Chromatin Diminution in Ascaris

描述（由申请人提供）：基因组的维护和稳定性是必不可少的，生物体的基因组很少发生变化。与之形成鲜明对比的是，染色质减少是一个程序化的过程，它从基因组中消除特定的DNA序列。在寄生线虫蛔虫（Ascaris）中，25%的基因组在体细胞谱系的第3至第5次卵裂（4至16个细胞阶段）中被消除，而种系基因组保持完整。在染色质减少过程中，重复和独特的序列（基因）都丢失了。这种消除导致染色体断裂和染色体末端的丢失，以及新染色体的产生。这一过程被认为是发育和种系建立所必需的一种基因沉默形式，然而，在蛔虫早期发育过程中，这种程序性消除如何促进种系向体细胞的转变，在发现100多年后仍然是一个谜。此外，染色体区域如何靶向消除的机制，染色体断裂的位置，DNA断裂如何产生，哪些序列丢失，以及如何选择丢失或保留特定序列的机制仍然未知。新的技术和方法将利用蛔虫独特的生物学和工具来检查染色质减少，定义消除和重新排列的序列，检查与减少相关的染色质修饰，测试消除的DNA在细胞分裂过程中如何不分离的新假设，并进一步了解小rna在染色质减少中的潜在作用。我们建议，蛔虫体细胞和生殖系基因组的全面比较将使我们能够第一次解决一些关于减少的核心问题，包括：发生了什么重排？哪些基因丢失了？断点之间是否存在共同的特性，可以让您了解如何定义断点？染色体断点是否在所有个体中大致相同的位置，还是在不同的个体中有所不同？此外，我们提出表观遗传染色质变化与减少过程有关，蛔虫22G内切sirna和相关的Argonaute CSR-1 RISC复合体通过标记蛔虫染色体区域以保留或消除来促进染色质减少。蛔虫是一种重要的人类病原体，它感染了超过10亿人。了解蛔虫基因的维持、改变以及基因表达改变的作用对于了解这种人类寄生虫的生物学非常重要。此外，了解DNA减少的分子调控、机制和后果不仅有助于深入了解DNA消除及其在线虫中的重要性，而且可能增加我们对这一现象以及生殖系、染色体和基因组生物学的总体理解。

DESCRIPTION (provided by applicant): Genome maintenance and stability are essential, and an organism's genome rarely changes. In striking contrast, chromatin diminution is a programmed process that eliminates specific DNA sequences from the genome. In the parasitic nematode, Ascaris, 25% of the genome is eliminated in the somatic lineages during the 3rd through 5th cleavage (4 to 16 cell stage), while the germline genome remains intact. Both repetitive and unique sequences (genes) are lost during chromatin diminution. The elimination results in chromosome breakage and the loss of chromosome termini as well as the generation of new chromosomes. This process is thought to be a form of gene silencing necessary for development and germline establishment, yet how this programmed elimination contributes to the germline to somatic transition in early Ascaris development remains a mystery more than 100 years after it was discovered. Furthermore, the mechanisms for how chromosomal regions are targeted for elimination, where the sites of chromosomal breakage are located, how DNA breaks are made, what sequences are lost, and how specific sequences are selected to be lost or retained remain unknown. New technologies and approaches will be leveraged to exploit the unique biology and tools in Ascaris to examine chromatin diminution and define eliminated and re-arranged sequences, to examine chromatin modifications associated with diminution, to test a new hypothesis for how eliminated DNA is not segregated during cell division, and to gain additional insight into the potential role of small RNAs in chromatin diminution. We propose that a comprehensive comparison of the somatic and germline genome in Ascaris will permit us to address for the first time a number of central questions regarding diminution including: What rearrangements occur? What genes are lost? Are there common features among the breakpoints that provide insight into how the breakpoints are defined? Are the chromosomal breakpoints at the same approximate location in all individuals or do they vary in different individuals? Furthermore, we propose that epigenetic chromatin changes are associated with the process of diminution and that Ascaris 22G endo-siRNAs and the associated Argonaute CSR-1 RISC complex contribute to chromatin diminution by marking regions of Ascaris chromosomes for retention or elimination. Ascaris is an important human pathogen as it infects over a billion people. Understanding gene maintenance, alterations, and the role of alterations in gene expression in Ascaris is important in understanding the biology of this human parasite. Furthermore, understanding the molecular regulators, mechanism, and consequences of diminution will not only provide insight into DNA elimination and its importance in nematodes, but is likely to increase our understanding of this phenomenon and germline, chromosome, and genome biology in general. PUBLIC HEALTH RELEVANCE: Parasitic nematodes remain a significant public health problem in many parts of the world. Ascaris alone infects upwards of 1 billion people and hinders socioeconomic development in endemic areas. We will carry out studies on an unusual form of programmed DNA elimination in Ascaris, chromatin diminution, important in the biology of the organism.