Abstract
Amplifying and sequencing DNA after bisulfite treatment of genomic DNA reveals the methylation state of cytosine residues at the highest resolution possible. However, a thorough analysis is required for statistical evaluation of methylation at all sites in each genomic region. Several software tools were developed to assist in quantitative evaluation of bisulfite sequencing data from complex methylation patterns occurring in plants. This chapter describes the application of Cytosine Methylation Analysis Tool for Everyone (CyMATE). From aligned sequences, CyMATE quantifies and illustrates general and pattern-specific methylation at CG, CHG, and CHH (H = A, C, or T) sites, both per sequence and per position. CyMATE is also able to perform a quality control of sequences and to detect redundancy among individual clones. The software is able to reveal methylation patterns on complementary strands by handling data from hairpin bisulfite sequencing. The tool is freely available for non-commercial use at http://www.cymate.org.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hetzl J, Foerster AM, Raidl G, Mittelsten Scheid O (2007) CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. Plant J 51(3):526–536
Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R (2008) Kismeth: analyzer of plant methylation states through bisulphite sequencing. BMC Bioinformatics 9:371–384
Grunau C, Schattevoy R, Mache N, Rosenthal A (2000) MethTools - a toolbox to visualize and analyze DNA methylation data. Nucleic Acids Res 28(5):1053–1058
Laird CD, Pleasant ND, Clark AD, Sneeden JL, Hassan KM, Manley NC et al (2004) Hairpin-bisulphite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc Natl Acad Sci USA 101(1):204–209
Miner BE, Stoger RJ, Burden AF, Laird CD, Hansen RS (2004) Molecular barcodes detect redundancy and contamination in hairpin-bisulphite PCR. Nucleic Acids Res 32(17):e135
Muellner C, Hetzl J (2008) CyMATEads: Reliable analysis of cytosine methylation in plant and animal DNA using bisulphite sequence data. Schriftenreihe Informatik 26:43–52
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Foerster, A.M., Hetzl, J., Müllner, C., Scheid, O.M. (2010). Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATE. In: Kovalchuk, I., Zemp, F. (eds) Plant Epigenetics. Methods in Molecular Biology™, vol 631. Humana Press. https://doi.org/10.1007/978-1-60761-646-7_2
Download citation
DOI: https://doi.org/10.1007/978-1-60761-646-7_2
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-645-0
Online ISBN: 978-1-60761-646-7
eBook Packages: Springer Protocols