Identification of SHORT VEGETATIVE PHASE putative targets through whole-genome expression analysis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE32397 | GEO | 2013/04/23
SECONDARY ACCESSION(S): PRJNA147927
REPOSITORIES: GEO
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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 regulated by SVP by means of Arabidopsis Tiling 1.0R Arrays (Affymetrix) during the two distinct phases of development. Arabidopsis thaliana seedlings and inflorescences were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. To evaluate the amount of SVP expression in the vegetative phase we used svp-41 single mutant 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 svp-41 agl24-2 ap1-12 triple mutant 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-32397 | biostudies-arrayexpress
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.
2013-04-23 | GSE33120 | GEO
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: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. 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:Six transcriptomes were generated for vegetative and reproductive plants of the lycophyte Selaginella nipponica, aiming at the molecular basis of the transition between the two growth phases, which is important to clarify the conservation of the SPL regulation in growth phase transition within land plants.
2021-01-01 | GSE164112 | 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: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:In plants, juvenile to adult phase transition is regulated by the sequential activity of two microRNAs: miR156 and miR172. A decline in miR156 and increase in miR172 abundance is associated with phase transition. There is very limited information on phase transition in economically important horticultural tree crops, which have a significantly long vegetative phase affecting fruit bearing. Here we profiled various molecular cues known to be involved in phase transition and flowering, including the microRNAs miR156 and miR172, in three horticultural tree crops avocado (Persea americana), mango (Mangifera indica) and macadamia (Macadamia integrifolia). We observed that miR156 expression decreases as these trees age and can potentially be used as a juvenility marker. Consistent with findings in annual plants, we also observed conserved regulation of the miR156-SPL3/4/5 regulatory module in these genetically distant tree crops, suggesting that this pathway may play a highly conserved role in vegetative identity. Meanwhile, the abundance of miR172 and its target AP2-like genes, as well as the accumulation level of SPL9 transcripts, were not related with plant age in these crops except in avocado where miR172 expression increased steadily. Finally, we demonstrate that various floral genes, including AP1 and SOC1 were upregulated in the reproductive phase and can be used as potential markers for the reproductive phase transition. Overall, this study provides an insight into the molecular associations of juvenility and phase transition in horticultural trees where crop breeding and improvement is encumbered by long juvenile phases.
2019-05-01 | GSE130476 | GEO
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.
2015-01-11 | GSE54881 | GEO