Advertisement

Bioinformatic Analysis of Methylation Patterns Using Bisulfite Sequencing Data

  • Jana AsselmanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1858)

Abstract

Epigenetic factors, including DNA methylation, play a crucial role in the development, behavior, and stress response of insects yet the analysis of DNA methylation patterns remains quite challenging. This chapter will introduce the different technologies for DNA methylation analysis and present a general methodology for the analysis of DNA methylation patterns using the commonly used technology of bisulfite sequencing. The chapter will give a short overview of the sequencing technology itself and will primarily focus on presenting the bioinformatic and statistical analysis methodology of bisulfite sequencing data to study DNA methylation patterns.

Key words

DNA methylation Bioinformatics Bisulfite sequencing 

References

  1. 1.
    Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9(6):465–476.  https://doi.org/10.1038/nrg2341 CrossRefPubMedGoogle Scholar
  2. 2.
    Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Dore LC, Weng X, Ji Q, Mets L, He C (2015) N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell 161(4):879–892.  https://doi.org/10.1016/j.cell.2015.04.010 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Greer EL, Blanco MA, Gu L, Sendinc E, Liu J, Aristizabal-Corrales D, Hsu CH, Aravind L, He C, Shi Y (2015) DNA methylation on N6-Adenine in C. elegans. Cell 161(4):868–878.  https://doi.org/10.1016/j.cell.2015.04.005 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Sun Q, Huang S, Wang X, Zhu Y, Chen Z, Chen D (2015) N6-methyladenine functions as a potential epigenetic mark in eukaryotes. Bioessays 37(11):1155–1162.  https://doi.org/10.1002/bies.201500076 CrossRefPubMedGoogle Scholar
  5. 5.
    Zhang G, Huang H, Liu D, Cheng Y, Liu X, Zhang W, Yin R, Zhang D, Zhang P, Liu J, Li C, Liu B, Luo Y, Zhu Y, Zhang N, He S, He C, Wang H, Chen D (2015) N6-methyladenine DNA modification in Drosophila. Cell 161(4):893–906.  https://doi.org/10.1016/j.cell.2015.04.018 CrossRefPubMedGoogle Scholar
  6. 6.
    Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11(3):191–203.  https://doi.org/10.1038/nrg2732 CrossRefPubMedGoogle Scholar
  7. 7.
    Kurdyukov S, Bullock M (2016) DNA methylation analysis: choosing the right method. Biology (Basel) 5(1).  https://doi.org/10.3390/biology5010003 CrossRefGoogle Scholar
  8. 8.
    Warnecke PM, Stirzaker C, Song J, Grunau C, Melki JR, Clark SJ (2002) Identification and resolution of artifacts in bisulfite sequencing. Methods 27(2):101–107CrossRefGoogle Scholar
  9. 9.
    Millar DS, Warnecke PM, Melki JR, Clark SJ (2002) Methylation sequencing from limiting DNA: embryonic, fixed, and microdissected cells. Methods 27(2):108–113CrossRefGoogle Scholar
  10. 10.
    Holmes EE, Jung M, Meller S, Leisse A, Sailer V, Zech J, Mengdehl M, Garbe LA, Uhl B, Kristiansen G, Dietrich D (2014) Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine. PLoS One 9(4):e93933.  https://doi.org/10.1371/journal.pone.0093933 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Gatzmann F, Lyko F (2018) Whole-genome bisulfite sequencing for the methylation analysis of insect genomes. In: Brown S, Pfrender M (eds) Insect genomics, methods in molecular biology, vol XXX. Springer-Nature, New YorkGoogle Scholar
  12. 12.
    Warnecke PM, Stirzaker C, Melki JR, Millar DS, Paul CL, Clark SJ (1997) Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res 25(21):4422–4426CrossRefGoogle Scholar
  13. 13.
    Krueger F, Kreck B, Franke A, Andrews SR (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9(2):145–151.  https://doi.org/10.1038/nmeth.1828 CrossRefPubMedGoogle Scholar
  14. 14.
    Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M (2006) Open software for biologists: from famine to feast. Nat Biotechnol 24(7):801–803.  https://doi.org/10.1038/nbt0706-801 CrossRefPubMedGoogle Scholar
  15. 15.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27(11):1571–1572.  https://doi.org/10.1093/bioinformatics/btr167 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25.  https://doi.org/10.1186/gb-2009-10-3-r25 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5(10):R80.  https://doi.org/10.1186/gb-2004-5-10-r80 CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA (2014) Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res 42(6):e43.  https://doi.org/10.1093/nar/gkt1325 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Bonasio R, Li Q, Lian J, Mutti NS, Jin L, Zhao H, Zhang P, Wen P, Xiang H, Ding Y, Jin Z, Shen SS, Wang Z, Wang W, Wang J, Berger SL, Liebig J, Zhang G, Reinberg D (2012) Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol 22(19):1755–1764.  https://doi.org/10.1016/j.cub.2012.07.042 CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Pegoraro M, Bafna A, Davies NJ, Shuker DM, Tauber E (2016) DNA methylation changes induced by long and short photoperiods in Nasonia. Genome Res 26(2):203–210.  https://doi.org/10.1101/gr.196204.115 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Rehan SM, Glastad KM, Lawson SP, Hunt BG (2016) The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata. Genome Biol Evol 8(5):1401–1410.  https://doi.org/10.1093/gbe/evw079 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13(10):R87.  https://doi.org/10.1186/gb-2012-13-10-r87 CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Hansen KD, Langmead B, Irizarry RA (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 13(10):R83.  https://doi.org/10.1186/gb-2012-13-10-r83 CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely KN (2015) Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res 43(21):e141.  https://doi.org/10.1093/nar/gkv715 CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Park Y, Wu H (2016) Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics 32(10):1446–1453.  https://doi.org/10.1093/bioinformatics/btw026 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab)Ghent UniversityGhentBelgium

Personalised recommendations