The Role of Somatic Transposition in Age-associated Genomic Instability

体细胞转座在与年龄相关的基因组不稳定中的作用

• 批准号: 9383309
• 负责人: NICOLA NERETTI
• 金额: $ 36.15万
• 依托单位: BROWN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2022-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9383309
• 关键词: Address; Adipose tissue; Affect; Age; Age of Onset; Aging; Aging-Related Process; Algorithms; Animals; Appearance; Area; Bioinformatics; Brain; Cell Aging; Cell physiology; Cells; Chromatin; Chronic Disease; Complex; Computing Methodologies; Consensus; DNA; DNA Insertion Elements; DNA Sequence; DNA sequencing; Data; Detection; Disease; Elements; Epigenetic Process; Etiology; Event; Frequencies; Future; Gene Expression; Gene Expression Regulation; Gene Mutation; Genetic; Genetic Transcription; Genome; Genomic Instability; Genomics; Goals; Heterochromatin; Heterogeneity; High-Throughput DNA Sequencing; High-Throughput Nucleotide Sequencing; Human; Human Genome; Individual; Intervention; Knowledge; Location; Methodology; Methods; Mitotic; Molecular; Molecular Computations; Mus; Muscle; Mutagenesis; Nature; Noise; Organism; Outcome; Output; Paste substance; Pattern; Pharmacology; Physiological; Positioning Attribute; Process; Publishing; RNA Splicing; Reporting; Research; Retrotransposition; Reverse Transcriptase Inhibitors; Role; Sampling; Somatic Cell; Structure; Therapeutic; Therapeutic Intervention; Tissues; Transcript; Viral; Work; base; cancer cell; derepression; experience; genome sequencing; genome-wide; human tissue; in vivo; innovation; neuronal cell body; novel; senescence; targeted treatment; tool; transcriptome; transcriptome sequencing; transcriptomics; translational impact; transposon/insertion element; whole genome

Project Summary Retrotransposable elements (RTEs) comprise approximately 45% of the human genome. RTEs are mobile DNA elements that can insert into new genomic positions using a copy and paste mechanism. This process, termed retrotransposition, can be deleterious at multiple levels by causing mutagenesis and genome structural instability, triggering epigenetic changes, and disrupting normal patterns of gene regulation. Numerous single- gene mutations in humans have been documented to result from germline retrotransposition. Organisms have evolved multiple transcriptional and post-transcriptional silencing mechanisms to protect their genomes against RTEs. Until recently RTEs were thought to be silent in the soma, however, new evidence points to activity in the brain and in cancer cells. Indeed, initial indications are that somatic retrotransposition is much more frequent than previously anticipated. We have reported that retrotransposition is activated during aging and cellular senescence, and hypothesized that it may represent a hitherto unappreciated molecular aging process. The long-term goal of our research is to determine the impact of retrotransposition on our genomes and transcriptomes during aging. As a first step, our objective in this proposal is to study, using high-throughput DNA and RNA sequencing methods, the mobilization of RTEs during cellular senescence and aging, and their impact on the transcriptome. In Aim 1 we will perform genome-wide high-throughput DNA sequencing of in senescent cells to determine where new insertions occur and to evaluate whether these events have the potential to exert deleterious effects by disrupting regions of the genome important for cell function. We have evidence that many new insertions likely occur in individual post-mitotic cells after they have ceased dividing. To comprehensively profile the spectrum and frequency of these events we will use single-cell whole genome DNA sequencing. In Aim 2 we will perform these same studies in the mouse to investigate to what degree different tissues are affected by increased retrotransposition with age. In Aim 3 we will investigate the effects of RTEs derepression and transposition on the transcriptome of senescent cells and in the aging mouse. Throughout our research plan we will apply interventive methods to modulate RTE activity to investigate the consequences on the landscape of somatic transposition as well as on the physiological function of the cells. Our research will employ innovative state-of-the-art high-throughput sequencing strategies, and we will develop new bioinformatic tools to integrate and validate the output from multiple algorithms. The information obtained will address the question: To what extent is retrotransposition damaging to the genomes of somatic cells in our bodies, and is this a plausible mechanism of aging? The experience gained and tools developed will be highly informative for future studies aimed at examining these processes directly in aging human tissues. Our efforts will also inform us whether proof-of-principle studies using interventions that inhibit retrotransposition should be investigated as potential therapeutics for age-associated diseases.

项目概要 逆转录转座元件 (RTE) 约占人类基因组的 45%。 RTE 是移动 DNA 可以使用复制和粘贴机制插入新的基因组位置的元素。这个过程，称为 逆转录转座可能通过引起突变和基因组结构在多个层面上产生有害作用 不稳定，引发表观遗传变化，并扰乱基因调控的正常模式。众多单 人类基因突变已被证明是由种系逆转座引起的。生物体有 进化出多种转录和转录后沉默机制来保护其基因组免受 RTE。直到最近，RTE 还被认为在体细胞中保持沉默，然而，新的证据表明，RTE 在体细胞中活动。 大脑和癌细胞中。事实上，初步迹象表明体细胞逆转座更为频繁 比之前预期的要多。我们已经报道逆转录转座在衰老和细胞衰老过程中被激活 衰老，并假设它可能代表了迄今为止未被认识到的分子衰老过程。这 我们研究的长期目标是确定逆转录转座对我们基因组的影响 衰老过程中的转录组。作为第一步，我们在本提案中的目标是使用高通量 DNA 进行研究 和 RNA 测序方法，细胞衰老和衰老过程中 RTE 的动员及其影响 在转录组上。在目标 1 中，我们将对衰老细胞进行全基因组高通量 DNA 测序 细胞来确定新插入发生的位置并评估这些事件是否有可能发挥作用 通过破坏对细胞功能重要的基因组区域而产生有害影响。我们有证据表明许多 在单个有丝分裂后细胞停止分裂后，可能会出现新的插入。为全面 为了分析这些事件的范围和频率，我们将使用单细胞全基因组 DNA 测序。在 目标 2 我们将在小鼠中进行相同的研究，以调查不同组织受到影响的程度 随着年龄的增长，逆转录转座增加。在目标 3 中，我们将研究 RTE 去抑制和 衰老细胞和衰老小鼠转录组的转座。在我们的整个研究计划中，我们 将采用干预方法来调节 RTE 活动，以调查对景观的影响 体细胞转座以及细胞的生理功能。我们的研究将采用创新的 最先进的高通量测序策略，我们将开发新的生物信息学工具来整合 并验证多种算法的输出。所获得的信息将解决以下问题： 逆转录转座对我们体内体细胞基因组的损害程度是否合理？ 衰老的机制？获得的经验和开发的工具将为未来的研究提供丰富的信息 旨在直接检查衰老人体组织中的这些过程。我们的努力也将告诉我们是否 应研究使用抑制逆转录转座干预措施的原理验证研究的潜力 与年龄相关的疾病的治疗。