title: A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis.
abstract: Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4, and 5) are critically necessary to maintaining this developmental state and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using integrated ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, exerted by sequence-specific binding to G-box (CACGTG) or PBE-box (CACATG) motifs in the target promoters genome-wide. In addition, expression analysis of selected genes in this set, in all triple pif-mutant combinations, provides evidence that the PIF quartet members collaborate to generate an expression pattern that is the product of a mosaic of differential transcriptional responsiveness of individual genes to the different PIFs and of differential regulatory activity of individual PIFs toward the different genes. Together with prior evidence that all four PIFs can bind to G-boxes, the data suggest that this collective activity may be exerted via shared occupancy of binding sites in target promoters.
authors: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America.
authors: Yu
authors: Y
authors: Zhang
authors: Oleg
authors: O
authors: Mayba
authors: Anne
authors: A
authors: Pfeiffer
authors: Hui
authors: H
authors: Shi
authors: James M
authors: JM
authors: Tepperman
authors: Terence P
authors: TP
authors: Speed
authors: Peter H
authors: PH
authors: Quail
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins; D051790:G-Box Binding Factors / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D008027:Light; D009024:Morphogenesis / Q000235:genetics*; D059372:Nucleotide Motifs / Q000235:genetics; D010834:Phytochrome / Q000235:genetics / Q000378:metabolism; D036226:Seedlings / Q000235:genetics / Q000254:growth & development; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D004268:DNA-Binding Proteins; D051790:G-Box Binding Factors; D010834:Phytochrome; C508068:At2g20180 protein, Arabidopsis; C116162:PIF3 protein, Arabidopsis; C459466:PIF4 protein, Arabidopsis; C497729:PIF5 protein, Arabidopsis
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