NASCArrays Information at The BAR

Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the experiment number. To download the CEL files, please click on the ftp link.

Description:In plants and animals, substantial evidence has implicated DNA methylation in the differential control of gene expression (Bird and Wolffe, 1999). For individual genes, different methylation patterns can be detected when different tissues are compared. These patterns are remarkably consistent among individuals of the same species, leading to the suggestion that methylation patterns are established during gametogenesis and change consistently throughout development (Monk et al, 1987). Several DNA methyltransferases have been identified in Arabidopsis (Genger et al, 1999). Mutations that reduce methylation have a pleiotropic effect on Arabidopsis morphology, indicating that many developmentally important genes are under methylation control. Assessment of DNA methylation patterns in Arabidopsis, however, have thus far been limited to the analysis of one or a few genes. Heterochromatin, in particular, is the most highly methylated portion of the genome ( Vongs et al, 1993 ), and our recent discovery of several genes (and ESTs) located within centromeric heterochromatin (Copenhaver et al., 1999) raises the possibility that these genes, in particular, may be highly sensitive to the state of DNA methylation. We would like to use microarray technology, combined with our analysis of heterochromatic DNA in the centromere regions to address the following questions: Which genes are regulated by DNA methylation? Do genes regulated by methylation reside in particular regions of the genome? Do patterns in heterochromatic regions differ from those in the euchromatic chromosome arms? As a first step toward answering these questions, we propose a 2-slide experiment that will compare gene expression patterns in normal seedlings, and in seedlings that have been treated to remove methylation. Specifically, we have treated Arabidopsis seedlings of the Columbia ecotype with 5-Aza-Deoxycytidine (an inhibitor of methyltransferase) for 10 days. Southern blotting has confirmed that this treatment is sufficient to eliminate DNA methylation at much of the centromeric heterochromatin. We have prepared mRNA from treated plants and from untreated controls, and would like to use this mRNA to identify all of the genes that differ in their expression patterns. Subsequently, we will correlate alterations in gene expression levels with the position of the genes on the chromosome, providing insight into the correlation between methylation state and overall chromatin structure.
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Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File