Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

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.

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

“…However, only our highly contiguous PacBio genome provides the structural context necessary to discern that these duplicates are tandems. The SVPlike gene cluster may be involved with flowering phenology, and the KCS6-like genes may be involved in cuticle buttressing of the thin, two-celled trap wall (78)(79)(80). The SVP-like genes appear to have diversified anciently, whereas the KCS6-like array occurs in a region of the genome without internal synteny, so it is likely more recent than the last U. gibba WGD.…”

DELLA proteins interact with FLC to repress flowering transition

“…Among 464 direct targets of FLC identified by ChIP‐seq, 163 (35.1%) were also affected in della ga1‐3 compared to ga1‐3 (Figure A). To further verify that FLC and DELLAs regulate gene expression in a concerted manner, previously published microarray data between svp‐41 ( short vegetative phase‐41 ) FLC FRI and svp‐41 flc FRI were compared to della ga1‐3 versus ga1‐3 (Cheminant et al ; Mateos et al ). Analysis of svp‐41 FLC FRI and svp‐41 flc‐3 FRI grown for 2 weeks under short day conditions showed that 562 genes expressed differentially, among which 139 (24.7%) were also identified in the comparison of della ga1‐3 versus ga1‐3 .…”

Effects of environmental variation during seed production on seed dormancy and germination

“…Supporting data is to be found in Chiang et al, 2009;Penfield and Hall, 2009;Chen et al, 2014;Kendall et al, 2011;Chiang et al, 2011;Deng et al, 2011;Mateos et al, 2015;Kaufmann et al, 2009;Vaistij et al 2012;Nakamura et al, 2011;Dave et al 2016;He et al 2016). Temperature-regulated genes are shown in blue.…”

“…In embryos this is likely affects levels of hormones and control of hormone signal transduction. For instance, FLC has not only been linked to regulation of ABA metabolism through CYTOCHROMEP450 707A (CYP707A) genes (Chiang et al, 2009;Deng et al, 2011), but also to indirect regulation of GA3OX1 via both TEMPRANILLO1 and APETALA1 (Mateos et al, 2015). It is very likely that understanding the environmental control of seed germination will require understanding in detail links between flowering time pathways which carry environmental signals and hormone metabolism and signalling.…”