Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA149369 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR354186.fastq.gz | Fastqsanger.gz | |||
| SRR354187.fastq.gz | Fastqsanger.gz | |||
| SRR354188.fastq.gz | Fastqsanger.gz | |||
| SRR354189.fastq.gz | Fastqsanger.gz | |||
| SRR354190.fastq.gz | Fastqsanger.gz |
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Project description:SVP is a key MADS-box transcription factor for Arabidopsis development since it acts both during vegetative and reproductive phases where it plays different roles probably by interacting with different partners to regulate specific sets of target genes. In fact, whereas SVP functions as a repressor of floral transition during the vegetative phase, it works as floral meristem gene during reproductive phase. We studied the behavior of SVP during two distinct developmental phases: the vegetative and reproductive phase. The aim of these studies is to identify subsets of genes that are directly bound by SVP by means of ChIP sequencing (Illumina Solexa Sequencing) approach during the two distinct phases of development. Arabidopsis thaliana seedlings and inflorescences were selected at successive stages of early development for chromatin extraction and subsequent immunoprecipitation using GFP antibody. The identification of genome wide binding sites of SVP using the ChIP-SEQ approach were performed in the vegetative phase using pSVP::SVP-GFP svp-41 and wild-type seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark); for the reproductive phase we used wild-type and pSVP::SVP-GFP svp-41 inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.
2013-04-23 | E-GEOD-33120 | biostudies-arrayexpress
Project description:Arabidopsis thaliana Transcriptome and chromatin immunoprecipitation sequencing
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Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-β and FLM-δ, which compete for interaction with the floral repressor SVP. The SVP/FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-δ complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change.
2013-09-19 | GSE48082 | 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.
2012-02-01 | GSE33297 | GEO
Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-M-NM-2 and FLM-M-NM-4, which compete for interaction with the floral repressor SVP. The SVP/FLM-M-NM-2 complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-M-NM-4 complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change. ChIP-seq A. thaliana FLM (3 replicates for gFLM and 2 replicates for FLM splice variants)
2013-09-19 | E-GEOD-48082 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation (ChIP)-sequencing of Arabidopsis plants in response to Spodoptera litura attack
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Project description:Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Transcript immunoprecipitation
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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:Chromatin immunoprecipitation and sequencing of pPLT2::PLT2-YFP in the root of plt1plt2 double mutant
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Project description:Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Small RNA immunoprecipitation
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