Pan-Epigenome Browser

Compare the epigenetic modifications of a collection of microbes

The incredible diversity of microbial life is not only driven by the different genes in their genomes, but also by the chemical structure of the DNA which encodes those genes – their “epigenome.”
The Pan-Epigenome Browser makes it easy to compare the epigenetic modifications from a group of organisms, identifying important patterns to learn something new about the microbial world.

Example Datasets

OrganismBrowserData FilesNum. GenomesNum. Motifs
Shigella dysenteriaelinklink2644
Escherichia colilinklink103389
Clostridioides difficilelinklink4034
Streptococcus equi subsp. equilinklink3520
Klebsiella pneumoniaelinklink3195

There are many different reasons why epigenetic modifications may be important for the biology of a particular bacterial strain:

  • Defense from invading genetic elements (e.g. plasmids, phage)
  • Regulation of gene expression
  • Phase variation

The large amount of variation in bacterial epigenetics has become much better appreciated with the advent of third-generation epigenome-aware platforms for genome sequencing. The primary platform which provides epigenetic information is PacBio SMRT Sequencing, while the Oxford Nanopore platform can also generate methylation information

Some key characteristics of bacterial epigenetic modification are:

  • Chemical modifications are made to DNA in the context of short nucleotide motifs (e.g. GATC)
  • Each type of modification may occur at a different molecular position within the nucleotide
  • Different strains of the same species will often have a distinct epigenetic profile (collection of motifs)

Input Data
The Pan-Epigenome Browser reads epigenome profiles which are produced by the PacBio analysis platform. Specifically, the motifs.csv file produced by the MotifMaker utility for each genome. It is strongly recommended to name each of the motif CSV files according to their source to avoid confusion (e.g. EcoliK12.motifs.csv).

Public Data
The public NCBI data repository accepts PacBio base modification files including the summary CSV format which is used by the Pan-Epigenome Browser. A complete list of datasets which include these files can be found here. Within that table, any of the files with BaseModification-MotifsSummary listed as their File Type should be compatible. In addition, the BioProjects containing base modification data can be found using the search term “has basemodification”[Properties]

Background Reading

Wilbanks, E.G., Doré, H., Ashby, M.H. et al. Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. ISME J 16, 1921–1931 (2022).

Fig. 1: Restriction-modification (RM) systems provide bacteria and archaea with a defense against foreign DNA by discriminating self from non-self DNA based on methylation patterns.