Chromatin diminution in nematodes

线虫中的染色质减少

• 批准号: 8898435
• 负责人: RICHARD E. DAVIS
• 金额: $ 31.33万
• 依托单位: UNIVERSITY OF COLORADO DENVER
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-20 至 2020-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8898435
• 关键词: Address; Area; Ascaris; Ascaris suum; Biological; Biology; Cell Lineage; Cell Nucleus; Cells; Centromere; ChIP-seq; Chromatin; Chromosomal Breaks; Chromosome Segregation; Chromosome Structures; Chromosomes; Complex; DNA; DNA Sequence; Data; Deposition; Development; Drug Targeting; Embryo; Eukaryota; Gene Expression; Genes; Genome; Genome Stability; Histone H3; Human; Immunohistochemistry; Kinetochores; Length; Location; Maintenance; Microtubules; Mitosis; Nematoda; Nuclear; Organism; Parasites; Parasitic nematode; Pathogenesis; Pathway interactions; Pharmacotherapy; Play; Process; Property; Proteins; Public Health; Resources; Role; Site; Small RNA; Somatic Cell; Staging; Testing; Tissues; Variant; base; centromere protein A; insight; neuronal cell body; new technology; novel; pathogen; programs; public health relevance; research study; segregation; socioeconomics; targeted sequencing; tool

 DESCRIPTION (provided by applicant): Ascaris is an important human pathogen infecting ~1 billion people. Understanding genome maintenance, genome alterations, and the role of these alterations in gene expression in Ascaris is important for understanding its biology and pathogenesis. Genomes rarely change. However, a few organisms undergo the wholesale genome change called chromatin diminution, a programmed process that eliminates specific DNA sequences from the genome. Many aspects of the phenomenon remain a mystery. We previously leveraged new technologies to characterize chromatin diminution in the parasitic nematode, Ascaris, We demonstrated that thirteen percent of the genome of the parasitic nematode Ascaris suum is eliminated in somatic cell lineages during the third through fifth cleavage (4 to 16 cell stage), while the germline genome remains intact. Unique sequences (including ~700 genes) are lost during chromatin diminution to form the somatic genome. The eliminated genes we identified are primarily expressed in the Ascaris germline and early embryo. This leads us to suggest that chromatin diminution in Ascaris is the essential, irreversible mechanism for silencing a subset of germline and early embryo expressed genes in somatic tissues required for distinguishing between the germline and soma. More than 100 years after it was first discovered, the mechanisms for how specific Ascaris chromosomal regions are targeted and selected for elimination or retention remain unknown. Two key mechanistic questions are: 1) How are the locations of the chromosomal breaks and boundary regions identified, marked, and cut? 2) What determines which chromosomal regions are retained or lost? We have formulated hypotheses regarding these key questions based on our preliminary data and propose to test these hypotheses in the specific aims. In preliminary experiments, we have shown that during Ascaris chromatin diminution, only those chromosomes that will be retained have extensive deposition of CENP-A (the key factor required for centromere formation and kinetochore assembly), whereas chromosomes destined for elimination have little CENP-A. This suggests a potential mechanistic explanation for how specific portions of chromosomes can be marked for retention or elimination. We propose to investigate the deposition and role of CENP-A as a mechanism for differential chromosome segregation in chromatin diminution. We further hypothesize that small RNAs and Argonautes play a role in Ascaris chromatin diminution. We have shown that specialized Argonautes associate with chromosomes that will be retained in Ascaris diminution mitosis, but not with chromosomes that are destined for elimination. We propose to investigate the role of these Argonautes and their associated small RNAs in nematode chromatin diminution and chromosome segregation. Analysis of Ascaris chromatin diminution promises to provide profound insights into genome stability, centromere specification, chromosome segregation and the contribution of Argonautes and small RNAs to chromosome function, segregation, and chromatin diminution. Our studies will not only provide insight into DNA elimination and its importance in nematodes, but is likely to increase our understanding of the germline, chromosomes, and genome biology in general. Finally, a better understanding of Ascaris chromosome organization and segregation and its small RNA pathways that differ from its human host may provide new insight into needed drug targets.

 描述（由申请人提供）：蛔虫是一种重要的人类病原体，感染约 10 亿人。了解蛔虫的基因组维护、基因组改变以及这些改变在基因表达中的作用对于了解其生物学和发病机制非常重要。然而，一些生物体经历了称为染色质减少的大规模基因组变化，这是一种从基因组中消除特定 DNA 序列的程序化过程，我们之前利用新技术来表征这一现象的许多方面仍然是个谜。寄生线虫蛔虫中的染色质减少，我们证明了寄生线虫蛔虫基因组的 13% 在第三至第五次卵裂（4 至 16 细胞阶段）的体细胞谱系中被消除，而种系基因组保持完整。在染色质减少形成体细胞基因组的过程中，独特的序列（包括约 700 个基因）丢失了，我们确定的被消除的基因主要在体细胞中表达。蛔虫种系和早期胚胎 这使我们认为，蛔虫中的染色质减少是 100 多年后体细胞组织中区分种系和体细胞所需的部分种系和早期胚胎表达基因沉默的重要的、不可逆的机制。首次发现后，如何靶向并选择特定蛔虫染色体区域以消除或保留的机制仍然未知：1）位置如何。 2）什么决定了哪些染色体区域被保留或丢失？我们根据我们的初步数据提出了关于这些关键问题的假设，并建议在特定目标中检验这些假设。在初步实验中，我们已经表明，在蛔虫染色质减少过程中，只有那些被保留的染色体才会大量沉积CENP-A（着丝粒形成和着丝粒组装所需的关键因子），而注定要消除的染色体几乎没有 CENP-A，这为如何标记染色体的特定部分以保留或消除提出了潜在的机制解释，我们研究了 CENP-A 作为差异染色体分离机制的沉积和作用。我们进一步研究了小 RNA 和 Argonautes 在蛔虫染色质减少中的作用。我们已经证明，特殊的 Argonautes 与保留在蛔虫中的染色体相关。我们建议研究这些 Argonautes 及其相关小 RNA 在线虫染色质减少和染色体分离中的作用，从而为蛔虫染色质减少提供深刻的见解。我们的研究不仅提供了染色体的规范、染色体分离以及 Argonautes 和小 RNA 对染色体功能、分离和染色质减少的贡献。深入了解 DNA 消除及其在线虫中的重要性，但可能会增加我们对种系、染色体和基因组生物学的总体了解，最后，更好地了解蛔虫染色体组织和分离及其不同于人类的小 RNA 途径。宿主可能会为所需的药物靶点提供新的见解。