Epigenetic natural variation in Arabidopsis thaliana

Vaughn, Matthew W., Tanurdzic, Milos, Lippman, Zachary, Jiang, Hongmei, Carrasquillo, Robert, Rabinowicz, Pablo D., Dedhia, Neilay, McCombie, W. Richard, Agier, Nicolas, Bulski, Agnes, Colot, Vincent, Doerge, R. W. and Martienssen, Robert A. (2007) Epigenetic natural variation in Arabidopsis thaliana. PloS Biology, 5 7: 1617-1629. doi:10.1371/journal.pbio.0050174

Author Vaughn, Matthew W.
Tanurdzic, Milos
Lippman, Zachary
Jiang, Hongmei
Carrasquillo, Robert
Rabinowicz, Pablo D.
Dedhia, Neilay
McCombie, W. Richard
Agier, Nicolas
Bulski, Agnes
Colot, Vincent
Doerge, R. W.
Martienssen, Robert A.
Title Epigenetic natural variation in Arabidopsis thaliana
Journal name PloS Biology   Check publisher's open access policy
ISSN 1544-9173
Publication date 2007-07
Sub-type Article (original research)
DOI 10.1371/journal.pbio.0050174
Open Access Status DOI
Volume 5
Issue 7
Start page 1617
End page 1629
Total pages 13
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
Abstract 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Biological Sciences Publications
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Citation counts: TR Web of Science Citation Count  Cited 246 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 266 times in Scopus Article | Citations
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Created: Mon, 08 Apr 2013, 22:07:01 EST by Gail Walter on behalf of Examinations