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.
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
- Characterize bacterial DNA modifications and methyltransferase recognition motifs
- Identify eukaryotic hyper- and hypo-methylated CpG islands to explore gene expression and regulation
Major epigenetic modifications detectable by SMRT Sequencing
Reference
Selected Resources
- Poulter, Russell T. M. et al. (2018) Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic Scientific Reports
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human Molecular Genetics
- Zhao, Liang et al. (2018) The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis. Harmful Algae
- Slager, Jelle et al. (2018) Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39 BioRxiv
- Frank, Jeroen et al. (2018) Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing. Scientific Reports
- Yadav, Vikas et al. (2018) RNAi is a critical determinant of centromere evolution in closely related fungi. Proceedings of the National Academy of Sciences of the United States of America
- Atack, John M et al. (2018) Phasevarions of bacterial pathogens: Methylomics sheds new light on old enemies. Trends in Microbiology
- Ardui, Simon et al. (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Research
- Kjærbølling, Inge et al. (2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proceedings of the National Academy of Sciences of the United States of America
- Beaulaurier, John et al. (2017) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology
- Ichikawa, Kazuki et al. (2017) Centromere evolution and CpG methylation during vertebrate speciation. Nature Communications
- Nell, Sandra et al. (2017) Genome and methylome variation in Helicobacter pylori with a cag pathogenicity island during early stages of human infection. Gastroenterology
- Deptula, Paulina et al. (2017) De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. BMC Genomics
- Edwards, Joan E et al. (2017) PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: Insights, challenges andopportunities. Frontiers in Microbiology
- Forde, Brian M. et al. (2017) SMRT Sequencing reveals differential patterns of methylation in two O111:H- Shiga toxigenic Escherichia coli isolates from a historic hemolytic uremic syndrome outbreak in Australia BioRxiv
- Zautner, Andreas E et al. (2017) Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT Sequencing Journal of Antimicrobial Chemotherapy
- Utturkar, Sagar M et al. (2017) A case study into microbial genome assembly gap sequences and finishing strategies. Frontiers in Microbiology
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Mondo, Stephen J et al. (2017) Widespread adenine N6-methylation of active genes in fungi. Nature Genetics
- Costa, Stephen K et al. (2017) Bypassing the restriction system to improve transformation ofStaphylococcus epidermidis. Journal of Bacteriology
- Elghraoui, Afif et al. (2017) SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics
- Chi, Kelly Rae et al. (2017) The RNA code comes into focus. Nature
- Cooper, Laurie P et al. (2017) DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus. Nucleic Acids Research
- Chen, Poyin et al. (2017) Comparative genomics reveals the diversity of restriction-modification systems and DNA methylation sites in Listeria monocytogenes. Applied and Environmental Microbiology
- Phelan, Jody et al. (2018) Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Scientific Reports
- Simões, Patrícia Martins et al. (2016) Single-molecule sequencing (PacBio) of the Staphylococcus capitis NRCS-A clone reveals the basis of multidrug resistance and adaptation to the Neonatal Intensive Care Unit environment. Frontiers in Microbiology
- Brykczynska, Urszula et al. (2016) CGG repeat-induced FMR1 silencing depends on the expansion size in human iPSCs and neurons carrying unmethylated full mutations. Stem Cell Reports
- Seong, Hoon Je et al. (2016) Methylome analysis of two Xanthomonas spp. using Single-Molecule Real-Time Sequencing. The Plant Pathology Journal
- Weigele, Peter et al. (2016) Biosynthesis and function of modified bases in bacteria and their viruses. Chemical Reviews
- Vassoler, Fair M et al. (2016) Transgenerational attenuation of opioid self-administration as a consequence of adolescent morphine exposure. Neuropharmacology
- Suzuki, Yuta et al. (2016) AgIn: Measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics
- Grunert, Marcel et al. (2016) Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases. Cardiovascular Research
- Dong, Jiaqiang et al. (2016) Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads. Proceedings of the National Academy of Sciences of the United States of America
- Anjum, Awais et al. (2016) Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168. Nucleic Acids Research
- Davis-Richardson, Austin G et al. (2016) Integrating DNA methylation and gene expression data in the development of the soybean-Bradyrhizobium N2-fixing symbiosis. Frontiers in Microbiology
- Poster: Liqing, Tian et al. (2018) Allelic specificity of immunoglobulin heavy chain (IGH@) translocation in B-cell acute lymphoblastic leukemia (B-ALL) unveiled by long-read sequencing
- Poster: Clark, Tyson A. et al. (2018) Amplification-free targeted enrichment and SMRT Sequencing of repeat-expansion genomic regions
- Poster: Clark, Tyson A. et al. (2017) Targeted enrichment without amplification and SMRT Sequencing of repeat-expansion disease causative genomic regions
- Poster: Ekholm, J. et al. (2016) Enrichment of unamplified DNA and long-read SMRT Sequencing to unlock repeat expansion disorders
- Poster: Ekholm, Jenny et al. (2016) Candidate gene screening using long-read sequencing
- Poster: Ekholm, Jenny et al. (2016) Enrichment of unamplified DNA and long-read SMRT Sequencing in unlocking the underlying biological disease mechanisms of repeat expansion disorders
- Presentation: Salit, Marc et al. (2015) Genome in a Bottle: You’ve sequenced. How well did you do?
- 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
- Korlach, Jonas (2017) Webinar: Addressing “NGS Dead Zones” with third generation PacBio sequencing
- Singh, Siddharth (2017) Webinar: Beginner’s Guide to PacBio SMRT Sequencing Data Analysis
- Turner, Stephen (2017) Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries
- Ameur, Adam (2017) AGBT Virtual Poster: Analysis method for amplification-free SMRT sequencing and assessment on repeat expansions in Huntington’s disease
- Auvignen, Petra (2017) AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria
- (2017) Tutorial: Base modification detection, base modification and motif analysis application [SMRT Link v5.0.0]
- (2017) Tutorial: SMRT Analysis overview and resequencing [SMRT Link v5.0.0]
- Ekholm, J. and Tsai, Y. and Greenberg, D. and Clark, T. (2016) ASHG Virtual Poster: Enrichment of unamplified DNA and long-read SMRT Sequencing to unlock repeat expansion disorders
- Suzuki, Yoshihiko (2016) AGBT Virtual Poster (Japanese): Meta-methylome of human gut microbiome using SMRT Sequencing
- Application Brief: Microbial whole genome sequencing – Best Practices. (2018)
- Sequel System Brochure: The premier solution for long-read sequencing. (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2018)
- PacBio Certified Service Providers (2018)
- Cancer Brochure: Discover the hidden landscape of cancer variants (2017)
- SMRT Analysis Brochure: Gain a deeper understanding of your sequencing data (2017)
- Case Study: Scientists advance understanding of microbial genomes, epigenomes and communities with SMRT Sequencing. (2016)
- Industrial Biotechnology Brochure: Fuel biotech discovery with confident characterization of microbes and their communities. (2016)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome. (2016)