RNA-Seq of early flowering Arabidopsis thaliana FLC mutants and wild type controls
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB89960 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR15083900.fastq.gz | Fastqsanger.gz | |||
| ERR15083901.fastq.gz | Fastqsanger.gz | |||
| ERR15083902.fastq.gz | Fastqsanger.gz | |||
| ERR15083903.fastq.gz | Fastqsanger.gz | |||
| ERR15083904.fastq.gz | Fastqsanger.gz |
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Project description:Plants of three different genotypes (FRI FLC, FRI flc and fri flc) were induced to flowering by shifting from short day conditions to long day conditions. FRI=FRIGIDA, FLC=FLOWERING LOCUS C.
2005-09-08 | E-TABM-19 | biostudies-arrayexpress
Project description:Arabiposis plants with conbinations of different FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) alleles grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0): fri FLC Columbia with introgressed FRI from Sf-2: FRI FLC Columbia with introgressed FRI and deleted FLC (flc-3): FRI flc Columbia with deleted FLC (flc-3): fri flc Time points: 0, 2, and 4 days after shift to long days Keywords = flowering Keywords: time-course
2003-08-06 | GSE577 | GEO
Project description:Quantitative variation in expression of the Arabidopsis floral repressor FLC influences whether plants overwinter before flowering or have a rapid cycling habit, enabling multiple generations a year. Genetic analysis has identified activators and repressors of FLC expression, but how they interact to set expression level is poorly understood. Here, we show that antagonistic functions of the FLC activator FRIGIDA (FRI), and the repressor FCA, at a specific stage of embryo development, determines FLC expression and flowering. FRI antagonizes an FCA-induced proximal polyadenylation to increase FLC expression and delay flowering. Sector analysis shows that FRI activity during the early heart stage of embryo development maximally delays flowering. Opposing functions of co-transcriptional regulators during an early embryonic developmental window thus set FLC expression levels and determine flowering time.
2021-03-19 | GSE166728 | GEO
Project description:The autonomous flowering pathway promotes flowering in rapid-flowering accessions of Arabidopsis thaliana by reducing the expression of the key flowering repressor gene FLC. Although previous studies identified several autonomous pathway components, little is known about how these components cooperate in the regulation of flowering time. Here, we identified an autonomous pathway complex (APC) composed of three known autonomous pathway components (FLD, LD, and SDG26) and three previously uncharacterized components (EFL2, EFL4, and APRF1). Loss-of-function mutations of all of these components result in increased FLC expression and delayed flowering. The late-flowering phenotype is independent of photoperiod and can be overcome by vernalization, supporting the inference that the complex regulates flowering time specifically through the autonomous pathway. Our ChIP-seq analyses indicated that the APC components are required for the suppression of the histone modifications (H3Ac, H3K4me3, and H3K36me3) associated with the activation of gene expression and for the promotion of the histone modification (H3K27me3) associated with the repression of gene expression at FLC. We also found that the C-terminal coiled-coil domain of SDG26 binds to DNA in vitro and that the DNA-binding ability mediates the association of SDG26 with FLC chromatin in vivo. These results reveal the molecular basis of the autonomous pathway.
2022-06-25 | GSE193251 | GEO
Project description:The autonomous flowering pathway promotes flowering in rapid-flowering accessions of Arabidopsis thaliana by reducing the expression of the key flowering repressor gene FLC. Although previous studies identified several autonomous pathway components, little is known about how these components cooperate in the regulation of flowering time. Here, we identified an autonomous pathway complex (APC) composed of three known autonomous pathway components (FLD, LD, and SDG26) and three previously uncharacterized components (EFL2, EFL4, and APRF1). Loss-of-function mutations of all of these components result in increased FLC expression and delayed flowering. The late-flowering phenotype is independent of photoperiod and can be overcome by vernalization, supporting the inference that the complex regulates flowering time specifically through the autonomous pathway. Our ChIP-seq analyses indicated that the APC components are required for the suppression of the histone modifications (H3Ac, H3K4me3, and H3K36me3) associated with the activation of gene expression and for the promotion of the histone modification (H3K27me3) associated with the repression of gene expression at FLC. We also found that the C-terminal coiled-coil domain of SDG26 binds to DNA in vitro and that the DNA-binding ability mediates the association of SDG26 with FLC chromatin in vivo. These results reveal the molecular basis of the autonomous pathway.
