The formation of Heterochromatin on evolving Y chromosomes

进化中的 Y 染色体上异染色质的形成

• 批准号: 10331018
• 负责人: Doris Bachtrog
• 金额: $ 41.92万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-01-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10331018
• 关键词: 3-Dimensional; Adopted; Appearance; Architecture; Binding; Biological Assay; Candidate Disease Gene; Cataloging; Catalogs; Cell physiology; Centromere; ChIP-seq; Chromatin; Chromatin Structure; Chromosomes; Coupled; DNA; DNA Binding; DNA Transposable Elements; Data; Deposition; Development; Disease; Drosophila genus; Drosophila melanogaster; Elements; Embryo; Epigenetic Process; Euchromatin; Eukaryota; Female; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Gene Silencing; Genes; Genome; Heterochromatin; Heterogeneity; Hi-C; Human Genome; Impairment; Knowledge; Link; Maps; Modeling; Molecular; Pathway interactions; Proteins; Protocols documentation; RNA; Regulation; Repetitive Sequence; Resolution; Resources; Sequence Analysis; Sex Chromatin; Signal Transduction; Site; Small RNA; Therapeutic; Time; Transcript; Transgenic Organisms; Variant; Work; Y Chromosome; Zinc Fingers; comparative; experimental study; genome integrity; genome-wide; genome-wide analysis; histone modification; nano; promoter; small hairpin RNA; spatiotemporal; telomere; temporal measurement; zygote

Most eukaryotes harbor a high proportion of transposable elements (TEs) in their genomes. Heterochromatin, a condensed chromatin state found at domains enriched for TEs and other repetitious elements, is important for silencing TEs and maintaining the integrity of the genome. Significant portions of eukaryotic genomes, including the Y chromosome, are heterochromatic, made up largely of repetitive sequences and possessing a distinctive chromatin structure associated with gene silencing. Heterochromatic regions have a high repeat content and are characterized by specific histone modifications, but the primary sequence elements that define specific chromosomal domains as preferred sites of heterochromatin assembly are not well understood. In addition, recent work has shown that the composition and organization of Drosophila heterochromatin is spatially heterogeneous and dynamic, and a variety of cellular pathways and molecular components create genetically inert heterochromatin, but only a subset of these components has been characterized. Our proposal aims to dissect the cis- and trans-acting cellular mechanisms involved in heterochromatin formation, by studying the genome-wide establishment of heterochromatin during early development in different wildtype and transgenic Drosophila strains and species. Recent studies suggest that small RNAs ⎯ possibly derived from transposable elements (TEs) ⎯ or specialized DNA-binding zinc finger proteins contribute to heterochromatin targeting. Using a combination of comparative sequence analysis, gene expression studies, small RNA profiling and ChIP-seq experiments across development to map histone modifications associated with heterochromatin and genome interaction maps, we will characterize the spatiotemporal heterogeneity of genome-wide heterochromatin establishment across development in Drosophila melanogaster and D. miranda, and catalog the establishment and maturation of inert chromatin in 3D during early development. This will reveal which sequences serve as nucleation sites for inactive chromatin, and how silencing chromatin spreads across the genome. The initial establishment of heterochromatin is driven by RNA and protein components that are maternally deposited into the fertilized egg. We will utilize the wealth of D. melanogaster resources to study heterochromatin formation in early embryos by depleting maternally deposited candidate genes involved in establishing heterochromatin in the developing embryo. Integrating our results across aims will provide a full picture of how heterochromatin is established in the early embryo, whether the initial establishment of closed chromatin proceeds in a sequential manner, and how it spreads across the repetitive regions of the genome. We will dissect the heterogeneous and dynamic composition of Drosophila heterochromatin across development and in embryos where components of the heterochromatin pathway are depleted using transgenic approaches. This will provide a full picture of the various molecular pathways and different molecular components involved in creating genetically inert heterochromatin.

大多数真核生物的基因组中都含有高比例的转座元件（TE）。异染色质，一种浓缩染色质 在富含 TE 和其他重复元素的域中发现的状态，对于沉默 TE 和维持 TE 的完整性非常重要 基因组。 真核基因组的重要部分，包括 Y 染色体，是异染色质的， 大部分由重复序列组成，并具有与相关的独特染色质结构 基因沉默。异色区域具有高重复含量，并具有特定的特征 组蛋白修饰，但定义特定染色体结构域的主要序列元件 因为异染色质组装的优选位点尚不清楚。此外，最近的工作还有 表明果蝇异染色质的组成和组织在空间上是 异质性和动态性，以及多种细胞途径和分子成分创造 遗传惰性异染色质，但仅对这些成分的一个子集进行了表征。 我们的建议旨在剖析参与的顺式和反式作用细胞机制 异染色质形成，通过研究异染色质在全基因组范围内的建立 不同野生型和转基因果蝇品系和物种的早期发育。最近的研究 表明小 RNA ⎯— 可能源自转座元件 (TE) ⎯— 或专门的 DNA 结合锌指蛋白有助于异染色质靶向。使用组合 比较序列分析、基因表达研究、小 RNA 分析和 ChIP-seq 跨发育实验绘制与异染色质相关的组蛋白修饰和 基因组相互作用图，我们将表征全基因组的时空异质性 黑腹果蝇和米兰达果蝇发育过程中异染色质的建立，以及 对早期发育过程中惰性染色质的建立和成熟进行 3D 分类。这 将揭示哪些序列充当非活性染色质的成核位点，以及如何沉默 染色质遍布整个基因组。异染色质的最初建立是由RNA驱动的 以及母体沉积到受精卵中的蛋白质成分。我们将利用 丰富的黑腹果蝇资源，通过耗尽来研究早期胚胎中异染色质的形成 母体沉积的候选基因参与发育中异染色质的建立 胚胎。 将我们的结果整合到各个目标中将提供异染色质如何在 早期胚胎，封闭染色质的初始建立是否按顺序进行 方式，以及它如何在基因组的重复区域中传播。我们将剖析 果蝇异染色质在整个发育过程中的异质和动态组成 使用转基因技术耗尽异染色质途径成分的胚胎 接近。这将提供各种分子途径和不同的全貌 参与产生遗传惰性异染色质的分子成分。