI: 10.1093/nar/gkaa082
• 发表时间: 2020
• 期刊: Nucleic Acids Research
• 影响因子: 14.9
• 作者: Zraly, Claudia B;Zakkar, Abdul;Perez, John Hertenstein;Ng, Jeffrey;White, Kevin P;Slattery, Matthew;Dingwall, Andrew K
• 通讯作者: Dingwall, Andrew K