Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA316877 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3313880.fastq.gz | Fastqsanger.gz | |||
| SRR3313881.fastq.gz | Fastqsanger.gz | |||
| SRR3313882.fastq.gz | Fastqsanger.gz | |||
| SRR3313873.fastq.gz | Fastqsanger.gz | |||
| SRR3313883.fastq.gz | Fastqsanger.gz |
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Project description:As a central component during Okazaki fragment maturation, flap endonuclease 1 (FEN1) removes the 5â flap and maintains genomic stability. Here, FEN1 was cloned as a suppressor of transcriptional gene silencing (TGS) from a forward genetic screen. FEN1 is abundant in the root and shoot apical meristems and FEN1-GFP shows a nucleolus-localized signal in tobacco cells. Arabidopsis fen1-1 mutant is hypersensitive to MMS and shows reduced telomere length. Interestingly, genome-wide ChIP-seq and RNA-seq results demonstrate that FEN1 mutation leads to a decrease in the H3K27me3 level and an increase in the expression of a subset of genes marked with H3K27me3. Overall, these results uncover a role for FEN1 in mediating TGS besides maintaining genome stability in Arabidopsis. To characterized the role of FEN1 in epigenetic silencing, we examine histone modification and RNA expression changes by whole-genome RNA sequencing; H3K27me3-, H3K4me3-, H3K9me2-, H3-ChIP-seq in A. thaliana transgenic wild type (TWT) and fen1 mutant
2016-05-28 | E-GEOD-79738 | biostudies-arrayexpress
Project description:As a central component during Okazaki fragment maturation, flap endonuclease 1 (FEN1) removes the 5’ flap and maintains genomic stability. Here, FEN1 was cloned as a suppressor of transcriptional gene silencing (TGS) from a forward genetic screen. FEN1 is abundant in the root and shoot apical meristems and FEN1-GFP shows a nucleolus-localized signal in tobacco cells. Arabidopsis fen1-1 mutant is hypersensitive to MMS and shows reduced telomere length. Interestingly, genome-wide ChIP-seq and RNA-seq results demonstrate that FEN1 mutation leads to a decrease in the H3K27me3 level and an increase in the expression of a subset of genes marked with H3K27me3. Overall, these results uncover a role for FEN1 in mediating TGS besides maintaining genome stability in Arabidopsis.
2016-05-28 | GSE79738 | GEO
Project description:Here we characterized a genetic regulatory system named as the hpDNA-assisted structure-guided nuclease mediating interference (HpSGNi) system, which was composed of flap endonuclease 1 (FEN1) and mis-hairpin DNA probe (mis-hpDNA). To investigate gene regulation effective of the HpSGNi system, we co-transformed HEK293A (human embryonic kidney epithelial cells) with plasmids encoding FEN1 with NES and two groups of mis-hpDNAs targeting the EGFP gene and negative control, respectively. RNA-seq was used to examine the regulation effective. We proved the HpSGNi system can knock down specific gene in human cells. At the same time, it indicated that a degree of off-targets occur in HpSGNi-treated cells.
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Project description:Here we characterized a flap endonuclease 1 (FEN1) plus hairpin DNA probe (hpDNA) system, called the HpSGN system, for both DNA and RNA editing without sequence limitation.To investigate the mRNA on/off target cleavage effective of the HpSGN system,we co-transformed HepG2 (liver hepatocellular cells) with plasmids encoding FEN1 with NES and two groups of hpDNAs targeting the mRNA of AFP (Alpha Fetoprotein) gene and CDK9 (Cyclin-dependent kinase 9) gene, respectively. RNA-seq was used to examine the on/off taget cleavage effective.We proved the HpSGN system can knock down specific mRNAs in human cells at a level of ~25%.At the same time,it indicated that a degree of off-targets occur in HpSGN-treated cells.
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Project description:We developed an artificial genome evolution system, which we termed ‘TAQing’, by introducing multiple genomic DNA double-strand breaks using a heat-activatable endonuclease in Arabidopsis plant. The heat-activated endonuclease, TaqI, induced random DSBs, which resulted in diverse types of chromosomal rearrangements including translocations. To evaluate the potential of TAQing in multicellular organisms, we tested it in diploid and tetraploid Arabidopsis plants. In 9 out of 96 TQ4 plants, we detected 22 large copy number variations (CNVs) events compared witn wild type plant genome, whereas no CNV was found in the 16 control tetraploid plants, and 12 TQ2 plants. The combination of artificially introduced DSBs with whole-genome duplication (WGD) in plants enabled more complex genome reorganization.
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Project description:Oxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PCO N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance, and are essential for root development and survival under oxygen limiting conditions in the soil. We determine the combined effects of ERFVIIs in controlling genome expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
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Project description:Transitive silencing of mobile small RNAs in Arabidopsis Pollen
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Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
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Project description:A link between RNA metabolism and silencing affecting Arabidopsis development
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Project description:Oxygen is a key signalling component of plant biology and, whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana. However, key features of the associated PCO N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance, and are essential for root development and survival under oxygen limiting conditions in the soil. We determine the combined effects of ERFVIIs in controlling genome expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine oxidation to sulphonic acid oxidation level of ERFVIIs was defined, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
2023-07-02 | PXD039288 | Pride