Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA97067 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. As part of a project for profiling replication origins in Arabidopsis thaliana, we have performed ChIP-chip analysis of the binding of ORC1 and CDC6, two proteins involved in initiation of DNA replication. Here, we provide the data of the ORC1-bound and CDC6-bound genomic sites using as control genomic DNA.
2011-02-06 | GSE21928 | GEO
Project description:gravity-Gravitational signature of synchronized cell cultures in particular cell cycle stages
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Project description:Cell cycle and cell death interaction in plants: PCNA, AtXRs and AtMIPS pathway.
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Project description:DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7α) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7α and its paralog, CDCA7β, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7α/β selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7α expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7α alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.
2024-12-16 | GSE283987 | GEO
Project description:Studies on the small compound PLU that induced cell mass formation in Arabidopsis thaliana
| PRJDB13246 | ENA
Project description:Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. Here we have profiled origins in Arabidopsis thaliana by high-throughput sequencing of purified nascent DNA strands. We have identified 1543 replication origins, which were uniformly distributed across the Arabidopsis genome and enriched in binding signals of two replication initiation proteins, CDC6 and ORC1. We have also analyzed novel epigenome maps of various histone modifications and found links between origins and epigenetic signatures, which differ from or have not been reported for other eukaryotic systems. Arabidopsis origins tend to be embedded in G+C-rich regions within the 5’ half of genes, enriched in histone H2A.Z, H3K4me2/3 and acetylated H4, and depleted of H3K4me1 and H3K9me2. Our data establish the basis for the understanding of the epigenetic specification of origins of replication in Arabidopsis and have implications for the mechanisms of origin specification in other eukaryotes. This SuperSeries is composed of the SubSeries listed below.
2011-02-06 | GSE21828 | GEO
Project description:Genome-wide demethylation of Arabidopsis endosperm
| PRJNA116929 | ENA
Project description:R1R2R3-Myb proteins represent an evolutionarily conserved class of Myb family proteins important for cell cycle regulation and differentiation in eukaryotic cells. In plants, this class of Myb proteins are believed to play important roles in cell cycle regulation through transcriptional regulation of G2/M phase-specific genes by binding to common cis-elements, called MSA elements. In Arabidopsis thaliana, MYB3R1 and MYB3R4 act as transcriptional activators and positively regulate cytokinesis by activating transcription of KNOLLE, which encodes a cytokinesis-specific syntaxin. Here, we show that the double mutation myb3r1 myb3r4 causes pleiotropic developmental defects, some of which are due to deficiency of KNOLLE whereas other are not, suggesting multiple target genes are involved. Consistently, microarray analysis of the double mutant revealed altered expression of many genes, among which G2/M-specific genes showed significant overrepresentation of the MSA motif and a strong tendency to be down-regulated by the double mutation. Our results demonstrate, on a genome-wide level, the importance of the MYB3R-MSA pathway for regulating G2/M-specific transcription. In addition, MYB3R1 and MYB3R4 may have diverse roles during plant development by regulating G2/M-specific genes with various functions, as well as genes possibly unrelated to the cell cycle.
2011-09-07 | GSE29433 | GEO
Project description:Transcript Profiling of Arabidopsis Plant Life Cycle
| PRJNA87627 | ENA
Project description:Genome-wide analysis of mRNA cleavage sites in Arabidopsis T87 cultured cell under heat stress condition
| PRJDB8951 | ENA