Bacterial Epigenomics: Coming of Age

  title={Bacterial Epigenomics: Coming of Age},
  author={Pedro H. Oliveira},
Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological significance of methylation. ABSTRACT Epigenetic DNA… 
2 Citations

Growth Condition Dependent Differences in Methylation Implies Transiently Differentiated DNA Methylation States in E. coli

Oxford Nanopore sequencing is used to profile DNA modification marks in three natural isolates of E. coli to 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.



Deciphering bacterial epigenomes using modern sequencing technologies

Advances in DNA sequencing technology have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes.

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community

This study used single-molecule real-time and circular consensus sequencing techniques to reveal the ‘metaepigenomes’ of a microbial community in the largest lake in Japan, Lake Biwa, and revealed 22 methylated motifs, nine of which were novel.

The Epigenomic Landscape of Prokaryotes

The results reveal the pervasive presence ofDNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.

Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond

A newfound diversity of DNA modifications and their potential for combinatorial interactions indicates that the epigenetic DNA code is substantially more complex than previously thought.

Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing.

It seems likely that 4mCmethylation of GGCC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of B. cenocepacia.

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

This work presents a novel SMRT sequencing-based framework, consisting of two complementary methods, for single molecule-level detection of DNA methylation and assessment of methyltransferase activity through single molecules-level long read-based epigenetic phasing, and shows that this method yields significantly improved resolution compared to existing population-level methods.

Identification of Novel Bacterial M.SssI DNA Methyltransferase Inhibitors

A set of novel M.SssI DNMT inhibitors, once confirmed in an orthogonal DNMT assay, may serve as a starting point to identify and characterize suitable lead candidates for further drug optimization.

Diverse DNA modification in marine prokaryotic and viral communities

Novel alternative motifs in the methylation system that are highly conserved in Alphaproteobacteria are revealed, illuminating the co-evolutionary history of themethylation system and host genome and highlighting diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses.

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.

High-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K12 is performed to describe the extent of cytosine methylation of bacterial DNA at single-base resolution, and it is speculated that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines.