Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE48082 | GEO | 2013/09/19
SECONDARY ACCESSION(S): PRJNA208886
REPOSITORIES: GEO
Similar Datasets
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:Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. However, it is unknown how the transcript level of FLM-β is down-regulated. Here we identify an RRM domain-containing protein, UBA2C, as a previously uncharacterized flowering repressor by forward genetic screening. We demonstrate that UBA2C directly binds to FLM chromatin and facilitates FLM transcription predominantly by inhibiting the histone H3K27 trimethylation, a histone mark related to transcriptional repression. At FLM chromatin, the histone H3K27 trimethylation is enhanced in response to increasing temperatures. Depletion of UBA2C weakens the response of FLM transcription and H3K27 trimethylation to temperature changes. UBA2C forms multiple puncta in the nucleus and the number of puncta increases with increasing temperatures. UBA2C contains a prion-like domain (PrLD) that is responsible for forming puncta in the nucleus in vivo. These results not only identify a previously unknown flowering-time regulator but also reveal the mechanism by which the regulator controls flowering time in response to temperature changes.
2021-10-28 | GSE165433 | GEO
Project description:Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. However, it is unknown how the transcript level of FLM-β is down-regulated. Here we identify an RRM domain-containing protein, UBA2C, as a previously uncharacterized flowering repressor by forward genetic screening. We demonstrate that UBA2C directly binds to FLM chromatin and facilitates FLM transcription predominantly by inhibiting the histone H3K27 trimethylation, a histone mark related to transcriptional repression. At FLM chromatin, the histone H3K27 trimethylation is enhanced in response to increasing temperatures. Depletion of UBA2C weakens the response of FLM transcription and H3K27 trimethylation to temperature changes. UBA2C forms multiple puncta in the nucleus and the number of puncta increases with increasing temperatures. UBA2C contains a prion-like domain (PrLD) that is responsible for forming puncta in the nucleus in vivo. These results not only identify a previously unknown flowering-time regulator but also reveal the mechanism by which the regulator controls flowering time in response to temperature changes.
2021-10-28 | GSE165432 | 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 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: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
Project description:Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana
| PRJNA208886 | ENA
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.
2015-01-11 | GSE57416 | GEO
Project description:Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well known. Due to global warming, understanding this ambient temperature pathway has become increasingly important. FLOWERING LOCUS M (FLM) is one critical flowering regulator of this pathway in Arabidopsis thaliana. We identified the Arabidopsis accession Kil-0 as an early flowering strain when compared to the common reference accession Col-0. Genetic mapping of this trait identified a causative region of around 31 kb at the bottom of chromosome one. Within this region, only FLOWERING LOCUS M (FLM) was expressed at a significantly lower level in Kil-0 when comparing RNA-seq (RNA sequencing) data from 10-day old Kil-0 and Col-0 plants grown at 21C. Furthermore, FLM was also the gene with the greatest reduction in gene expression between Kil-0 and Col-0 when we specifically analyzed 267 genes with a role in flowering time regulation what strongly suggested that FLM is the major locus that results in accelerated flowering in Kil-0.
2015-08-28 | E-MTAB-4473 | biostudies-arrayexpress