PIF4 (PHYTOCHROME INTERACTING FACTOR 4) is a nuclear basic helix-loop-helix (bHLH, subgroup 15) transcription factor of Arabidopsis thaliana that binds G-box and E-box (CACGTG/CA[CT]GTG) cis-elements in light-regulated promoters and acts as a central, growth-promoting regulator integrating light, temperature and hormone cues. It functions as a negative component of phytochrome B (phyB) red-light signaling, where photoactivated phyB (Pfr) binds PIF4 and promotes its degradation, restraining cell elongation in the light. PIF4 is the master positive regulator of thermomorphogenesis, whereby warm ambient temperature stabilizes and activates PIF4 to drive hypocotyl elongation, acting together with the coactivator HEMERA (HMR) and the Mediator subunit MED14 to activate auxin biosynthesis and auxin-signaling genes. PIF4 also relays blue-light cues through direct interaction with cryptochromes CRY1/CRY2, and integrates gibberellin (via DELLA proteins) and brassinosteroid (via BZR1) signaling at shared growth-gene targets. It forms homodimers and heterodimers (including non-DNA-binding heterodimers with HFR1 that inhibit its activity) and its abundance and activity are tuned by phosphorylation (PP6/FyPP phosphatases) and stress-responsive degradation. PIF4 localizes to the nucleus, is expressed mainly in leaves, stems and seedlings, and shows a circadian expression rhythm.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: PIF4 is a bHLH transcription factor that binds sequence-specific cis-elements (G-box/E-box) in light-regulated promoters to regulate gene expression. This is a core molecular function. Reason: Sequence-specific DNA-binding transcription factor activity is the defining, experimentally established molecular function of PIF4; the IEA InterPro mapping is strongly corroborated by direct evidence. Supporting Evidence: PMID:12006496 PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters. file:ARATH/PIF4/PIF4-deep-research-falcon.md The PIF family (including PIF4) is described as binding |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: PIF4 is a nuclear transcription factor; nuclear localization is established experimentally and is essential for its function. Reason: Nuclear localization is a core, experimentally confirmed cellular component for this transcription factor. Supporting Evidence: PMID:12006496 PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters. file:ARATH/PIF4/PIF4-deep-research-falcon.md PIF4 is a nuclear transcription factor acting at chromatin |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: As a DNA-binding transcription factor, PIF4 regulates transcription of light- and temperature-responsive target genes. A more specific term (regulation of transcription by RNA polymerase II) is also annotated. Reason: The annotation is correct but generic; PIF4 is a Pol II transcription factor, so the RNA polymerase II-specific term better captures its role. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:12006496 PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters. |
| GO:0010017 red or far-red light signaling pathway | IEA GO_REF:0000117 | ACCEPT | Summary: PIF4 is a core component of phytochrome (red/far-red) light signaling, acting as a negative regulator of phyB signaling. Reason: Participation in red/far-red light signaling is a core, experimentally established function of PIF4 as a phytochrome-interacting factor. Supporting Evidence: PMID:12006496 which binds selectively to the biologically active Pfr form of phyB, but has little affinity for phyA file:ARATH/PIF4/PIF4-deep-research-falcon.md Direct interaction of nuclear, active phyB with PIF4 (and other PIFs) triggers |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: As a bHLH factor, PIF4 dimerizes to bind DNA; it forms homodimers and heterodimers (e.g. non-DNA-binding heterodimers with HFR1). Dimerization is intrinsic to bHLH transcription-factor function. Reason: Protein dimerization is a core molecular function of bHLH transcription factors and is experimentally documented for PIF4 (homodimerization for DNA binding; HFR1 heterodimerization). Supporting Evidence: PMID:19851283 HFR1 directly inhibits these PIFs by forming non-DNA-binding heterodimers with PIF4 and PIF5. |
| GO:0005515 protein binding | IPI PMID:18216857 A molecular framework for light and gibberellin control of c... | MARK AS OVER ANNOTATED | Summary: PIF4 is bound and inhibited by DELLA proteins, which block its DNA-recognition domain, integrating light and gibberellin control of cell elongation. Reason: Bare "protein binding" is uninformative as a function (per curation guidelines). The real, curated DELLA-PIF4 interaction is biologically meaningful but the generic term adds nothing beyond the informative MF/BP terms; the interaction is retained in the notes. Supporting Evidence: PMID:18216857 DELLAs block PIF4 transcriptional activity by binding the DNA-recognition domain of this factor |
