Abstract
Members of the PIF quartet (PIFq; PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. However, a comprehensive definition of the PIFq-regulated transcriptome under SD is still lacking. We have recently shown that SD and free-running (LL) conditions correspond to “growth” and “no growth” conditions, respectively, correlating with greater abundance of PIF protein in SD. Here, we present a genomic analysis whereby we first define SD-regulated genes at dawn compared to LL in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, we have identified 349 PIF/SD-regulated genes, approximately 55% induced and 42% repressed by both SD and PIFq. Comparison with available databases indicates that PIF/SD-induced and PIF/SD-repressed sets are differently phased at dawn and mid-morning, respectively. In addition, we found that whereas rhythmicity of the PIF/SD-induced gene set is lost in LL, most PIF/SD-repressed genes keep their rhythmicity in LL, suggesting differential regulation of both gene sets by the circadian clock. Moreover, we also uncovered distinct overrepresented functions in the induced and repressed gene sets, in accord with previous studies in other examined PIF-regulated processes. Interestingly, promoter analyses showed that, whereas PIF/SD-induced genes are enriched in direct PIF targets, PIF/SD-repressed genes are mostly indirectly regulated by the PIFs and might be more enriched in ABA-regulated genes.
Highlights
Environmental light conditions change within each day and season, and plants have adapted to these oscillations in solar energy by timing their physiological responses to specific times of the day and/or the year
Pifq seedlings in SD display SS1.5F alterations in the expression of 538 genes relative to the SD-grown wild type (WT-SD vs. pifq-SD; Figure 1B and Supplementary Figure S1; see Dataset S1 online for the gene list). Of these 538 genes, 349 (64.8%) are identical to those altered in expression in the WT by exposure to the long night of SD (Figure 1B and Supplementary Figure S1). Of these common 349 SS1.5F genes, 191 (54.7%) are SD- and PIFinduced, and 145 (41.5%) are SD- and PIF-repressed, and were designated PIF/SD-induced and PIF/SD-repressed, respectively (Dataset S1)
A considerable additional number of the SS1.5F genes that respond to SD in the pifq mutant only (PIFregulated only, purple symbols) respond in the WT in SD compared to LL, albeit to a lesser extent compared to the fold change (FC) difference between WT and pifq (Figure 1C and Supplementary Figure S2B)
Summary
Environmental light conditions change within each day and season, and plants have adapted to these oscillations in solar energy (and the related changes in temperature and water availability) by timing their physiological responses to specific times of the day and/or the year. PIFq Contribution to Diurnal Gene Expression of phy function resides in the ability to bind in its photoactivated state to the PIF (Phy-Interacting Factor) family of basic helixloop-helix (bHLH) transcriptional regulators (Ni et al, 1999; Bae and Choi, 2008; Leivar and Monte, 2014; Xu et al, 2015). After seed germination and emergence into sunlight, Arabidopsis seedlings are subjected to alternating light/dark cycles Hypocotyl elongation under these conditions depends on the duration of the dark period in a non-linear fashion, and it is accelerated in the long nights of short-day (SD) photoperiods (Niwa et al, 2009). We have recently shown that the transcriptional activity of PIF3 (and possibly of the other PIFq members) is inhibited by the core component of the circadian clock TOC1 to gate hypocotyl elongation to the end of the night (Soy et al, 2016)
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