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 interecotype 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.
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dig-inia-es-20.500.12792-58452020-12-15T09:55:06Z Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers Cervera, M. T. Ruiz-García, L. Martínez-Zapater, J. M. 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 interecotype 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. 2020-10-22T21:27:37Z 2020-10-22T21:27:37Z 2002 journal article http://hdl.handle.net/20.500.12792/5845 10.1007/s00438-002-0772-4 eng Attribution-NonCommercial-ShareAlike 4.0 International http://creativecommons.org/licenses/by-nc-sa/4.0/ open access |
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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 interecotype 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. |
format |
journal article |
author |
Cervera, M. T. Ruiz-García, L. Martínez-Zapater, J. M. |
spellingShingle |
Cervera, M. T. Ruiz-García, L. Martínez-Zapater, J. M. Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers |
author_facet |
Cervera, M. T. Ruiz-García, L. Martínez-Zapater, J. M. |
author_sort |
Cervera, M. T. |
title |
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers |
title_short |
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers |
title_full |
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers |
title_fullStr |
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers |
title_full_unstemmed |
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers |
title_sort |
analysis of dna methylation in arabidopsis thaliana based on methylation-sensitive aflp markers |
publishDate |
2002 |
url |
http://hdl.handle.net/20.500.12792/5845 |
work_keys_str_mv |
AT cerveramt analysisofdnamethylationinarabidopsisthalianabasedonmethylationsensitiveaflpmarkers AT ruizgarcial analysisofdnamethylationinarabidopsisthalianabasedonmethylationsensitiveaflpmarkers AT martinezzapaterjm analysisofdnamethylationinarabidopsisthalianabasedonmethylationsensitiveaflpmarkers |
_version_ |
1758004702241357824 |