Arabidopsis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA669593 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12880900_1.fastq.gz | Fastqsanger.gz | |||
| SRR12880900_2.fastq.gz | Fastqsanger.gz | |||
| SRR12880901_1.fastq.gz | Fastqsanger.gz | |||
| SRR12880901_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE24494: cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE24831: cgh_colvsc24_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE24835: cgh_colvscvi_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25049: h3k4me2_c24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25050: h3k27me3_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25051: h3k27me3_cvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25052: h3k27me3_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25053: h3k4me2_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25054: h3k4me2_cvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25056: h3k4me2_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25057: h3k27me3_colxc24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25058: h3k27me3_c24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25059: h3k27me3_col(c24)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25060: h3k4me2_colxc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25061: h3k4me2_col_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions Refer to individual Series
2011-05-17 | E-GEOD-24836 | biostudies-arrayexpress
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295118 | GEO
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295116 | GEO
Project description:Reduced DNA methylation in Arabidopsis allopolyploids induces genome-specific changes in gene expression
| PRJNA103309 | 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:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295119 | GEO
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295117 | GEO
Project description:Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
| PRJNA99003 | ENA
Project description:The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter-enhancer interactions and DNA loop stabilization
| EGAS00001007411 | EGA
Project description:Genome-wide analysis of gene expression has documented differential gene expression between closely related species in plants or animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In Arabidopsis, 15-43% of genes are expressed differently between the related species, A. thaliana and A. arenosa, and the majority of them are nonadditvely expressed (differently from mid-parent value) in allotetraploids relative to the parents. The gene expression variation is associated with transcriptional and posttranscriptional mechanisms. Although transcriptional regulation by epigenetic mechanisms plays a role in nonadditive gene expression, the effects of posttranscriptional regulation on nonadditive gene expression is largely unknown. Here we reported a comprehensive genome-wide analysis of mRNA decay in Arabidopsis allotetraploids using oligo gene microarrays. Among ~26,000 annotated genes on the arrays, over 1% of genes showed a rapid decay rate with an estimated half-life of less than 60 min, and these genes are known as genes with unstable transcripts (GUTs). Interestingly, 30% of GUTs matched the nonadditively expressed genes, and their expression levels were significantly negatively correlated. These nonadditively expressed GUTs are highly enriched with a 2-8-fold increase compared to the proportion of all genes in the Gene Ontology (GO) classifications in response to stress, abiotic and biotic stimulus, signal transduction, and transcription. The data are consistent with the enrichment of nonadditvely-expressed genes in those categories in allopolyploids of Arabidopsis, wheat and cotton. Interestingly, the GUTs include some key transcription factors including circadian clock regulators, suggesting a mechanism for rapid response to light signalling and clock regulation in allotetraploids. These data collectively suggest an important role of mRNA stability in nonadditive expression of homoeologous genes in allopolyploids.
2011-09-16 | GSE26065 | GEO