Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli

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dc.citation.issue2
dc.citation.volume13
dc.contributor.authorBreckell GL
dc.contributor.authorSilander OK
dc.coverage.spatialEngland
dc.date.accessioned2024-01-08T23:45:14Z
dc.date.accessioned2024-07-25T06:32:20Z
dc.date.available2022-12-01
dc.date.available2024-01-08T23:45:14Z
dc.date.available2024-07-25T06:32:20Z
dc.date.issued2023-02
dc.description.abstractDNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia 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 entire 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 differentiate 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 show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
dc.description.confidentialfalse
dc.description.notesBreckell, G. L., Silander, O. K. “Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli” First published in “G3”, December 2022. 10.1093/g3journal/jkac310en
dc.edition.editionFebruary 2023
dc.format.paginationjkac310-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/36454087
dc.identifier.citationBreckell GL, Silander OK. (2023). Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli.. G3 (Bethesda). 13. 2. (pp. jkac310-).
dc.identifier.doi10.1093/g3journal/jkac310
dc.identifier.eissn2160-1836
dc.identifier.elements-typejournal-article
dc.identifier.issn2160-1836
dc.identifier.numberjkac310
dc.identifier.pii6858946
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70376
dc.languageeng
dc.publisherOxford University Press on behalf of the Genetics Society of America
dc.publisher.urihttps://academic.oup.com/g3journal/article/13/2/jkac310/6858946
dc.relation.isPartOfG3 (Bethesda)
dc.rights(c) The author/sen
dc.rights.licenseCC BYen
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectE coli
dc.subjectDNA methylation
dc.subjectnanopore
dc.subjectDNA Methylation
dc.subjectEscherichia coli
dc.subjectGenomics
dc.subjectCell Differentiation
dc.subjectDNA
dc.subjectEpigenesis, Genetic
dc.titleGrowth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli
dc.typeJournal article
pubs.elements-id458508
pubs.organisational-groupOther
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