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Kismeth: analyzer of plant methylation states through bisulfite sequencing.

Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R - BMC Bioinformatics (2008)

Bottom Line: 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.Kismeth can also be used to study methylation states in different tissues and disease cells compared to a reference sequence.

View Article: PubMed Central - HTML - PubMed

Affiliation: gruntman@cshl.edu

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.

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Comparison of methylation between WT Laer versus ago4-1 mutants using Kismeth. This is a comparison of methylation profiles for WT Laer against ago4-1 mutants for MEA-ISR, a repetitive element [12]. The top graph shows the WT while the bottom panel shows the ago4-1 mutant. The methylation of the CHG and CHH cytosines is reduced in the ago4-1 mutant as compared to the WT, while the CG cytosines are unaffected.
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Figure 10: Comparison of methylation between WT Laer versus ago4-1 mutants using Kismeth. This is a comparison of methylation profiles for WT Laer against ago4-1 mutants for MEA-ISR, a repetitive element [12]. The top graph shows the WT while the bottom panel shows the ago4-1 mutant. The methylation of the CHG and CHH cytosines is reduced in the ago4-1 mutant as compared to the WT, while the CG cytosines are unaffected.

Mentions: In the wild type plant, high levels of methylated Cs in CG, CHG, and CHH contexts were observed (the example datasets called Laer that can be downloaded from the Kismeth website); whereas those in ago4-1 (example dataset available on the Kismeth website, labeled ago4-1) have a decrease in CHG and CHH methylation, with CG methylation unchanged (Figure 10). The dot plots shown in Figure 11 agree with the observations from Figure 10, that there is a reduction in CHG and CHH methylation by comparing the graphs for the two datasets. Thus, Kismeth allows for a quick evaluation of biologically-relevant, global methylation changes.


Kismeth: analyzer of plant methylation states through bisulfite sequencing.

Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R - BMC Bioinformatics (2008)

Comparison of methylation between WT Laer versus ago4-1 mutants using Kismeth. This is a comparison of methylation profiles for WT Laer against ago4-1 mutants for MEA-ISR, a repetitive element [12]. The top graph shows the WT while the bottom panel shows the ago4-1 mutant. The methylation of the CHG and CHH cytosines is reduced in the ago4-1 mutant as compared to the WT, while the CG cytosines are unaffected.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553349&req=5

Figure 10: Comparison of methylation between WT Laer versus ago4-1 mutants using Kismeth. This is a comparison of methylation profiles for WT Laer against ago4-1 mutants for MEA-ISR, a repetitive element [12]. The top graph shows the WT while the bottom panel shows the ago4-1 mutant. The methylation of the CHG and CHH cytosines is reduced in the ago4-1 mutant as compared to the WT, while the CG cytosines are unaffected.
Mentions: In the wild type plant, high levels of methylated Cs in CG, CHG, and CHH contexts were observed (the example datasets called Laer that can be downloaded from the Kismeth website); whereas those in ago4-1 (example dataset available on the Kismeth website, labeled ago4-1) have a decrease in CHG and CHH methylation, with CG methylation unchanged (Figure 10). The dot plots shown in Figure 11 agree with the observations from Figure 10, that there is a reduction in CHG and CHH methylation by comparing the graphs for the two datasets. Thus, Kismeth allows for a quick evaluation of biologically-relevant, global methylation changes.

Bottom Line: 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.Kismeth can also be used to study methylation states in different tissues and disease cells compared to a reference sequence.

View Article: PubMed Central - HTML - PubMed

Affiliation: gruntman@cshl.edu

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.

Show MeSH