biostudies-arrayexpressOlin SilanderEscherichia coliMinKnowhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-12128We performed genomic sequencing of whole-genome amplified DNA and native DNA isolated during growth in one of five conditions. We sequenced the DNA using Oxford Nanopore and compared the signals from the whole genome amplified DNA to the native DNA to infer sites at which the native DNA was methylated. The file names here are denoted via the strain name (SC419, SC452, or SC469), the growth condition (37C M9, 42C M9, 25C M9, rich media LB, 96 hours of growth), and in two cases, the replicate culture (M9_rep1 and M9_rep2)biostudies-arrayexpressSample Collection - Cell harvested at mid-exponential phase unless otherwise specified (e.g. at 96 hours)Sequencing - Oxford Nanopore MinIONLibrary Construction - Oxford Nanopore RBK-004Growth Protocol - Minimal glucose media (M9) or rich media (LB)Sample Treatment - grown at cold stress (25C), no stress (37C), or heat stress (42C)Nucleic Acid Extraction - Promega Wizard kitOrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSequence Alignment - aligned with minimap2Data Transformation - normalisation by sampling reads across the genome to ensure even genomic coverageUnknownTranscriptomicsGenomicsProteomicsMinIONDNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. It is not well established whether methylation also frequently serves a more general epigenetic function, modifying bacterial phenotypes in a heritable manner. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of E. coli . We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiates into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results provide new insights into the dynamics of methylation during bacterial growth, and provide evidence of differentiated cell states, a transient analogue to what is observed in the differentiation of cell types in multicellular organisms.methylation profiling by high throughput sequencingEscherichia coliGrowth Condition Dependent Differences in Methylation Implies Transiently Differentiated DNA Methylation States in E. coliGeorgia Breckell, Olin K. SilanderOlin SilanderfalseGenomic sequencing of E. coli natural isolates to identify methylated basesWe performed genomic sequencing of whole-genome amplified DNA and native DNA isolated during growth in one of five conditions. We sequenced the DNA using Oxford Nanopore and compared the signals from the whole genome amplified DNA to the native DNA to infer sites at which the native DNA was methylated. The file names here are denoted via the strain name (SC419, SC452, or SC469), the growth condition (37C M9, 42C M9, 25C M9, rich media LB, 96 hours of growth), and in two cases, the replicate culture (M9_rep1 and M9_rep2)2022-09-22T00:00:00Z2022-10-10T20:05:18.074Z2022-10-10T20:05:18.074ZE-MTAB-12128ERP140502EFO_0002944EFO_0004170EFO_0003789EFO_0002761EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_000396910.1101/2022.03.24.485589