High Resolution Characterization of Bacterial Epigenomes and Microbiome

项目摘要/摘要 我的长期目标是全面了解细菌的多样性、异质性和功能 表观基因组在基础科学和生物医学方面的影响。在细菌世界里，甲基化腺嘌呤 而胞嘧啶残基之前被认为只与下列限制修饰系统有关 提供抵御外来基因组入侵的防御机制。然而，越来越多的证据支持这一点 它们还在调节细胞周期、基因表达、毒力、产孢量、生物被膜等方面发挥重要作用。 形成、微生物-宿主相互作用和抗生素耐药性。高效高分辨率的细菌图谱分析 直到单分子实时检测技术(SMRT)的出现，DNA甲基化才成为可能 测序。这项技术使我们能够在单核苷酸上鉴定第一个细菌甲基组 决议。越来越多的细菌正在被定性，从中有了令人兴奋的发现 已经做好了。然而，这些研究也揭示了细菌的意想不到的复杂性和多样性 甲基组，呼吁开发新技术、分析和实验方法，以便 更全面地了解细菌表观基因组。在这个R35项目中，我们将在我们的进展基础上再接再厉 在过去的五年里，我做出了进一步发展更广泛范围的综合研究计划的努力 整合两个正在进行的重点R01项目。最重要的主题是地图， 细菌甲基组的特征和开发，以更好地了解单个细菌和 微生物群落。我们将沿着四个相辅相成的主题发展这一研究计划。第一，要 更全面地绘制细菌甲基组图，我们将继续创新技术开发，以 在完整性和分辨率方面都有重大改进。第二，做得更好 阐明细菌的表观遗传调控，我们将结合计算和实验方法来 确定不同细菌生物体中特定甲基化事件的优先顺序和功能特征。第三, 为了系统地将细菌甲基组研究从培养的单个细菌扩展到微生物组，我们将 描述细菌表观遗传学对不同类型扰动的反应。最后，我们将提供 为便于广泛使用，我们将软件作为一个集成包进行开发，并组织相关会议 帮助更广泛社区的教程。结合在一起，我们预计这个项目将提供广泛的 适用于微生物学和微生物群落的方法，并发现新的生物学见解 单个细菌和微生物组的表观遗传调控。

PROJECT SUMMARY/ABSTRACT My long term goal is to comprehensively understand the diversity, heterogeneity and functions of bacterial epigenomes both in terms of basic science and biomedical impact. In the bacterial world, methylated adenine and cytosine residues was previously thought to be only associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. However, increasing evidence supports that they also play important roles in the regulation of cell cycle, gene expression, virulence, sporulation, biofilm formation, microbe-host interaction and antibiotic resistance. Efficient and high resolution profiling of bacterial DNA methylation events has not been possible until the advent of Single Molecule Real-Time (SMRT) sequencing. This technique enabled us to characterize the first bacterial methylome at single nucleotide resolution. A fast growing number of bacteria are being characterized, from which exciting discoveries have been made. However, these studies have also revealed unexpected complexity and diversity in bacterial methylomes, calling for the development new technologies, analytical and experimental methods in order to more comprehensively understand bacterial epigenomes. In this R35 project, we will build on the progress we have made in the past five years to further develop an integrated research program with a broader scope integrating two ongoing focused R01 projects. The overarching theme is focused on the mapping, characterization and exploitation of bacterial methylomes to better understand individual bacteria and microbiome community. We will develop this research program along four complementary themes. First, to more comprehensively map bacterial methylome, we will continue to innovate on technology development to make significant improvements both in terms of in terms of completeness and resolution. Second, to better elucidate epigenetic regulation in bacteria, we will combine computational and experimental approaches to prioritize and functionally characterize specific methylation events across different bacterial organisms. Third, to systematically expand bacterial methylome research from cultured individual bacteria to microbiome, we will characterize bacterial epigenetics in response to different types of perturbations. Last, we will provide the software we develop as an integrated package to ease broad usage, and organize relevant conference tutorials to help the broader community. Combined together, we expect this project to provide broadly applicable methods to the microbiology and microbiome community, and discover novel biological insights into epigenetic regulation in individual bacteria and microbiome.