The gateway to new biological discoveries
Epigenetic modifications affect a broad range of biological processes, including gene expression, host-pathogen interactions, environmental response, DNA damage, and DNA repair1. Epigenetics also play a significant role in the inheritance of traits from one generation to the next. While more than 20 types of epigenetic and DNA-damage modifications have been identified, most scientists have only been able to study one type, cytosine methylation, using indirect detection methods. The ability to directly detect these changes is critical for understanding the impact of DNA modification on a wide variety of natural processes and disease responses.
Characterize the epigenetic landscape of your genome
Single Molecule, Real-Time (SMRT) Sequencing directly detects epigenetic modifications by measuring kinetic variation during base incorporation. By capturing these modifications simultaneously with sequence data, this method eliminates the need for special sample preparation and additional sequencing.
PacBio Systems provide a direct view of epigenetic modification
To learn more about how SMRT Sequencing simultaneously captures genomic and epigenetic information, contact us.
- Davis, B. M., et al., (2013) Entering the era of bacterial epigenomics with single molecule real time DNA sequencing. Current Opinion in Microbiology. 16 (2), 192–198.
- Forde, Brian M et al. (2015) Lineage-specific methyltransferases define the methylome of the globally disseminated Escherichia coli ST131 clone. mBio
- O'Callaghan, A et al. (2015) Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems. BMC Genomics
- Cameron, David R et al. (2015) Insights on virulence from the complete genome of Staphylococcus capitis. Frontiers in Microbiology
- Atack, John M et al. (2015) A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae. Nature Communications
- Lee, Woon Ching et al. (2015) The complete methylome of Helicobacter pylori UM032. BMC Genomics
- Huo, Wenwen et al. (2015) Genome modification in Enterococcus faecalis OG1RF assessed by bisulfite sequencing and Single-Molecule Real-Time Sequencing. Journal of Bacteriology
- Beaulaurier, John et al. (2015) Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nature Communications
- Eutsey, Rory A et al. (2015) Genetic stabilization of the drug-resistant PMEN1 Pneumococcus lineage by its distinctive DpnIII restriction-modification system. mBio
- Li, Jun-Jie et al. (2015) Complete nucleotide sequences of bla(CTX-M)-harboring IncF plasmids from community-associated Escherichia coli strains in the United States. Antimicrobial Agents and Chemotherapy
- Heyn, Holger et al. (2015) An adenine code for DNA: A second life for N6-methyladenine. Cell
- Greer, Eric Lieberman et al. (2015) DNA methylation on N6-adenine in C. elegans. Cell
- Monk, Ian R et al. (2015) Complete bypass of restriction systems for major Staphylococcus aureus lineages. mBio
- Beatson, Scott A et al. (2015) Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition. Infection and Immunity
- Yang, Yao et al. (2015) Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics
- Agarwal, Prasoon et al. (2015) CGGBP1 mitigates cytosine methylation at repetitive DNA sequences. BMC Genomics
- Seib, Kate L et al. (2015) Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis. Nucleic Acids Research
- Suzuki, Yuta et al. (2015) Landscape of CpG methylation of individual repetitive elements bioRxiv
- Ouellette, Matthew et al. (2015) Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. Frontiers in Microbiology
- Pirone-Davies, Cary et al. (2015) Genome-wide methylation patterns in Salmonella enterica subsp. enterica serovars. PLoS One
- Utturkar, Sagar M et al. (2015) Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Scientific Data
- Feng, Z et al. (2015) qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data. Nucleic Acids Research
- O'Loughlin, Jason L et al. (2015) Analysis of the Campylobacter jejuni genome by SMRT DNA Sequencing identifies restriction-modification motifs. PLoS One
- Goldfarb, Tamara et al. (2015) BREX is a novel phage resistance system widespread in microbial genomes. The EMBO Journal
- Roberts, Richard J et al. (2015) REBASE–a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Research
- Poster: Korlach, J. et al. (2015) Epigenome characterization of human genomes using the PacBio platform
- Poster: Korlach, Jonas et al. (2015) Whole genome sequencing and epigenome characterization of cancer cells using the PacBio platform.
- Poster: Hall, Richard J et al. (2015) A workflow for the analysis of contigs from the metagenomic shotgun assembly of SMRT Sequencing data
- Conference Presentation: Korlach, Jonas (2015) ASHG Workshop Presentation: Going beyond the $1,000 genome?: the future of high quality de novo human genomes, epigenomes and transcriptomes?
- Case Studies and Interviews: Case Study: With SMRT Sequencing for genomes, transcriptomes, and epigenomes, scientists are overcoming barriers in plant and animal research (2016)
- Brochures: Bring the “W” back to Whole genome sequencing (2015)
- Brochures: Sequel System – Introducing the scalable platform for SMRT Sequencing (2015)
- Brochures: Gain a deeper understanding of your sequencing data (2015)
- Brochures: Revolutionize genomics with SMRT Sequencing (2015)
- Brochures: Novel insights into microbial and viral complexity. (2015)
- Service Provider and Core Lab Profiles: Long reads yield complete microbial genomes and improved large genome assemblies at the Institute for Genome Sciences. (2015)