Roles for Global Chromatin Structure in C. elegans Longevity

描述(由申请人提供)：最近的研究揭示了许多进化上保守的遗传途径对长寿很重要。相比之下，人们对表观遗传变化在生物衰老中的作用知之甚少。表观遗传学变化，如DNA甲基化水平或模式的改变和翻译后组蛋白修饰，已经在各种老化的哺乳动物组织和老化的人类同卵双胞胎中观察到。在酵母、蠕虫和苍蝇中，几种组蛋白修饰酶已被证明在决定寿命方面发挥关键作用。因此，新出现的证据表明染色质结构和寿命之间存在机械联系。这项建议的目的是探索线虫的全球染色质结构如何随年龄的变化而变化。由于DNA甲基化在线虫中几乎检测不到，组蛋白的翻译后修饰可能是线虫染色质状态的主要调节机制。线虫的整体染色质状态如何随着年龄的变化而变化是完全未知的。在目标1中，我们建议使用芯片序列技术来确定不同年龄线虫中几种主要的组蛋白修饰的基因组分布和丰度。在目标2中，我们建议使用RNA-seq技术来综合检测不同年龄线虫的转录图谱。尽管先前已经使用微阵列研究来检测线虫衰老过程中的转录图谱，但微阵列研究具有多方面的局限性，并且RNA-SEQ技术通常被认为提供了更全面的基因表达图谱的视图。我们计划比较CHIP-SEQ和RNA-SEQ的结果，以高度自信地识别显示年龄相关变化的基因，即使是低水平表达的基因和那些只显示微妙表达变化的基因。比较CHIP-SEQ和RNA-SEQ的结果还将揭示选择性剪接转录本以及以前未被注释的新转录本(包括非编码RNA)中随年龄的变化。由于先前基因表达研究的局限性，这些变化以前可能没有揭示出来。比较CHIP-SEQ和RNA-SEQ数据还将提供对染色质状态的洞察，这有助于确定依赖年龄的mRNA表达变化。一些与年龄相关的组蛋白修饰和mRNA表达变化可能是衰老的有价值的分子标记物。重要的是，其中一些变化可能指向决定长寿的监管因素。我们提出的研究将首次在全球范围内描述染色质状态如何随着线虫的年龄而受到影响。考虑到线虫和哺乳动物之间调节寿命的遗传途径之间的高度保守性，我们预计影响线虫寿命的一些表观遗传机制也将在哺乳动物中保守。与公共健康相关：该应用程序建议研究基因组的某些特殊功能如何影响衰老，这些特殊功能通过多轮细胞分裂稳定遗传，但不涉及DNA序列的变化。这些表观遗传特征通常涉及DNA或有助于紧凑DNA的蛋白质的特定装饰，它们的适当维护对于细胞和生物保持某些特征至关重要。到目前为止，人们对这些表观遗传特征如何影响衰老和年龄相关性疾病知之甚少，我们的研究建议使用两种不同的综合方法来研究这些特征的变化如何影响强大的模式系统土壤线虫的寿命。我们提议的研究可能会导致未来的治疗开发，旨在改善健康衰老和减轻年龄依赖性疾病。

DESCRIPTION (provided by applicant): Recent research has revealed many evolutionarily conserved genetic pathways important for longevity. In contrast, relatively little is known about the role of epigenetic changes in organismal aging. Epigenetic changes, such as altered levels or patterns of DNA methylation and post-translational histone modifications, have been observed in a variety of aging mammalian tissues and in aging human monozygotic twins. In yeast, worms, and flies, several histone modifying enzymes have been shown to play critical roles in determining longevity. Thus, emerging evidence points to a mechanistic link between chromatin structure and longevity. The goal of this proposal is to explore how global chromatin structure changes with aging in C. elegans. Because DNA methylation is nearly undetectable in C. elegans, post-translational modification of histones is likely the major regulatory mechanism of chromatin state in C. elegans. How the global chromatin state changes with age in C. elegans is completely unknown. In Aim 1, we propose to determine the genomic distribution and abundance of several major histone modifications in C. elegans of different age using the ChIP-seq technique. In Aim 2, we propose to comprehensively examine the transcriptional profiles of C. elegans at different age using the RNA-seq technique. Although the transcriptional profiles of C. elegans through aging have previously been examined using microarray studies, microarray studies have multiple limitations and the RNA-seq technique is generally considered to provide a much more comprehensive view of gene expression profiles. We plan to compare the ChIP-seq and the RNA-seq results to identify, with high confidence, the genes that show age-dependent changes, even for genes that are expressed at low levels and those that only show subtle expression changes. Comparing the ChIP-seq and the RNA-seq results will also reveal age-dependent changes in alternatively spliced transcripts, as well as novel transcripts that have not been previously annotated, including non- coding RNAs. These changes are likely not revealed previously due to the limitations of previous gene expression studies. Comparing the ChIP-seq and RNA-seq data will also provide insights into the chromatin state that help specify age-dependent mRNA expression changes. Some of the age-dependent histone modification and mRNA expression changes may represent valuable molecular markers of aging. Importantly, some of these changes may point to regulatory factors that contribute to longevity determination. Our proposed research will be the first to globally profile how chromatin state is impacted as C. elegans age. Considering the high degree of conservation between the genetic pathways that modulate longevity in C. elegans and mammals, we anticipate that some of the epigenetic mechanisms that impact C. elegans longevity will also be conserved in mammals. PUBLIC HEALTH RELEVANCE: This application proposes to investigate how aging is impacted by certain special features of the genome that are stably inherited through multiple rounds of cell division, but do not involve changes in the DNA sequence. These epigenetic features often involve specific decorations of the DNA or the proteins that help compact DNA, and their proper maintenance is critically important for cells and organisms to maintain certain characteristics. To date, very little is known about how these epigenetic features affect aging and age-dependent diseases, and our research proposes to use two different comprehensive approaches to examine how changes in these features affect longevity in the powerful model system soil nematode. Our proposed research may lead to future therapeutic development that aims to improve healthy aging and alleviate age-dependent diseases.