An MRG-mediated chromatin switch operates at the SOC1 gene to modulate abiotic stress responses during the onset of flowering
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ABSTRACT:
PROVIDER: PRJNA592188 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14154284.fastq.gz | Fastqsanger.gz | |||
| SRR14154285.fastq.gz | Fastqsanger.gz | |||
| SRR14154286.fastq.gz | Fastqsanger.gz | |||
| SRR14154287.fastq.gz | Fastqsanger.gz | |||
| SRR14154288.fastq.gz | Fastqsanger.gz |
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Project description:The mechanisms underlying the precise integration of environmental and developmental signals necessary for plant adaptation to suboptimal environments remain obscure. Here we show that a chromatin switch, mediated by MRG proteins, acts on the floral activator SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) to coordinate flowering initiation with plant responsiveness to adverse conditions. SOC1 constitutes a central hub in a mechanism that tunes down stress responses likely to optimize plant reproductive success and fitness
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Project description:A comparative study ware made to know the abiotic stress tolerance machanism between tolerant and susceptible plants at flowering stage. The tolerance in response to abiotic stresses are sum of expression of thousands of genes at a particular stage.
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Project description:A comparative study ware made to know the abiotic stress tolerance machanism between tolerant and susceptible plants at flowering stage. The tolerance in response to abiotic stresses are sum of expression of thousands of genes at a particular stage. Tomato plants were exposed to drought and heat stress for RNA extraction and hybridization on Affymetrix microarrays. To study the molecular mechanism of abiotic stress tolerance to increase the tolerance in tomato plants, transcripts of tolerant and susceptible plants at flowering stage were compared in response to heat and water stress.
2010-06-23 | E-GEOD-22304 | biostudies-arrayexpress
Project description:14-3-3 proteins are involved in a number of developmental processes in plants, largely acting through the control of transcription factor localization within the cytoplasm or nucleus. The temperate Pooideae grass 14-3-3 gene GF14h in particular was previously found to be co-expressed with flowering activators in the vernalization pathway, leading to the hypotheses that its protein product is involved in vernalization responsive flowering and/or cold acclimation. To test predictions of these non-exclusive hypotheses, and to assess functional conservation broadly across angiosperms, we generated CRISPR lines of GF14h in Brachypodium distachyon (Pooideae) and compared their mutant phenotypes with those of the co-orthologous Arabidopsis thaliana (Brassicaceae) grf9 T-DNA mutant. Contrary to our first prediction, we found that rather than promoting flowering as part of the vernalization pathway, both BdGF14h and AtGRF9 repress flowering under different conditions. Our data also support a conserved role for GF14h/GRF9 genes in the promotion of growth at the expense of abiotic stress resilience. We discuss these results in the light of crop improvement and climate change.
2024-12-16 | GSE240619 | GEO
Project description:The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator. A. thaliana SOC1 ChIP-seq w. control, 3 replicates
2013-04-09 | E-GEOD-45846 | biostudies-arrayexpress
Project description:The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
2013-04-09 | GSE45846 | GEO
Project description:We compared wild type N2 to mrg-1 mutants L1 larvae. Genes tend to be upregulated rather than downregulated in these mutants. Comparison to available ChIPseq datasets indicates that the upregulated genes are heterochromatic and are not enriched for H3K36 methylation, indicating that MRG-1 loss derepresses heterochromatin indirectly.
2019-04-11 | GSE115998 | GEO
Project description:The floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). Genes encoding proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes bound by SOC1 and SVP, indicating their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was directly regulated by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)-like genes that repress FT and SOC1 expression were downregulated by SOC1, but upregulated by SVP, revealing a complex feedback regulation among key genes determining the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self-activation and repression by SVP contribute to the regulation of SOC1 expression. In addition, ChIP-chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2-like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings reveal that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks underpinning the integration of flowering signals during the floral transition. soc1-101D and 35S:SVP ChIPed with SOC1 or SVP polyclonal antibody respectively vs. soc1-2 or svp-41 in Arabidopsis 9-day-old whole seedlings
2012-02-01 | E-GEOD-33297 | 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. 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 floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). Genes encoding proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes bound by SOC1 and SVP, indicating their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was directly regulated by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)-like genes that repress FT and SOC1 expression were downregulated by SOC1, but upregulated by SVP, revealing a complex feedback regulation among key genes determining the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self-activation and repression by SVP contribute to the regulation of SOC1 expression. In addition, ChIP-chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2-like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings reveal that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks underpinning the integration of flowering signals during the floral transition.
2012-02-01 | GSE33297 | GEO