Chromatin diminution in nematodes

线虫中的染色质减少

• 批准号: 9204381
• 负责人: RICHARD E. DAVIS
• 金额: $ 57.49万
• 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/9204381
• 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; Testing; Tissues; Variant; base; centromere protein A; chromosomal location; experimental study; insight; neuronal cell body; new technology; new therapeutic target; novel; pathogen; public health relevance; segregation; socioeconomics; 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。基因组很少改变。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。这种现象的许多方面仍然是个谜。我们之前利用新技术来表征寄生线虫蛔虫中染色质减少的特征，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。在形成体细胞基因组的染色质减少过程中，独特的序列（包括约 700 个基因）会丢失。我们确定的消除基因主要在蛔虫种系和早期胚胎中表达。这使我们认为蛔虫中的染色质减少是沉默体细胞组织中区分种系和体细胞所需的种系和早期胚胎表达基因的子集的重要的、不可逆的机制。在首次发现蛔虫100多年后，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。两个关键的机制问题是：1）如何识别、标记和切割染色体断裂和边界区域的位置？ 2）什么决定了哪些染色体区域被保留或丢失？我们根据初步数据对这些关键问题提出了假设，并建议在特定目标中检验这些假设。在初步实验中，我们发现，在蛔虫染色质减少过程中，只有那些将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），而注定要被消除的染色体则几乎没有CENP-A。这为染色体的特定部分如何被标记为保留或消除提供了潜在的机制解释。我们建议研究 CENP-A 的沉积和作用，作为染色质减少中差异染色体分离的机制。我们进一步假设小 RNA 和 Argonautes 在蛔虫染色质减少中发挥作用。我们已经证明，特殊的阿尔戈英雄与蛔虫缩小有丝分裂中保留的染色体相关，但与注定要消除的染色体无关。我们打算研究这些 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。对蛔虫染色质减少的分析有望为基因组稳定性、着丝粒规范、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提供深刻的见解。我们的研究不仅将深入了解 DNA 消除及其在线虫中的重要性，而且可能会增加我们对种系、染色体和基因组生物学的总体理解。最后，更好地了解蛔虫染色体组织和分离及其不同于人类宿主的小RNA途径可能会为所需的药物靶点提供新的见解。