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ABSTRACT:
PROVIDER: PRJEB90358 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Viola odorata (sweet violet) genome assembly, ddVioOdor1
| PRJEB70564 | ENA
Project description:Viola odorata (sweet violet), genomic and transcriptomic data
| PRJEB69495 | ENA
Project description:Viola odorata (sweet violet) genome assembly, ddVioOdor1, alternate haplotype
| PRJEB70565 | ENA
Project description:Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant species A. thaliana and A. arenosa. Here we report that reduced DNA methylation in met1-RNAi A. suecica lines altered the expression of ~200 genes encoding transposons, centromeric and heterochromatic RNAs, and predicted proteins. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes but not of the repressed genes and led to increased mobility of En/Spm-like transposons in met1-RNAi A. suecica lines. Compared to A. arenosa centromeres, A. thaliana centromeres were hypermethylated, which correlates with higher levels of small RNA accumulation in A. thaliana centromeres than that in A. arenosa centromeres. Derepression of the genes examined was primarily derived from A. thaliana subgenome, and A. arenosa genes are less affected by methylation defects. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 was maintained in resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810, which was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that a subset of A. thaliana and A. arenosa genes are differentially methylated in natural allopolyploids, and some A. thaliana genes including centromeres are subjected to transcriptional repression and genome-specific RNA-mediated DNA methylation in Arabidopsis allopolyploids. Keywords: gene expression in reduced DNA methylation lines in Arabidopsis allotetraploids
2008-03-30 | GSE9512 | GEO
Project description:Hybridization to Affymetrix tiling array Ath 1.0R performed using cDNA from Arabidopsis suecica var. Sue-1
2011-01-01 | E-MEXP-2968 | biostudies-arrayexpress
Project description:To find the possible molecular mechanism of myopia protection by violet light, we performed expression microarray analysis of chick chorioretinal tissue. The mRNA were obtained at day 13 from the following four groups: control eyes with or without violet light exposure and covered eyes with or without violet light exposure, and then the gene expression pattern was compared among them. Principle component analysis, which is to find major patterns of variability in gene expression, was performed and we found that the largest gene population (PC1, positive: n = 138, negative: n = 292) was affected by violet light treatment. On the other hand, the second largest gene population (PC2, positive: n = 120, negative: n = 23) was affected in the eyes covered with a plastic lens. The previously reported myopia-related genes such as Bmp2, Ednrb, Fgf2, Igf1, Il18, Irbp, Lumican, Sfrp1, Tgfb1, Vegfa, Vip, and Wnt2b were not found in the PC1 group in vivo, which indicates that they responded less to violet light. In the PC1 group, only one myopia protective gene, EGR1 (ZENK, zif268), was found among the previously reported myopia related genes.
2017-03-08 | GSE90118 | GEO