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.

真核细胞的发育过程由称为增强子的 DNA 元件控制。 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 元件不同，在染色体内具有独特的结构。负责在细胞核中包装 DNA 的组蛋白的酶促修饰可能会产生结构差异。 该项目重点研究修饰增强子元件的酶，以及它们的作用如何帮助在发育过程中的正确时间和位置打开关键基因。这项工作将采用多学科方法进行，结合遗传、生物化学和高通量生物信息学工具，以果蝇（Drosophila melanogaster）作为模式生物。 由于控制基因在发育过程中如何、何时、何地开启和关闭的机制在整个进化过程中都是保守的，因此这些结果应该会对从酵母到人类产生深远的影响。 该项目将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。 学生还学习如何提出科学假设、独立进行实验和解释结果、准备口头和书面总结并发表他们的工作以及为不同科学职业提供强大技术知识基础的技能。后生动物 COMPASS 相关的共激活剂复合物催化甲基化赖氨酸 4 (H3K4) 上的组蛋白 H3，与控制真核基因转录相关的表观遗传标记。果蝇中的 Cmi/Trr COMPASS 样复合物负责 H3K4 的单甲基化，并与对正常发育重要的转录因子合作调节增强子活性。 Trr 提供组蛋白甲基转移酶活性，而 Cmi 在两个保守簇中含有植物同源结构域锌指，这两个簇与核小体中的染色体压缩共同进化了 15 亿年。尽管在转录控制中具有保守性和重要性，但人们尚不清楚类 COMPASS 复合物如何在发育过程中启动和维持增强子活性。该项目重点研究保守的 PHD 指结构域在染色质识别和依赖于精确增强子控制的关键细胞信号传导途径中的作用。利用多功能果蝇遗传模型系统，该项目测试了广泛的假设 (1) Cmi 和同源脊椎动物蛋白中发现的聚集的 PHD 结构域贡献了重要的表观遗传组蛋白阅读器功能，可驱动基因增强子的正确启动和调节；(2)果蝇 COMPASS 样共激活子复合物调节增强子利用的时间，以整合关键的发育信号。该项目的目标之一是探索保守 PHD 簇中指状结构域的组合功能，这对于正确的增强子调节至关重要。 PHD 指结构域和靶向突变的结构建模研究，结合染色质关联的体外和体内测量，将定义 Cmi 和哺乳动物 PHD 指结构域的组蛋白识别和结合特性，并进一步阐明 COMPASS 增强子控制的机制类复合物。结合发育、遗传和分子分析（ChIP-seq、RNA-seq、染色质捕获）的第二个目标将扩大我们对体内靶基因调控的理解，帮助将特定增强子表观遗传标记与 COMPASS 样复杂功能关联起来，并提供重要的新功能。关于染色质调控保守机制的见解。

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

COMPASS Ascending: Emerging clues regarding the roles of MLL3/KMT2C and MLL2/KMT2D proteins in cancer

• DOI: 10.1016/j.canlet.2019.05.024
• 发表时间: 2019-01-01
• 期刊: CANCER LETTERS
• 影响因子: 9.7
• 作者: Fagan, Richard J.;Dingwall, Andrew K.
• 通讯作者: Dingwall, Andrew K.