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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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Front page of the website. The reference sequence file and a file containing the results of bisulfite sequencing are uploaded in this page. The results are presented as shown in figures 2 and 3. Example datasets described in the text can be downloaded from this page. The parameters used in the program can also be modified through text boxes on this page.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2553349&req=5

Figure 1: Front page of the website. The reference sequence file and a file containing the results of bisulfite sequencing are uploaded in this page. The results are presented as shown in figures 2 and 3. Example datasets described in the text can be downloaded from this page. The parameters used in the program can also be modified through text boxes on this page.

Mentions: Both files are uploaded on the front page shown in figure 1. Example files from the pilot study described in the application section are available through a link on the front page of Kismeth. The question mark on the front page provides a manual (or answers to questions) for the tool. Kismeth will perform the analysis and return a synopsis table and graph, shown in figures 2 and 3, summarizing the statistics for the sequence as a whole. The graph shows the fraction of methylation at each cytosine position along the reference sequence, allowing a quick estimate of the rates of methylation in different regions (Figure 3). The data underlying the graph, the methylation states of various kinds of cytosines in the sequence, is also available either for browsing on the web (the View links) or as downloadable comma separated value (csv) files (the download links) which can be imported into spreadsheet programs.


Kismeth: analyzer of plant methylation states through bisulfite sequencing.

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

Front page of the website. The reference sequence file and a file containing the results of bisulfite sequencing are uploaded in this page. The results are presented as shown in figures 2 and 3. Example datasets described in the text can be downloaded from this page. The parameters used in the program can also be modified through text boxes on this page.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Front page of the website. The reference sequence file and a file containing the results of bisulfite sequencing are uploaded in this page. The results are presented as shown in figures 2 and 3. Example datasets described in the text can be downloaded from this page. The parameters used in the program can also be modified through text boxes on this page.
Mentions: Both files are uploaded on the front page shown in figure 1. Example files from the pilot study described in the application section are available through a link on the front page of Kismeth. The question mark on the front page provides a manual (or answers to questions) for the tool. Kismeth will perform the analysis and return a synopsis table and graph, shown in figures 2 and 3, summarizing the statistics for the sequence as a whole. The graph shows the fraction of methylation at each cytosine position along the reference sequence, allowing a quick estimate of the rates of methylation in different regions (Figure 3). The data underlying the graph, the methylation states of various kinds of cytosines in the sequence, is also available either for browsing on the web (the View links) or as downloadable comma separated value (csv) files (the download links) which can be imported into spreadsheet programs.

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