Epigenetic natural variation in Arabidopsis thaliana

Vaughn, M. W., Tanurdzic, M., Lippman, Z. B., Jiang, H., Carrasquillo, R., Rabinowicz, P. D., Dedhia, N., McCombie, W. R., Agier, N., Bulski, A., Colot, V., Doerge, R. W., Martienssen, R. A. (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology, 5 (7). pp. 1617-1629. ISSN 1544-9173

[img]
Preview
PDF
Epigenetic_natural_variation_in_Arabidopsis_thaliana.pdf - Published Version

Download (726Kb)
URL: http://www.ncbi.nlm.nih.gov/pubmed/17579518
DOI: 10.1371/journal.pbio.0050174

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.

Item Type: Paper
Uncontrolled Keywords: GENOMIC TILING MICROARRAYS DNA METHYLATION PATTERNS TRANSPOSABLE ELEMENTS CG METHYLATION GENE INHERITANCE PLANTS ALLELES SITES WIDE
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
organism description > plant behavior
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics
CSHL Authors:
Communities: CSHL labs > Lippman lab
CSHL labs > Martienssen lab
CSHL labs > McCombie lab
Watson School > Publications
Depositing User: CSHL Librarian
Date Deposited: 02 Sep 2011 19:22
Last Modified: 22 Sep 2014 15:17
PMCID: PMC1892575
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15271

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving