Microbial epigenetics

DNA methylation is an important component of microbial defense against foreign DNA, but restriction-modification (R-M) systems can also drive bacterial evolution by increasing double strand breaks and C-T mutations and alter the transcription of genes affecting pathogenicity and virulence.

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Directly detect epigenetic modifications with HiFi sequencing

HiFi sequencing directly detects DNA modifications in native DNA from variations in the polymerase kinetics of DNA base incorporation, without the need for arduous chemical conversion protocols like bisulfite treatment.

  • Detect genome-wide m6A and m4C R-M system motifs at coverage levels recommended for assembly
  • Obtain complete genomes with annotations for epigenetic modification
  • Reveal phase variation of R-M genes that regulate batteries of genes involved in pathogenesis, host adaption, and antibiotic resistance

Workflow: from DNA to microbial methylome

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Sample + library preparation

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Sequencing

  • Simultaneously generate whole genome and epigenome data by sequencing on a Sequel II system

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Data analysis

Spotlight

Microbial DNA methylation signatures detected with SMRT sequencing improves metagenomic binning and plasmid tracking

Scientists used bacterial DNA methylation profiles as endogenous epigenetics barcodes to computationally bin individual reads and assembled contigs by species or strain. This research also enabled linking of plasmids and other mobile genetic elements to their host genomes to improve the strain-level resolution of metagenomes. Explore this research further:

Beaulaurier, J. et al., (2017). Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology. ePub ahead of print.

Beaulaurier 2017_Figure 1

Spotlight

Revealing methylation fingerprints to evade the host defenses that thwart genome engineering

SyngenicDNA is a novel stealth-by-engineering approach: editing out recognition motifs specific to a host’s R-M systems makes foreign DNA invisible. The stealth-by-engineering approach, facilitated by SMRT sequencing, improves bacterial transformation efficiency by up to 70,000-fold and can unlock myriad applications of bacterial genetic engineering in basic research, industrial biology, synthetic biology, and translational science. Explore this research further:

Johnston, C. D., et al. (2018). SyngenicDNA: stealth-based evasion of restriction-modification barriers during bacterial genetic engineering. BioRxiv preprint.

SMRT sequencing to identify R-M system motifs for de novo synthesis and production of SyngenicDNA plasmid or minicircle image - PacBio

Spotlight

Methylomes — a new frontier in prokaryotic biology

SMRT sequencing sheds light on the methylomes of 230 prokaryotic organisms, uncovering potentially broader roles of DNA methylation in genome biology. Explore this research further:

Blow, M.J. et al., (2016). The epigenomic landscape of prokaryotesPLoS Genetics, 12(2), p.e1005854.

Epigenomic landscape of prokaryotes

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