Kismeth: Analyzer of plant methylation states through bisulfite sequencing
Open Access
- 11 September 2008
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 9 (1), 371
- https://doi.org/10.1186/1471-2105-9-371
Abstract
Background There is great interest in probing the temporal and spatial patterns of cytosine methylation states in genomes of a variety of organisms. It is hoped that this will shed light on the biological roles of DNA methylation in the epigenetic control of gene expression. Bisulfite sequencing refers to the treatment of isolated DNA with sodium bisulfite to convert unmethylated cytosine to uracil, with PCR converting the uracil to thymidine followed by sequencing of the resultant DNA to detect DNA methylation. For the study of DNA methylation, plants provide an excellent model system, since they can tolerate major changes in their DNA methylation patterns and have long been studied for the effects of DNA methylation on transposons and epimutations. However, in contrast to the situation in animals, there aren't many tools that analyze bisulfite data in plants, which can exhibit methylation of cytosines in a variety of sequence contexts (CG, CHG, and CHH). Results Kismeth http://katahdin.mssm.edu/kismeth is a web-based tool for bisulfite sequencing analysis. Kismeth was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. Conclusion Kismeth simplifies bisulfite sequencing analysis. It is the only publicly available tool for the design of bisulfite primers for plants, and one of the few tools for the analysis of methylation patterns in plants. It facilitates analysis at both global and local scales, demonstrated in the examples cited in the text, allowing dissection of the genetic pathways involved in DNA methylation. Kismeth can also be used to study methylation states in different tissues and disease cells compared to a reference sequence.Keywords
This publication has 17 references indexed in Scilit:
- Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 SequencingCancer Research, 2007
- CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencingThe Plant Journal, 2007
- Maintenance of DNA Methylation during theArabidopsisLife Cycle Is Essential for Parental ImprintingTHE PLANT CELL ONLINE, 2006
- DNA Methylation Is Critical for Arabidopsis Embryogenesis and Seed ViabilityTHE PLANT CELL ONLINE, 2006
- Gardening the genome: DNA methylation in Arabidopsis thalianaNature Reviews Genetics, 2005
- Role of transposable elements in heterochromatin and epigenetic controlNature, 2004
- DNA METHYLATION AND EPIGENETICSAnnual Review of Plant Biology, 2004
- Worms gang up on bacteriaNature Reviews Genetics, 2002
- DNA methylation patterns and epigenetic memoryGenes & Development, 2002
- Mobilization of transposons by a mutation abolishing full DNA methylation in ArabidopsisNature, 2001