Project description:This SuperSeries is composed of the following subset Series: GSE16503: Genomic DNA concentration series in Allele Specific Expression study GSE16504: Genomic DNA mixture series in Allele Specific Expression study GSE16505: Genomic DNA 1:1 mixtures in Allele Specific Expression study GSE16506: mRNA samples in Allele Specific Expression study Refer to individual Series
Project description:Ecotype-specific differences in genome methylation were assayed in Arabidopsis Col and Ler variations using genomic tiling microarrays. Comparative genome hybridization was also performed so that the contribution of ecotype-specific amplifications and deletions could be estimated and integrated into the analysis of differential DNA methylation. Keywords: methylation analysis and comparative genome hybridization
Project description:Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.
Project description:The mechanistic connection between the THO/TREX complex and RdDM remains poorly understood. To address this, we performed EMS mutagenesis in a transgenic Col-0 background harboring pro2×35S::LUC and pro2×35S::NPTII reporters and homozygous for rdr6, and identified a low-fluorescence mutant, tho2-8. Unlike null alleles, tho2-8 is a viable homozygous allele, offering a unique opportunity to explore THO2 function in DNA methylation. Here, we report that THO2 is required for proper siRNA accumulation and RdDM activity, revealing a previously uncharacterized role for the THO/TREX complex in epigenetic gene silencing. This study expands our understanding of the molecular coordination between RNA metabolism and epigenetic regulation in plants.
