High Resolution Characterization of Bacterial Epigenomes and Microbiome

项目概要/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。在细菌世界中，甲基化腺嘌呤 而胞嘧啶残基以前被认为只与限制修饰系统有关， 提供一种防御机制来抵御外来基因组的入侵。然而，越来越多的证据表明， 它们在细胞周期、基因表达、毒力、孢子形成、生物被膜等方面也起着重要的调节作用 形成、微生物-宿主相互作用和抗生素抗性。高效和高分辨率的细菌谱分析 DNA甲基化事件直到单分子实时（SMRT）的出现才成为可能。 测序这项技术使我们能够表征第一个细菌甲基化组在单核苷酸 分辨率越来越多的细菌正在被鉴定，从中有了令人兴奋的发现。 被制造了。然而，这些研究也揭示了细菌中意想不到的复杂性和多样性， 甲基化，呼吁开发新技术，分析和实验方法，以 更全面地了解细菌表观基因组。在这个R35项目中，我们将在我们所取得的进展的基础上， 在过去的五年里，我们进一步发展了一个范围更广的综合研究计划， 整合两个正在进行的重点R 01项目。首要主题是侧重于绘图， 细菌甲基化组的表征和开发，以更好地了解单个细菌， 微生物群落我们将沿着沿着四个互补的主题发展这个研究计划。一是 更全面地绘制细菌甲基化组，我们将继续在技术开发上创新， 在完整性和分辨率方面都有显著的改进。第二，为了更好 阐明细菌中的表观遗传调控，我们将结合联合收割机计算和实验方法， 区分不同细菌生物体中的特定甲基化事件的优先级并在功能上表征。第三、 为了系统地将细菌甲基化组研究从培养的单个细菌扩展到微生物组，我们将 表征细菌表观遗传学对不同类型扰动的响应。最后，我们将提供 我们开发软件作为一个集成包，以方便广泛使用，并组织相关会议 教程，以帮助更广泛的社区。结合在一起，我们预计该项目将提供广泛的 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， 在个体细菌和微生物组中的表观遗传调节。

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.