Skip to main content
SpringerLink
Log in

High-Throughput Sequencing of the Methylome Using Two-Base Encoding

  • Protocol
  • First Online:
Bioinformatics and Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 910))

Abstract

Methylation of Cytosine together with other epigenetic traits plays an important role in the development and regulation of both healthy and diseased cells. Changes in the methylation patterns have been shown to be associated with the development of cancer, growth, neurodevelopmental, and endocrine disorders (Laird PW, Nat Rev Genet 11:191–203, 2010; Tost J, Mol Biotechnol 44:71–81, 2010; Zuo T et al., Epigenomics 1:331–345, 2009). Thus, studying the methylation pattern can give important insights to the underlying causes of disease and development. A method for studying the methylome on a single base resolution is described, using bisulfite sequencing in combination with the high-throughput SOLiDTM sequencing technology.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Laird PW (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11:191–203

    Article  PubMed  CAS  Google Scholar 

  2. Tost J (2010) DNA methylation: an introduction to the biology and the disease-associated changes of a promising biomarker. Mol Biotechnol 44:71–81

    Article  PubMed  CAS  Google Scholar 

  3. Zuo T, Tycko B, Liu T-M et al (2009) Methods in DNA methylation profiling. Epigenomics 1:331–345

    Article  PubMed  CAS  Google Scholar 

  4. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465–476

    Article  PubMed  CAS  Google Scholar 

  5. Illingworth RS, Bird AP (2009) CpG islands—‘a rough guide’. FEBS Lett 583:1713–1720

    Article  PubMed  CAS  Google Scholar 

  6. Reik W, Dean W, Walter J (2001) Epigenetic reprogramming in mammalian development. Science 293:1089–1093

    Article  PubMed  CAS  Google Scholar 

  7. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683–692

    Article  PubMed  CAS  Google Scholar 

  8. Laird PW (2005) Cancer epigenetics. Hum Mol Genet 14:R65–R76

    Article  PubMed  CAS  Google Scholar 

  9. Ehrlich M (2002) DNA methylation in cancer: too much, but also too little. Oncogene 21:5400–5413

    Article  PubMed  CAS  Google Scholar 

  10. Edwards JR, O’Donnell AH, Rollins RA et al (2010) Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Res 20: 972–980

    Article  PubMed  CAS  Google Scholar 

  11. Bormann Chung CA, Boyd VL, McKernan KJ et al (2010) Whole methylome analysis by ultra-deep sequencing using two-base encoding. PLoS One. doi:10.1371/journal.pone.0009320

    Google Scholar 

  12. Laurent L, Wong E, Li G et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20:320–331

    Article  PubMed  CAS  Google Scholar 

  13. Li N, Ye M, Li Y et al (2010) Whole genome DNA methylation analysis based on high ­throughput sequencing technology. Methods 52(3): 203–212. doi:10.1016/j.ymeth.2010.04.009

    Article  PubMed  Google Scholar 

  14. Xiang H, Zhu J, Chen Q et al (2010) Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 28:516–520

    Article  PubMed  CAS  Google Scholar 

  15. Lister R, O’Malley RC, Tonti-Filippini J et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536

    Article  PubMed  CAS  Google Scholar 

  16. Lister R, Pelizzola M, Dowen RH et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322

    Article  PubMed  CAS  Google Scholar 

  17. Zemach A, McDaniel IE, Silva P et al (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916–919

    Article  PubMed  CAS  Google Scholar 

  18. Hsieh T-F, Ibarra CA, Silva P et al (2009) Genome-wide demethylation of arabidopsis endosperm. Science 324:1451–1454

    Article  PubMed  CAS  Google Scholar 

  19. Homer N, Merriman B, Nelson S (2009) Local alignment of two-base encoded DNA sequence. BMC Bioinformatics 10:175

    Article  PubMed  Google Scholar 

  20. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  PubMed  CAS  Google Scholar 

  21. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145

    Article  PubMed  CAS  Google Scholar 

  22. McKernan KJ, Peckham HE, Costa GL et al (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:1527–1541

    Article  PubMed  CAS  Google Scholar 

  23. Ranade SS, Chung CB, Zon G et al (2009) Preparation of genome-wide DNA fragment libraries using bisulfite in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection. Anal Biochem 390:126–135

    Article  PubMed  CAS  Google Scholar 

  24. Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  Google Scholar 

  25. Marnellos G, Krissinger D, Meredith G D et al. (2010) Genome-wide methylation data analysis on the SOLiDTM System. 60th Annual Meeting of The American Society of Human Genetics, Washington, DC, 5 November 2010, abstract #1337

    Google Scholar 

  26. Meredith GD, Dudas M, Levandowsky E et al. (2010) Efficient whole-genome DNA methylation analysis of the Human Reference Genome (HuRef). 60th Annual Meeting of The American Society of Human Genetics, Washington, DC, 5 November 2010, abstract #1385

    Google Scholar 

  27. Meredith GD, Marnellos G, D’Ippolito A et al. (2010) Efficient whole-genome DNA methylation analysis of the human fibroblast cell-line IMR-90 and the plant A. thaliana. Epigenetics Europe Conference, Select Biosciences, Dublin, Ireland, 14–15 September 2010, abstract # 323

    Google Scholar 

  28. Ondov BD, Cochran C, Landers M et al (2010) An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System. Bioinformatics 26:1901–1902

    Article  PubMed  CAS  Google Scholar 

  29. Chen P-Y, Cokus S, Pellegrini M (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11:203

    Article  PubMed  CAS  Google Scholar 

  30. Cokus SJ, Feng S, Zhang X et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219

    Article  PubMed  CAS  Google Scholar 

  31. Harris EY, Ponts N, Levchuk A et al (2010) BRAT: bisulfite-treated reads analysis tool. Bioinformatics 26:572–573

    Article  PubMed  CAS  Google Scholar 

  32. Smith AD, Chung W-Y, Hodges E et al (2009) Updates to the RMAP short-read mapping software. Bioinformatics 25:2841–2842

    Article  PubMed  CAS  Google Scholar 

  33. Xi Y, Li W (2009) BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10:232

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

I like to thank my colleagues Clarence Lee and Tim Harkins for their support and guidance on this work and Quynh Doan, Robert Nutter, and Vrunda Sheth for their valuable comments and tips.

Author information

Authors and Affiliations

  1. Life Technologies, Foster City, CA, USA

    Christina A. Bormann Chung

Authors
  1. Christina A. Bormann Chung
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christina A. Bormann Chung .

Editor information

Editors and Affiliations

  1. , Department of Pathology, The University of New Mexico, Camino de Salud 915, Albuquerque, 87131, New Mexico, USA

    Richard S. Larson

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media New York

About this protocol

Cite this protocol

Chung, C.A.B. (2012). High-Throughput Sequencing of the Methylome Using Two-Base Encoding. In: Larson, R. (eds) Bioinformatics and Drug Discovery. Methods in Molecular Biology, vol 910. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-965-5_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-965-5_5

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-964-8

  • Online ISBN: 978-1-61779-965-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation