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Insect Genomics pp 141–156Cite as

Whole-Genome Bisulfite Sequencing for the Methylation Analysis of Insect Genomes

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1858))

Abstract

DNA methylation is a conserved epigenetic modification of animal genomes, but genome methylation patterns appear surprisingly diverse in insects. Whole-genome bisulfite sequencing (WGBS) represents a sensitive and robust method for the characterization of genome-wide methylation patterns at single-base resolution. Here, we describe a step-by-step protocol for the generation and analysis of WGBS datasets using standard Illumina sequencing platforms. In comparison to whole-genome sequencing, WGBS has additional caveats that require particular attention and are highlighted in this chapter.

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References

  1. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514

    Article  CAS  Google Scholar 

  2. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9(6):465–476

    Article  CAS  Google Scholar 

  3. Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13(7):484–492

    Article  CAS  Google Scholar 

  4. Schubeler D (2015) Function and information content of DNA methylation. Nature 517(7534):321–326. https://doi.org/10.1038/nature14192

    Article  CAS  PubMed  Google Scholar 

  5. Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl:245–254

    Article  Google Scholar 

  6. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107(19):8689–8694

    Article  CAS  Google Scholar 

  7. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328(5980):916–919

    Article  CAS  Google Scholar 

  8. Falckenhayn C, Boerjan B, Raddatz G, Frohme M, Schoofs L, Lyko F (2013) Characterization of genome methylation patterns in the desert locust Schistocerca gregaria. J Exp Biol 216. (Pt 8:1423–1429. https://doi.org/10.1242/jeb.080754

    Article  CAS  PubMed  Google Scholar 

  9. Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R (2010) The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol 8(11):e1000506

    Article  Google Scholar 

  10. Raddatz G, Guzzardo PM, Olova N, Fantappie MR, Rampp M, Schaefer M, Reik W, Hannon GJ, Lyko F (2013) Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proc Natl Acad Sci U S A 110(21):8627–8631

    Article  Google Scholar 

  11. Falckenhayn C, Carneiro VC, de Mendonca Amarante A, Schmid K, Hanna K, Kang S, Helm M, Dimopoulos G, Fantappie MR, Lyko F (2016) Comprehensive DNA methylation analysis of the Aedes aegypti genome. Sci Rep 6:36444. https://doi.org/10.1038/srep36444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Evolution of DNA methylation across insects. Mol Biol Evol 34(3):654–665. https://doi.org/10.1093/molbev/msw264

    Article  CAS  PubMed  Google Scholar 

  13. Clark SJ, Harrison J, Paul CL, Frommer M (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22(15):2990–2997

    Article  CAS  Google Scholar 

  14. Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5(1):e8888. https://doi.org/10.1371/journal.pone.0008888

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lister R, Ecker JR (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 19(6):959–966

    Article  CAS  Google Scholar 

  16. Lyko F, Maleszka R (2011) Insects as innovative models for functional studies of DNA methylation. Trends Genet 27(4):127–131

    Article  CAS  Google Scholar 

  17. Asselman J (2018) Bioinformatic analysis of methylation patterns using bisulfite sequencing data. In: Brown S, Pfrender ME (eds) Insect genomics, methods in molecular biology, vol XXX. Springer-Nature, New York

    Google Scholar 

  18. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  Google Scholar 

  20. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/map format and SAMtools. Bioinformatics. 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352

    Article  Google Scholar 

  21. Feng H, Conneely KN, Wu H (2014) A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res 42(8):e69. https://doi.org/10.1093/nar/gku154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM (2013) An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One 8(12):e85024. https://doi.org/10.1371/journal.pone.0085024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sinha R, Stanley G, Gulati GS, Ezran C, Travaglini KJ, Wei E, Chan CKF, Nabhan AN, Su T, Morganti RM, Conley SD, Chaib H, Red-Horse K, Longaker MT, Snyder MP, Krasnow MA, Weissman IL (2017) Index switching causes “Spreading-Of-Signal” among multiplexed samples in illumina HiSeq 4000 DNA sequencing. BioRxiv. https://doi.org/10.1101/125724

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Acknowledgments

We thank Günter Raddatz, Stephan Wolf, Nicolle Diessl, and the DKFZ Genomics and Proteomics Core Facility for helpful discussions.

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Authors and Affiliations

  1. Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany

    Fanny Gatzmann & Frank Lyko

Authors
  1. Fanny Gatzmann
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  2. Frank Lyko
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Corresponding author

Correspondence to Frank Lyko .

Editor information

Editors and Affiliations

  1. Division of Biology, Kansas State University, Manhattan, NY, USA

    Susan J. Brown

  2. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA

    Michael E. Pfrender

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Gatzmann, F., Lyko, F. (2019). Whole-Genome Bisulfite Sequencing for the Methylation Analysis of Insect Genomes. In: Brown, S., Pfrender, M. (eds) Insect Genomics. Methods in Molecular Biology, vol 1858. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8775-7_11

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  • DOI: https://doi.org/10.1007/978-1-4939-8775-7_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8774-0

  • Online ISBN: 978-1-4939-8775-7

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