ArticlePLoS genetics2013
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.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 218 papers.
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Who cites it
218 citing papers in PubMed, 412 citations in OpenAlex.
- BR-ENHANCED EXPRESSION 1/2/3 fine-tune plant photomorphogenesis by regulating the phyA/B-SPA1 cascade.The Plant cell · 2026Article
- DNA-binding activity of PIF7 links phytochrome B signaling to plant responses to vegetation proximity.Plant physiology · 2026Article
- Hexokinase 1 facilitates post-germinative seedling growth through its catalytic function.The Plant journal : for cell and molecular biology · 2026Article
- Twenty-five years of photobodies: formation, composition, and the 2-compartment logic of phytochrome B signaling.Plant physiology · 2026Review
- BrPIF4/BrBBX24-BrHB52-mediated hypocotyl modularity unlocks mechanized harvesting potential inHorticulture research · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis.Nature communications · 2025Article
- Involvement of Phytochrome-Interacting Factors in High-Irradiance Adaptation.International journal of molecular sciences · 2025Article
- PHYB and PIF3 repress OLE4 expression to regulate hypocotyl length and ABA signaling in Arabidopsis.BMC plant biology · 2025Article
- Challenges in Applying DNA-Binding Protein Predictors to Biological Research.International journal of molecular sciences · 2025Article
- Light-regulated dual-targeting of NUCLEAR CONTROL OF PEP ACTIVITY establishes photomorphogenesis via interorganellar communication.Plant physiology · 2025Article
- Phytochrome B and phytochrome-interacting-factor4 modulate tree seasonal growth in cold environments.Nature communications · 2025Article
- A 65-kb deletion survey identifies a distalProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Analysis of the Genes from Gibberellin, Jasmonate, and Auxin Signaling Under Drought Stress: A Genome-Wide Approach in Castor Bean (Plants (Basel, Switzerland) · 2025Article
- Transcriptional Dynamics Underlying Somatic Embryogenesis inPlants (Basel, Switzerland) · 2025Article
- Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence.BMC plant biology · 2024Article
- Phytochrome interacting factor 3 mediates low light signaling to regulate isorhynchophylline biosynthesis in Uncaria rhynchophylla.Scientific reports · 2024Article
- MPK4-mediated phosphorylation of PHYTOCHROME INTERACTING FACTOR4 controls thermosensing by regulating histone variant H2A.Z deposition.The Plant cell · 2024Article
- SlDELLA interacts with SlPIF4 to regulate arbuscular mycorrhizal symbiosis and phosphate uptake in tomato.Horticulture research · 2024Article
- A circadian clock output functions independently of phyB to sustain daytime PIF3 degradation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
158 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.