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. (July 2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology, 5 (7). pp. 1617-1629. ISSN 1544-9173
Preview |
PDF
Epigenetic_natural_variation_in_Arabidopsis_thaliana.pdf - Published Version Download (743kB) |
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 School of Biological Sciences > Publications |
| Depositing User: | CSHL Librarian |
| Date: | July 2007 |
| Date Deposited: | 02 Sep 2011 19:22 |
| Last Modified: | 22 Sep 2014 15:17 |
| PMCID: | PMC1892575 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/15271 |
Actions (login required)
 |
Administrator's edit/view item |