Characterize the epigenetic landscape of your genome
Directly detect epigenetic changes during sequencing to open the door to easier exploration of DNA modification to connect genotype with phenotype.
Epigenetics
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. With SMRT Sequencing you can:
- Understand the effects of epigenetics on a broad range of biological processes, including gene expression, host-pathogen interactions, environmental response, DNA damage, and DNA repair
- Uncover the role of epigenetics in the inheritance of traits from one generation to the next
Explore further with workflows and tools for Epigenetics customized for your research focus
- Microbial Epigenetics – Characterize DNA modifications and methyltransferase recognition motifs
- Eukaryotic Epigenetics – Identify hyper- and hypo-methylated CpG islands to explore gene expression and regulation
Selected Resources
- Kondratyev, Nikolay et al. (2018) Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation. Clinical epigenetics
- Hiraoka, Satoshi et al. (2018) Metaepigenomic analysis reveals the unexplored diversity of DNA methylations in an environmental prokaryotic community BioRxiv
- Zhou, Chao et al. (2018) Identification and analysis of adenine N6-methylation sites in the rice genome. Nature plants
- Kumari, Romika et al. (2018) PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA
- Atack, John M et al. (2018) Phasevarions of bacterial pathogens: Methylomics sheds new light on old enemies. Trends in microbiology
- Ameur, Adam et al. (2018) Single-molecule sequencing: Towards clinical applications Trends in biotechnology
- 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
- Zhao, Liang et al. (2018) The highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis. Harmful algae
- 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
- 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
- Wu, Tao P et al. (2016) DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature
- Blow, Matthew J et al. (2016) The epigenomic landscape of prokaryotes. PLoS genetics
- Roberts, Richard J et al. (2015) REBASE–a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic acids research
- Korlach, Jonas et al. (2012) Going beyond five bases in DNA sequencing. Current opinion in structural biology
- Flusberg, Benjamin A et al. (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nature methods
- Poster: Ekholm, J. et al. (2018) Amplification-free, CRISPR-Cas9 targeted enrichment and SMRT Sequencing of repeat-expansion disease causative genomic regions
- 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
- 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]
- PacBio Certified Service Providers (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Application Brief: Microbial whole genome sequencing – Best Practices (2018)
- Cancer Brochure: Discover the hidden landscape of cancer variants (2017)
- SMRT Analysis Brochure: Gain a deeper understanding of your sequencing data (2017)