Expression data from Arabidopsis seedling during plastid development
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ABSTRACT:
PROVIDER: PRJNA605424 | ENA |
REPOSITORIES: ENA
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Project description:For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary. We employed a gene expression profiling approach in order to elucidate the changes in gene expression that occur at different stages of plastid development.
2020-02-07 | GSE144694 | GEO
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Project description:Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus
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Project description:Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus.
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Project description:Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.
2026-08-05 | GSE317463 | GEO
Project description:Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.
2026-08-05 | GSE308159 | GEO
Project description:Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.
2026-08-05 | GSE308160 | GEO
Project description:Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.
2026-08-05 | GSE308349 | GEO
Project description:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development.
2013-07-22 | GSE30910 | GEO
Project description:Plastids communicate with the nucleus through retrograde signaling pathways that coordinate nuclear and plastid gene expression to support plant development and environmental adaptation. However, how plastid regulatory factors are dynamically controlled to modulate these signals remains largely unknown. Here we identify a proteostasis mechanism that regulates plastid retrograde signaling through the ubiquitin–26S proteasome system. We show that the nuclear-encoded plastid RNA-editing factor MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2) is targeted for degradation by a Skp1–Cullin1–F-box (SCF) ubiquitin ligase assembled with the MORF2-INTERACTING F-BOX (MIF) protein. MIF physically associates with MORF2 and promotes its ubiquitylation and proteasome-dependent turnover. Genetic and physiological analyses reveal that this pathway balances early plant development. MIF overexpression suppresses seedling growth and disrupts chloroplast structure and function, whereas mif null mutants or MORF2 overaccumulation retard seed germination and reduce photosynthetic efficiency. Transcriptomic profiling and RNA-editing analyses further demonstrate that MIF-dependent MORF2 turnover modulates plastid RNA editing and retrograde signaling pathways. Together, our results uncover a previously unrecognized cytoplasmic regulatory layer that links ubiquitin-mediated proteostasis to plastid RNA editing and retrograde signaling. This mechanism enables plants to coordinate seed germination and chloroplast development during early seedling establishment.
2026-04-16 | GSE325043 | GEO