Bacterial epigenomics, it’s just the time

With the applications of multi-omics approaches to examine the epigenome, the?eld of epigenetics is poised to change. We focus on the integration of omics approaches as applied to DNA modi?cation for high-throughput approaches

The bacterial epigenome is a dynamic feature that changes during growth in response to external stimuli, and thereby facilitating adjustment to varying environmental conditions. Many techniques have been developed to quantify methylation, the number of modi?ed nucleotides, and improve detection resolution. Bisul?te sequencing was the?rst method used for determining DNA methylation via sequencing. NGS has paved the way for numerous large-scale sequencing efforts, which will increase the discovery of methylation density, location and catalytic enzymes.

The explosive production of epigenomes in the coming years predicts the need for new computational tools and platforms to run large-scale data analysis for genome and epigenetic annotation. Databases for high-throughput analysis of physical and functional protein-protein interactions include STRING, which predicts protein-protein interaction networks for a single genome are highly needed. The future challenges are exciting and?lled with many opportunities to make new discoveries that de?ne epigenomics in the role of the bacterial life cycle in the era of multi-omics integration.

The precursors of cells commit to their fate in a step-by-step differentiation process, which is driven by a multitude of inputs and is accompanied by epigenetic measures strengthening the commitment decisions. The preparation for sexual reproduction is a three-step process consisting of erasure of somatic signatures in the germ cell precursors via a comprehensive reprogramming process, establishment of sex-specific and germ cell-specific epigenetic signatures and transcription profiles and finally, the post-fertilization removal of these signatures to trigger the embryonic developmental program and beginning of a new life cycle.

DNA methylation is common in eukaryotes ranging from fungi to vertebrates, although its significance and function in these organisms varies greatly. The predominant positioning of 5mC in the symmetrical CpG context led to the early proposal of DNA methylation inheritance through semiconservative DNA replication,

5-hydroxymethylcytosine (5hmC) and the recent discovery of the ten-eleven translocation (Tet) family of dioxygenases suggest new possibilities of active DNA demethylation.

It is now clear that passive DNA demethylation is the most parsimonious mechanism of both PGCs and preimplantation embryos and is probably sufficient for that purpose.

Epigenetic reprogramming differs in details among mammalian species, suggesting that demethylation–methylation in the embryo are novel mechanisms.