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Project description:Characterizing the FIONA1 protein in Arabidopsis revealing its methyl transferase activity influencing level of FLC transcripts plus the pleiotropic phenotype obsersed in fio mutants
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Project description:The transition to flowering in plants is controlled by a regulatory network that responds to both developmental and environmental signals. The MADS-box genes FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major flowering repressors that enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod. FLC and SVP physically interact in vivo and mutation of each gene causes early flowering while the double mutant is more extreme. The molecular mechanisms underlying these genetic interactions are mostly unknown. We addressed the regulatory input of these two key transcription factors (TFs) both individually and as a complex at the genome-wide level through ChIP-seq and microarray expression analysis in single and double mutants. Analysis of each TF demonstrated that the complex acts predominantly via functional redundancy in the repression of flowering. SVP and FLC bind to the same regions of the flowering genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) but do not require the presence of the other to bind. However, genome-wide identification of SVP and FLC occupancy events revealed that their binding scenarios are quantitatively and qualitatively affected by the presence of the cognate partner. A subgroup of genes whose regulation by these TFs depends exclusively on combinatorial binding of both proteins was identified, demonstrating a qualitatively essential role of the SVP-FLC complex. Some of these genes are involved in the control of flowering through direct and indirect regulation of Gibberellin-related processes. Cis-regulatory elements enriched only at such complex-bound sites were identified. Thus the regulatory output mediated by SVP and FLC reveals substantial flexibility, leading to dependent and independent DNA binding that enables additive, cooperative and repressive modes of co-regulation. In total 48 samples; 24 leaf samples corresponding to two different growing conditions, 24 apex samples corresponding to two different growing conditions.
2015-01-11 | E-GEOD-57416 | biostudies-arrayexpress
Project description:The transition to flowering in plants is controlled by a regulatory network that responds to both developmental and environmental signals. The MADS-box genes FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major flowering repressors that enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod. FLC and SVP physically interact in vivo and mutation of each gene causes early flowering while the double mutant is more extreme. The molecular mechanisms underlying these genetic interactions are mostly unknown. We addressed the regulatory input of these two key transcription factors (TFs) both individually and as a complex at the genome-wide level through ChIP-seq and microarray expression analysis in single and double mutants. Analysis of each TF demonstrated that the complex acts predominantly via functional redundancy in the repression of flowering. SVP and FLC bind to the same regions of the flowering genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) but do not require the presence of the other to bind. However, genome-wide identification of SVP and FLC occupancy events revealed that their binding scenarios are quantitatively and qualitatively affected by the presence of the cognate partner. A subgroup of genes whose regulation by these TFs depends exclusively on combinatorial binding of both proteins was identified, demonstrating a qualitatively essential role of the SVP-FLC complex. Some of these genes are involved in the control of flowering through direct and indirect regulation of Gibberellin-related processes. Cis-regulatory elements enriched only at such complex-bound sites were identified. Thus the regulatory output mediated by SVP and FLC reveals substantial flexibility, leading to dependent and independent DNA binding that enables additive, cooperative and repressive modes of co-regulation.
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Project description:The MADS-box transcription factors FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major transcriptional repressors controlling flowering time. They enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod, acting at least in part by blocking transcription of the floral pathway integrators. As other MADS-box transcription factors, FLC and SVP can interact in vivo forming multimeric complexes. Mutations in either FLC or SVP lead to similar early flowering, suggesting that FLC-SVP interaction might be the major control unit. Here we have analyzed the coordinated regulatory modes of these two key transcription factors at a genome-wide level through ChIP-seq and gene expression microarrays. Genome-wide identification of SVP and FLC DNA-binding occupancy events revealed that their binding scenarios are strongly yet differently affected by the presence of the cognate partner both at a quantitative as well as a qualitative level. Also, we identified a subgroup of genes whose regulation exclusively depends on the combinatorial binding of these two proteins, strengthening the role of the SVP-FLC complex. Some of these genes are involved in the control of flowering through direct and indirect regulation of Gibberellin-related genes such as GA2ox8, DDF1 and TEM1. Interestingly, we identified cis-regulatory elements enriched uniquely at complex-bound sites. This study decoded the regulatory code mediated by the major flowering repressors SVP and FLC.
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Project description:FIONA1-mediated methylation of the 3'UTR of FLC affects FLC transcript levels and flowering in Arabidopsis
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