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Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing

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Plant Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1610))

Abstract

DNA methylation is one of the most prominent epigenetic marks and is particularly complex in plant genomes. Whole-genome bisulfite sequencing (WGBS) using short reads has become the standard tool to study genome-wide patterns of DNA methylation. The goal of the present protocol is to enable readers to perform WGBS on both the wet lab and the computational side. We briefly outline important steps in bisulfite library preparation, then focus on the different aspects of DNA methylation analysis, from read mapping to identifying biologically relevant differential methylation between different samples.

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References

  1. Pikaard CS, Mittelsten Scheid O (2014) Epigenetic regulation in plants. Cold Spring Harb Perspect Biol 6(12):a019315. doi:10.1101/cshperspect.a019315

    Article  PubMed  PubMed Central  Google Scholar 

  2. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126(6):1189–1201. doi:10.1016/j.cell.2006.08.003

    Article  CAS  PubMed  Google Scholar 

  3. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39(1):61–69. doi:10.1038/ng1929

    Article  CAS  PubMed  Google Scholar 

  4. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89(5):1827–1831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Cokus SJ, Feng SH, Zhang XY, Chen ZG, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184):215–219. doi:10.1038/nature06745

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523–536. doi:10.1016/j.cell.2008.03.029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Robinson MD, Kahraman A, Law CW, Lindsay H, Nowicka M, Weber LM, Zhou X (2014) Statistical methods for detecting differentially methylated loci and regions. Front Genet 5:324. doi:10.3389/fgene.2014.00324

    Article  PubMed  PubMed Central  Google Scholar 

  8. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315–322. doi:10.1038/nature08514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Becker C, Hagmann J, Muller J, Koenig D, Stegle O, Borgwardt K, Weigel D (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480(7376):245–249. doi:10.1038/nature10555

    Article  CAS  PubMed  Google Scholar 

  10. Hagmann J, Becker C, Muller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D (2015) Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet 11(1):e1004920. doi:10.1371/journal.pgen.1004920

    Article  PubMed  PubMed Central  Google Scholar 

  11. van Gurp TP, Wagemaker NC, Wouters B, Vergeer P, Ouborg JN, Verhoeven KJ (2016) epiGBS: reference-free reduced representation bisulfite sequencing. Nat Methods 13(4):322–324. doi:10.1038/nmeth.3763

    Article  PubMed  Google Scholar 

  12. Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD (2011) Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146(6):1029–1041. doi:10.1016/j.cell.2011.08.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100(16):9440–9445. doi:10.1073/pnas.1530509100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by the Max Planck Society.

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Authors and Affiliations

  1. Computomics GmbH, Christophstr. 32, 72072, Tübingen, Germany

    Jörg Hagmann

  2. Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany

    Claude Becker

  3. Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, 1030, Austria

    Claude Becker

Authors
  1. Jörg Hagmann
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  2. Claude Becker
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Corresponding author

Correspondence to Claude Becker .

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Editors and Affiliations

  1. Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria

    Wolfgang Busch

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Hagmann, J., Becker, C. (2017). Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing. In: Busch, W. (eds) Plant Genomics. Methods in Molecular Biology, vol 1610. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7003-2_5

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  • DOI: https://doi.org/10.1007/978-1-4939-7003-2_5

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7001-8

  • Online ISBN: 978-1-4939-7003-2

  • eBook Packages: Springer Protocols

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