Causes and functional consequences of chromatin evolution

染色质进化的原因和功能后果

• 批准号: 9380609
• 负责人: Mia Tauna Levine
• 金额: $ 18.38万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-11 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9380609
• 关键词: Aging; Amino Acids; Biological; Biology; Blood; CRISPR/Cas technology; Cell physiology; Cellular biology; Chromatin; Chromosome Segregation; Complex; Conflict (Psychology); Congenital Abnormality; DNA; DNA Packaging; DNA Sequence; Developmental Process; Disease; Drosophila melanogaster; Elements; Engineering; Evolution; Genes; Genetic; Genome; Genomic Instability; Genomics; Heterochromatin; Infertility; Left; Malignant Neoplasms; Mediating; Molecular; Mutation; Proteins; Race; Recurrence; Research; Sex Chromosomes; Shapes; Testing; Testis; Time; Transgenic Organisms; Trisomy; X Chromosome; Y Chromosome; arm; cancer type; chromatin protein; genetic approach; genetic element; genetic information; genome integrity; innovation; insight; pressure; programs; telomere; transmission process; tumor; virtual

PROJECT SUMMARY DNA packaging into chromatin mediates chromosome segregation, telomere protection, genome integrity, and other essential, conserved cellular processes. However, many chromatin proteins are strikingly unconserved— domains and residues evolve rapidly between even closely related species. This paradox of conserved, chromatin-dependent functions supported by fast-evolving chromatin proteins suggests that maintaining essential cellular processes requires recurrent innovation. The biological significance of this innovation is virtually unexplored. With few exceptions, we understand neither the evolutionary forces that shape contemporary chromatin proteins nor the chromatin-dependent functions modified by recent adaptation. Nevertheless, aberrant chromatin packaging is the hallmark of many blood and tumor cancers, chromosomal birth defects, and aging. My lab integrates evolutionary genomics, transgenics, cell biology, and classical genetics to identify the evolutionary pressures that drive recurrent DNA packaging innovation and the consequences for fundamental, chromatin-dependent cellular and developmental processes. We utilize the classic evolutionary framework of a “molecular arms race” between a host genome and its selfish genetic elements to gain new insights into the causes and functional consequences of DNA packaging evolution. We focus specifically on adaptively evolving chromatin proteins that package the gene-poor, repeat-rich, and fast- evolving “heterochromatic” DNA sequence enriched at telomeres and along the sex chromosomes. We hypothesize that selfish genetic elements, which thrive in heterochromatin, antagonize sex chromosome and telomere packaging proteins. Consistent with this hypothesis, these heterochromatin proteins harbor the distinct DNA signature left behind by intra-genomic conflict—the rapid accumulation of amino acid-changing mutations over evolutionary time (i.e., positive selection). To empirically test the hypothesis that recurrent bouts of selfish element evasion and heterochromatin protein suppression drive these signatures of adaptation, we engineer “evolutionary mismatches” between contemporary Drosophila melanogaster selfish elements and “resurrected” versions of fast-evolving host proteins. Specifically, we leverage CRISPR/Cas9-mediated editing to delete or to swap in an ancestrally reconstructed host gene. Our preliminary results indicate that “mal- adapted” telomere proteins de-repress telomere-embedded selfish elements. Similarly, deleting young, testis- restricted heterochromatin proteins unleashes a selfish X chromosome that sabotages Y chromosome transmission. Our “reverse evolutionary genetics” approach offers us the unique opportunity to (1) identify selfish elements and their targets and (2) elucidate the mechanisms by which selfish elements gain a transmission advantage and by which chromatin proteins suppress them. By identifying the biological causes and consequences of heterochromatin protein innovation, our research program provides new insights into how rapid evolution renders our genome vulnerable to chromatin-mediated disease and infertility.

项目概要 DNA 包装到染色质中介导染色体分离、端粒保护、基因组完整性和 其他重要的、保守的细胞过程。然而，许多染色质蛋白是惊人的不保守—— 即使是密切相关的物种之间的结构域和残基也会快速进化。这种保守的悖论， 由快速进化的染色质蛋白支持的染色质依赖性功能表明，维持 重要的细胞过程需要不断的创新。这项创新的生物学意义是 几乎未经探索。除了极少数例外，我们都不了解塑造事物的进化力量 现代染色质蛋白或最近适应所改变的染色质依赖性功能。 然而，异常的染色质包装是许多血液和肿瘤癌症、染色体 出生缺陷和衰老。我的实验室整合了进化基因组学、转基因学、细胞生物学和经典 遗传学来识别驱动周期性 DNA 包装创新的进化压力以及 对基本的染色质依赖性细胞和发育过程的影响。我们利用 宿主基因组与其自私遗传之间“分子军备竞赛”的经典进化框架 获得对 DNA 包装进化的原因和功能后果的新见解。我们 特别关注适应性进化的染色质蛋白，这些蛋白包装了基因贫乏、重复丰富和快速的基因组。 不断进化的“异染色质”DNA序列在端粒和性染色体上富集。我们 假设自私的遗传因素在异染色质中大量繁殖，拮抗性染色体， 端粒包装蛋白。与这一假设一致，这些异染色质蛋白具有 基因组内冲突留下的独特 DNA 特征——氨基酸变化的快速积累 进化过程中的突变（即正选择）。实证检验复发性假设 自私元素逃避和异染色质蛋白抑制的发作驱动了这些适应特征， 我们设计了当代果蝇自私元素和 快速进化的宿主蛋白的“复活​​”版本。具体来说，我们利用 CRISPR/Cas9 介导的编辑 删除或交换祖先重建的宿主基因。我们的初步结果表明“恶意 适应的“端粒蛋白去抑制端粒嵌入的自私元素。同样，删除年轻的睾丸- 受限异染色质蛋白释放自私的 X 染色体，破坏 Y 染色体 传播。我们的“逆向进化遗传学”方法为我们提供了独特的机会（1）识别 自私分子及其目标；（2）阐明自私分子获得利益的机制。 传输优势以及染色质蛋白通过哪些方式抑制它们。通过确定生物学原因 以及异染色质蛋白创新的后果，我们的研究项目提供了新的见解 快速的进化使我们的基因组容易受到染色质介导的疾病和不孕症的影响。