Detect epigenetics without compromising discovery
Epigenetic modifications play an important role in the biology of eukaryotes. A prime example is the impact of DNA methylation on gene expression, imprinting, and X chromosome inactivation. Additionally, the deregulation of epigenetic machinery has been implicated in Mendelian disease, human cancer, and drug resistance1,2. While the most commonly used methods for determining CpG methylation rely on targeted approaches, these methods are restricted by indirect detection and the limitations of many sequencing technologies.
Discover more with SMRT epigenetics
By pairing high throughput with long reads, the PacBio Systems offer scalable solutions for assessing CpG methylation in eukaryotic genomes. When using Single Molecule, Real-Time (SMRT) Sequencing, genome-wide regional methylation information is generated with no additional sample preparation. For targeted applications, SMRT bisulfite sequencing marries bisulfite samples with highly multiplexed, quantitative long-read sequencing, accurately measuring CpG methylation across ~1.5 kb regions.
Workflow: from DNA to epigenetic information
- Library preparation
- SMRT Sequencing with PacBio Systems
- Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared with the PacBio RS II
- Achieve ~10 kb average read lengths, with some reads as long as 60 kb Average read lengths 10–15 kb
Featured research: whole genome sequencing and epigenome characterization of cancer cells
PacBio sequencing was used to characterize the cancer genomes of both drug-sensitive and drug-resistant PC-9 cells. Large-scale changes in the methylation status were observed, allowing researchers to explore the function of methylation on drug sensitivity3.
Explore this research further.
To learn more about how you can use SMRT Sequencing for eukaryotic epigenetics, contact us.
- Fahrner, J.A. and Bjornson, H.T. (2014) Mendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annual Reviews Genomics and Human Genetics. 15, 269-293.
- Baylin, S.B. and Herman J.G. (2000) DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends in Genetics. 16(4),168–174.
- Korlach, J., et al., (2015, February) Whole genome sequencing and epigenome characterization of cancer cells using the PacBio platform. Poster presented at Advances in Genome Biology and Technology., Marco Island, FL.
- Chi, Kelly Rae et al. (2017) The RNA code comes into focus. Nature
- 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
- Wu, Tao P et al. (2016) DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature
- 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
- 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
- Davis, Caleb F et al. (2014) The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell
- Pham, Thang T et al. (2016) Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications. Molecular Genetics and Genomics
- Pfeifer, Gerd P et al. (2016) Epigenetics: An elusive DNA base in mammals. Nature
- Marx, Vivien et al. (2016) Genetics: profiling DNA methylation and beyond. Nature Methods
- Richards, Stephen et al. (2015) It’s more than stamp collecting: how genome sequencing can unify biological research. Trends in Genetics
- Chavez, Lukas et al. (2014) Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea. Proceedings of the National Academy of Sciences of the United States of America
- Clark, Tyson A et al. (2011) Direct detection and sequencing of damaged DNA bases. Genome Integrity
- 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
- 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: Yeadon, Jane et al. (2014) Integrative biology of a fungus: Using PacBio SMRT Sequencing to interrogate the genome, epigenome, and transcriptome of Neurospora crassa.
- Presentation: Morishita, Shinichi et al. (2015) Understanding methylome, metagenome, structural variants using SMRT Sequencing
- 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
- Korlach, Jonas (2015) ASHG PacBio Workshop: Going beyond the $1,000 genome? – the future of high quality de novo human genomes, epigenomes and transcriptomes?
- Suzuki, Yuta (2015) AGBT Virtual Poster: Observing heterozygotic DNA methylation patterns in diploid genomes using kinetics data from the PacBio RS
- Suzuki, Yuta (2015) Customer Experience: SMRT Sequencing for generating data for haplotype-specific epigenetic analysis
- Scott, Stuart (2014) ASHG PacBio Workshop: Long-read multiplexed amplicon sequencing – applications for epigenetics and pharmacogenetics
- Cancer Brochure: Discover the hidden landscape of cancer variants (2017)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2017)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome. (2016)
- Case Study: With SMRT Sequencing for genomes, transcriptomes, and epigenomes, scientists are overcoming barriers in plant and animal research. (2015)