Kismeth: Analyzer of plant methylation states through bisulfite sequencing |
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Authors: | Eyal Gruntman Yijun Qi R Keith Slotkin Ted Roeder Robert A Martienssen Ravi Sachidanandam |
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Institution: | (1) Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA;(2) National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, PR China;(3) Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA |
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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). |
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