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