Combinatorial complexity in a transcriptionally-centered signaling hub in Arabidopsis

Authors: PFEIFFER, A - University Of California; SHI, H - University Of California; TEPPERMAN, J - University Of California; ZHANG, Y - University Of California; QUAIL, P - University Of California

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2014
Publication Date: 11/13/2014
Citation: Pfeiffer, A., Shi, H., Tepperman, J.M., Zhang, Y., Quail, P.H. 2014. Combinatorial complexity in a transcriptionally-centered signaling hub in Arabidopsis. Molecular Plant. 7(11):1598-1618.

Interpretive Summary: Seedlings emerging from buried seed into subterranean darkness use a developmental strategy, termed skotomorphogenesis, to rapidly reach the soil surface. Four transcription factors, called PIFs (for Phytochrome (phy)-Interacting Factors) are collectively functionally essential for this strategy. Emergence into sunlight, activates the cell’s phy photosensory receptors that then bind to the PIFs and induce their rapid degradation, thereby triggering a major redirection of gene expression that switches the seedling to photomorphogenic (normal green-plant) development. This work identifies genes that are direct targets of PIF regulation across the entire genome, and shows that the contribution of each PIF to this activity is different, despite the fact that all four PIFs bind to the same DNA-recognition motifs, even in fully shared genes. These findings suggest a model whereby each PIF interacts differentially with the local gene-promoter context in a way that can significantly modulate simple occupancy-based determination of the expression level.

Technical Abstract: A subfamily of four Phytochrome (phy)-Interacting bHLH transcription Factors (PIFs) collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoactivated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a transition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process. To identify the direct targets of PIF transcriptional regulation genome-wide, we analyzed the DNA-binding sites for all four PIFs by ChIP-seq analysis, and defined the genes transcriptionally regulated by each PIF, using RNA-seq analysis of pif mutants. Despite the absence of detectable differences in DNA-binding-motif recognition between the PIFs, the data show a spectrum of regulatory patterns, ranging from single PIF dominance to equal contributions by all four. Similarly, a broad array of promoter architectures was found, ranging from single PIF-binding sites, containing single sequence motifs, through multiple PIF-binding sites, each containing one or more motifs, with each site occupied preferentially by one to multiple PIFs. Quantitative analysis of the promoter occupancy and expression level induced by each PIF revealed an intriguing pattern. Although there is no robust correlation broadly across the target-gene population, examination of individual genes that are shared targets of multiple PIFs shows a gradation in correlation from strongly positive, through uncorrelated, to negative. This finding suggests a dual-layered mechanism of transcriptional regulation, comprising both a continuum of binding-site occupancy by each PIF and a superimposed layer of local regulation that acts differentially on each PIF, to modulate its intrinsic transcriptional activation capacity at each site, in a quantitative pattern that varies between the individual PIFs from gene to gene. These findings provide a framework for probing the mechanisms by which transcription factors with overlapping direct-target genes integrate and selectively transduce signals to their target networks.