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Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers

Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/HpaII and EcoRI/MspI patterns in different ecotypes revealed that 35–43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Molecular Genetics and Genomics Springer Journals

Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers

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References (54)

Publisher
Springer Journals
Copyright
Copyright © 2002 by Springer-Verlag
Subject
Life Sciences; Cell Biology; Biochemistry, general; Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics
ISSN
1617-4615
eISSN
1617-4623
DOI
10.1007/s00438-002-0772-4
pmid
12471452
Publisher site
See Article on Publisher Site

Abstract

AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/HpaII and EcoRI/MspI patterns in different ecotypes revealed that 35–43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation.

Journal

Molecular Genetics and Genomics – Springer Journals

Published: Dec 8, 2002

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