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Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings

ABSTRACT: Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings

PROVIDER: PRJNA448672 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6936280.fastq.gz	Fastqsanger.gz
	SRR6936281.fastq.gz	Fastqsanger.gz
	SRR6936282.fastq.gz	Fastqsanger.gz
	SRR6936283.fastq.gz	Fastqsanger.gz
	SRR6936284.fastq.gz	Fastqsanger.gz

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Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings

Project description:Background: Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (e.g., HY5, HFR1, PAP1 and others) in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic bases for the constitutive photomorphogenic phenotypes of spaQ remain unknown. Results: Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild type in the dark. Comparison of the RNAseq data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Moreover, a large number of genes (~2790) are predominantly regulated by SPA proteins and not by COP1, suggesting that SPA proteins might regulate many biological processes independently of COP1. Conclusions: Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling expression of a large number of genes in concert with COP1, likely through regulating the abundance of downstream transcription factors in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and –independent manner in regulating many biological processes and developmental pathways in Arabidopsis.

2018-11-05 | GSE112662 | GEO

SPA regulation of light induced gene expressions in dark-grown Arabidopsis thaliana

Project description:The total mRNA and polysomal RNA expression profiles of wild type (Col-0) and the quadruple spa mutant (spaQ) were analyzed under dark or in 4 hour light treated condition. The gene expression changed in spaQ mutant was analyzed and compared with Col-0.

2024-03-10 | GSE233765 | GEO

Effects of a 6h-long treatment with 90 mM sucrose to 4-d old, dark grown Arabidopsis seedlings

Project description:Dark grown Arabidopsis seedlings (Columbia gl1) were grown in the dark at 23°C for 4 days before adding 90 mM sucrose for 6h. Keywords: Response to nutrients; sugar sensing

2005-12-03 | GSE3704 | GEO

ATH1 Transcriptome profiling of dark grown photoreceptor mutants seedlings of Arabidopsis

Project description:Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment. Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses

2005-09-04 | GSE3038 | GEO

Transcriptome profiling of dark grown photoreceptor mutants seedlings of Arabidopsis ATH1

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SPA regulation of light induced gene expressions in dark-grown Arabidopsis thaliana

Project description:SPA regulation of light induced gene expressions in dark-grown Arabidopsis thaliana

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Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings.

Project description:Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (TFs; e.g. ELONGATED HYPOCOTYL (HY5), LONG HYPOCOTYL IN FAR-RED 1 (HFR1), PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1) and others] in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic basis for the constitute photomorphogenic phenotype of spaQ remains unknown. Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild-type in the dark. Comparison of the RNA sequencing (RNA-Seq) data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling gene expression in concert with COP1, likely through regulating the abundance of downstream TFs in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and -independent manner in regulating many biological processes and developmental pathways in Arabidopsis.

| S-EPMC8630753 | biostudies-literature

Transcription profiling of Arabidopsis dark grown photoreceptor mutants seedlings

Project description:Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment. Experiment Overall Design: We analysed the transcriptome profile in dark grown seedlings of the WT, and phyA phyB photoreceptor mutants. All seedlings have the same treatment (3d grown in complete darkness). We have two samples for each genotype that represent two replicates in each case.

2008-06-12 | E-GEOD-3002 | biostudies-arrayexpress

Whole-genome transcriptome profiling of dark-grown cryptochrome 2 over-expressing indica rice seedlings

Project description:We found that indica rice cryptochrome 2 overexpression (OsiCRY2) seedlings exhibited partial photomorphogenesis in dark. Therefore, we decided to use microarray technique to determine the genes whose expression would have been altered in dark.

2025-04-02 | GSE200963 | GEO

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Project description:Transcriptome analysis of dark grown wild-type and lon1-1 mutant seedlings

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