Epigenetic natural variation in Arabidopsis thaliana.
Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2007-07-01
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| Series: | PLoS Biology |
| Online Access: | http://europepmc.org/articles/PMC1892575?pdf=render |
| _version_ | 1831548535596646400 |
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| author | Matthew W Vaughn Milos Tanurdzić Zachary Lippman Hongmei Jiang Robert Carrasquillo Pablo D Rabinowicz Neilay Dedhia W Richard McCombie Nicolas Agier Agnès Bulski Vincent Colot R W Doerge Robert A Martienssen |
| author_facet | Matthew W Vaughn Milos Tanurdzić Zachary Lippman Hongmei Jiang Robert Carrasquillo Pablo D Rabinowicz Neilay Dedhia W Richard McCombie Nicolas Agier Agnès Bulski Vincent Colot R W Doerge Robert A Martienssen |
| author_sort | Matthew W Vaughn |
| collection | DOAJ |
| description | Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F(2) families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means. |
| first_indexed | 2024-12-17T02:21:23Z |
| format | Article |
| id | doaj.art-dd8d3263f2654a5dbd3afc8a14c3c819 |
| institution | Directory Open Access Journal |
| issn | 1544-9173 1545-7885 |
| language | English |
| last_indexed | 2024-12-17T02:21:23Z |
| publishDate | 2007-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj.art-dd8d3263f2654a5dbd3afc8a14c3c8192022-12-21T22:07:16ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852007-07-0157e17410.1371/journal.pbio.0050174Epigenetic natural variation in Arabidopsis thaliana.Matthew W VaughnMilos TanurdzićZachary LippmanHongmei JiangRobert CarrasquilloPablo D RabinowiczNeilay DedhiaW Richard McCombieNicolas AgierAgnès BulskiVincent ColotR W DoergeRobert A MartienssenCytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F(2) families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.http://europepmc.org/articles/PMC1892575?pdf=render |
| spellingShingle | Matthew W Vaughn Milos Tanurdzić Zachary Lippman Hongmei Jiang Robert Carrasquillo Pablo D Rabinowicz Neilay Dedhia W Richard McCombie Nicolas Agier Agnès Bulski Vincent Colot R W Doerge Robert A Martienssen Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology |
| title | Epigenetic natural variation in Arabidopsis thaliana. |
| title_full | Epigenetic natural variation in Arabidopsis thaliana. |
| title_fullStr | Epigenetic natural variation in Arabidopsis thaliana. |
| title_full_unstemmed | Epigenetic natural variation in Arabidopsis thaliana. |
| title_short | Epigenetic natural variation in Arabidopsis thaliana. |
| title_sort | epigenetic natural variation in arabidopsis thaliana |
| url | http://europepmc.org/articles/PMC1892575?pdf=render |
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