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.

大多数真核生物在其基因组中含有高比例的转座因子（TE）。异染色质，一种浓缩的染色质 在富含TE和其他重复元件的结构域中发现的这种状态，对于沉默TE和维持DNA序列的完整性是重要的。 基因组 真核生物基因组的重要部分，包括Y染色体，是异染色质的， 大部分是重复序列，并具有与之相关的独特染色质结构， 基因沉默异染色质区域具有高重复含量，并且具有特异性的特征。 组蛋白修饰，但定义特定染色体结构域的一级序列元件 因为异染色质装配的优选位点还不清楚。此外，最近的工作 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，但只有一个子集的这些组件已被确定。 我们的建议旨在剖析涉及的顺式和反式作用的细胞机制， 异染色质的形成，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种的早期发育。最近的研究 提示小RNA可能来源于转座因子（TEs）， DNA结合锌指蛋白有助于异染色质靶向。结合使用 比较序列分析、基因表达研究、小RNA分析和ChIP-seq 在整个发育过程中进行实验，以绘制与异染色质相关的组蛋白修饰， 基因组相互作用图，我们将描述时空异质性的基因组范围内的 异染色质在果蝇和果蝇发育过程中的建立。米兰达，和 对早期发育过程中惰性染色质的建立和成熟进行3D编目。这 将揭示哪些序列作为非活性染色质的成核位点， 染色质遍布整个基因组。异染色质最初的形成是由RNA驱动的 和蛋白质成分，这些成分是母体沉积到受精卵中的。我们将利用 财富D黑腹动物资源研究异染色质形成的早期胚胎， 在发育中参与异染色质形成的母体沉积的候选基因 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细胞中建立的完整图像 在早期胚胎中，封闭染色质的最初建立是否以顺序的方式进行， 方式，以及它如何在基因组的重复区域中传播。我们将解剖 果蝇异染色质在不同发育阶段和不同发育阶段中异质性和动态组成 使用转基因技术消除异染色质途径组分的胚胎 接近。这将提供各种分子途径的全貌和不同的 参与产生遗传惰性异染色质的分子成分。