Abstract
BackgroundThe initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants. The MADS-box transcription factors (TFs) FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) form a complex to repress the expression of genes that initiate flowering in Arabidopsis. Both TFs play a central role in the regulatory network by conferring seasonal patterns of flowering. However, their interdependence and biological relevance when acting as a complex have not been extensively studied.ResultsWe characterized the effects of both TFs individually and as a complex on flowering initiation using transcriptome profiling and DNA-binding occupancy. We find four major clusters regulating transcriptional responses, and that DNA binding scenarios are highly affected by the presence of the cognate partner. Remarkably, we identify genes whose regulation depends exclusively on simultaneous action of both proteins, thus distinguishing between the specificity of the SVP:FLC complex and that of each TF acting individually. The downstream targets of the SVP:FLC complex include a higher proportion of genes regulating floral induction, whereas those bound by either TF independently are biased towards floral development. Many genes involved in gibberellin-related processes are bound by the SVP:FLC complex, suggesting that direct regulation of gibberellin metabolism by FLC and SVP contributes to their effects on flowering.ConclusionsThe regulatory codes controlled by SVP and FLC were deciphered at the genome-wide level revealing substantial flexibility based on dependent and independent DNA binding that may contribute to variation and robustness in the regulation of flowering.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0597-1) contains supplementary material, which is available to authorized users.
Highlights
The initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants
We examined the individual and combined activities of the MADS-box transcription factor (TF) SHORT VEGETATIVE PHASE (SVP) and FLOWERING LOCUS C (FLC), which, as flowering repressors that control the effect of environmental cues on floral induction, fulfil key functions within the network controlling flowering in Arabidopsis thaliana
Transcriptional network controlled by FLC and SVP in leaves and apices FLC and SVP delay flowering by repressing the expression of target genes such as FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) in the leaves and apices, respectively [30,31,34], and were reported to participate in the same protein complex [12]
Summary
The initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants. The MADS-box transcription factors (TFs) FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) form a complex to repress the expression of genes that initiate flowering in Arabidopsis. Both TFs play a central role in the regulatory network by conferring seasonal patterns of flowering. The initiation of flowering is the first step in reproductive development, and is controlled by a complex regulatory network that converges on the transcription of a small number of floral integrator genes [1,2]. We examined the individual and combined activities of the MADS-box TFs SHORT VEGETATIVE PHASE (SVP) and FLOWERING LOCUS C (FLC), which, as flowering repressors that control the effect of environmental cues on floral induction, fulfil key functions within the network controlling flowering in Arabidopsis thaliana
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