Methods for Multiscale and Integrative Characterization of Bacterial Epigenomes

细菌表观基因组的多尺度和综合表征方法

• 批准号: 9334272
• 负责人: Gang Fang
• 金额: $ 43.94万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-08 至 2020-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9334272
• 关键词: Address; Adenine; Antibiotic Resistance; Bacteria; Bacterial DNA; Bacterial Genome; Biodiversity; Biological; Biological Process; Biotechnology; Bypass; Cell Cycle Regulation; Collection; Communicable Diseases; Communities; Complement; Computer software; Cytosine; DNA Methylation; DNA Modification Process; DNA Restriction-Modification Enzymes; Data; Defense Mechanisms; Detection; Development; Dimensions; Discipline; Dissection; Drug resistance; Environment; Epigenetic Process; Event; Gene Expression; Gene Expression Regulation; Generations; Genes; Genetic Transcription; Genome; Genomic Segment; Global Change; Goals; Health; Heterogeneity; Human Microbiome; Immune system; Invaded; Mediating; Metabolism; Metagenomics; Methodology; Methods; Methylation; Molecular; Molecular Profiling; Mus; Nature; Nucleotides; Phenotype; Play; Population; Process; Research; Resolution; Role; Sequencing By Hybridizations; Software Tools; Systems Biology; Techniques; Technology; Testing; Time; Virulence; Work; base; clinically relevant; clinically significant; commensal microbes; design; epigenetic variation; epigenome; epigenomics; innovation; insight; interest; method development; methylome; new technology; novel; pathogen; programs; public health relevance; response; single molecule; statistics; tool; whole genome

 DESCRIPTION (provided by applicant): In the bacterial world, methylated adenine and cytosine residues are most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. In addition, some forms of them also play important roles in the regulation of cell cycle, gene expression, virulence, and antibiotic resistance. Efficient and high resolution profiling of bacterial methylation events has not been possible until the recent advent of Single Molecule Real-Time sequencing (SMRTseq) technique that can detect N6-methyladenine (6mA) and 4-methylcytosine (4mC) residues, the two major types of methylation in the bacterial world, in addition to 5-methylcytosine (5mC). This technique enabled us to characterize one of the first whole-genome bacterial methylomes, the entire set of methylations, at single- nucleotide resolution. A fast growing number of bacteria are being characterized, revealing unexpected degrees of complexity and diversity in bacterial methylomes. However, existing methods using SMRTseq data mainly carried out at population levels cannot resolve epigenetic heterogeneity that often exists in a single population and empowers bacteria to better adapt to changing conditions. Also, SMRTseq has its own limitations that call for combinations with other existing complementary techniques. Last but not least, previous studies have mostly focused on gene-specific mechanisms of methylation-mediated regulation of gene expression, which only account for a very small fraction of global changes of gene expression induced by epigenetic perturbations. Motivated by both the unique advantages of SMRTseq and these emerging challenges, we propose to develop novel methods for multiscale detection and integrative functional characterization of bacterial DNA methylation. The novel methods will combine innovative developments across multiple disciplines: hybrid sequencing design, multi-dimensional molecular profiling, statistics and systems biology. They will enable the better understanding of the mechanisms and dynamics of epigenetic heterogeneity in different types of bacteria, and advance the integration of epigenetic variations into a systems biology framework for bacteria. We will apply these methods to study a diverse collection of bacteria with different methylome complexity, methylation-related phenotypes and clinical significance. We will also implement all the methods developed over the project period in an integrated program for the broader research community. The impact will not be restricted to current research on bacterial methylomes, but also to bacterial research in which DNA methylations are assumed to be independent of the biological processes of interest, partly due to the lack of techniques and tools. These include some that have important clinical relevance: virulence, antibiotic resistance and persistence that are causing critical health crisis

 描述（由适用提供）：在细菌世界中，甲基化的腺嘌呤和胞嘧啶耐药性最常与限制模型系统有关，这些系统提供了防御机制，以防止入侵外国基因组。此外，其中某些形式在细胞周期，基因表达，病毒和抗生素耐药性的调节中也起着重要作用。直到最近可以检测N6-甲基二氨酸（6MA）和4-甲基二氨基（4MC）保留的单分子实时测序（SMRTSEQ）技术的高效且高分辨率的分析，直到单分子实时测序（SMRTSEQ）技术的近期推进，该技术是细菌世界中两种主要类型的甲基化。这项技术使我们能够表征单核苷酸分辨率的第一个全基因组细菌之一，即整个甲基化。快速增长的细菌是 被表征，揭示了细菌甲基组的复杂性和多样性的意外程度。但是，使用SMRTSEQ数据主要在人群水平上进行的现有方法无法解决经常存在于单个人群中的表观遗传异质性，并使细菌能够更好地适应不断变化的条件。此外，SMRTSEQ有自己的局限性，可以与其他现有的完整技术组合。最后但并非最不重要的一点是，以前的研究主要集中在甲基化介导的基因表达调节的基因特异性机制上，这仅是表观遗传扰动引起的基因表达的全球变化的很小一部分。由SMRTSEQ的独特优势和这些新出现的挑战的动机，我们建议开发新的多尺度检测方法和细菌DNA甲基化的综合功能表征。这种新方法将结合跨多个学科的创新发展：混合测序设计，多维分子分析，统计和系统生物学。它们将更好地了解不同类型细菌中表观遗传异质性的机制和动力学，并将表观遗传变异的整合到细菌的系统生物学框架中。我们将应用这些方法来研究具有不同甲基化复杂性，与甲基化相关表型和临床意义不同的细菌收集。我们还将在项目期间为更广泛的研究社区的集成计划中实施所有开发的方法。影响不仅限于当前对细菌甲基瘤的研究，而且还限于细菌研究，其中假定DNA甲基化为与感兴趣的生物学过程无关，部分原因是缺乏技术和工具。其中包括一些具有重要临床相关性的：病毒，抗生素耐药性和持续性，导致严重的健康危机