| GO:0005515 protein binding | IPI PMID:19851283 Inhibition of the shade avoidance response by formation of n... | MARK AS OVER ANNOTATED | Summary: PIF4 forms non-DNA-binding heterodimers with HFR1, which inhibits PIF4 activity and limits the shade-avoidance response. Reason: Bare "protein binding" is uninformative; the specific HFR1 heterodimerization is captured by protein dimerization activity (GO:0046983) and described in the notes. Supporting Evidence: PMID:19851283 HFR1 directly inhibits these PIFs by forming non-DNA-binding heterodimers with PIF4 and PIF5. |
| GO:0005515 protein binding | IPI PMID:22820378 Interaction between BZR1 and PIF4 integrates brassinosteroid... | MARK AS OVER ANNOTATED | Summary: PIF4 directly interacts with the brassinosteroid-activated transcription factor BZR1; the BZR1-PIF4 module co-binds thousands of common targets to integrate brassinosteroid and environmental signals. Reason: Bare "protein binding" is uninformative as a function; the specific, important BZR1 interaction is documented in the notes and core function framing. Supporting Evidence: PMID:22820378 direct interaction between the dark- and heat-activated transcription factor phytochrome-interacting factor 4 (PIF4) and the BR-activated transcription factor BZR1 |
| GO:0005515 protein binding | IPI PMID:40726285 Salt-responsive SSN1 condensation in nucleus facilitates PIF... | MARK AS OVER ANNOTATED | Summary: Under salt stress, PIF4 co-condenses with the repressor SSN1 (and SOS2) in nuclear salt bodies, facilitating PIF4 degradation to regulate salt tolerance. Reason: Bare "protein binding" is uninformative; the SSN1/SOS2 interaction is a stress-specific regulatory mechanism captured in the notes, not a core MF. Supporting Evidence: PMID:40726285 SSN1 also co-condenses with another negative regulator PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) |
| GO:0003677 DNA binding | IPI PMID:38958765 Atmospheric nitrogen dioxide suppresses the activity of phyt... | MODIFY | Summary: PIF4 binds the promoter regions of its auxin-pathway target genes (e.g. SAUR46, SAUR67), as shown by ChIP; atmospheric NO2 suppresses this binding. Note PIF4 binds DNA directly (not via a protein partner), so the IPI/protein-interaction framing is best represented as sequence-specific DNA binding. Reason: PIF4 binds specific promoter cis-elements (G-box/E-box); the generic DNA binding term is better represented by sequence-specific DNA binding. Proposed replacements: sequence-specific DNA binding Supporting Evidence: PMID:38958765 NO2 inhibited the binding of PIF4 to the promoter regions of two of its target genes, SAUR46 and SAUR67 |
| GO:0006357 regulation of transcription by RNA polymerase II | IMP PMID:36063057 PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosenso... | ACCEPT | Summary: PIF4, with its coactivator HMR and the Mediator subunit MED14, activates thermoresponsive growth genes (auxin biosynthesis/signaling), demonstrating Pol II transcriptional regulation by PIF4. Reason: Regulation of Pol II transcription is a core, experimentally supported molecular activity of PIF4 at target promoters. Supporting Evidence: PMID:36063057 PIF4 and its co-activator HEMERA (HMR) promote plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin |
| GO:0009408 response to heat | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | KEEP AS NON CORE | Summary: PIF4 transcript is up-regulated by heat (IEP, expression-pattern evidence). PIF4 is independently and strongly established as a central effector of warm-temperature (thermomorphogenic) growth. Reason: The IEP evidence reflects PIF4 expression responding to heat. While PIF4's thermomorphogenesis role is core (captured by GO:0140922), the generic "response to heat" term is peripheral relative to that specific function. Supporting Evidence: file:ARATH/PIF4/PIF4-notes.md up-regulated by salt (NaCl), cold, heat |
| GO:0009409 response to cold | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | KEEP AS NON CORE | Summary: PIF4 transcript is up-regulated by cold (IEP, expression-pattern evidence). This reflects PIF4 gene regulation by temperature rather than a defined causal role of PIF4 in a cold-response pathway. Reason: Expression-correlation (IEP) evidence; peripheral/pleiotropic relative to PIF4's core transcriptional and thermomorphogenic functions. Supporting Evidence: file:ARATH/PIF4/PIF4-notes.md up-regulated by salt (NaCl), cold, heat |
| GO:0009723 response to ethylene | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | KEEP AS NON CORE | Summary: PIF4 transcript is down-regulated by ethylene (ACC) (IEP, expression-pattern evidence), reflecting regulation of PIF4 expression rather than a defined causal role of PIF4 in ethylene response. Reason: Expression-correlation (IEP) evidence; peripheral relative to PIF4's core functions. Supporting Evidence: file:ARATH/PIF4/PIF4-notes.md down-regulated by ethylene (ACC) and auxin (IAA) |
| GO:0009733 response to auxin | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | KEEP AS NON CORE | Summary: PIF4 transcript is down-regulated by auxin (IAA) (IEP, expression-pattern evidence). Note PIF4 acts primarily upstream of auxin (regulating auxin biosynthesis/signaling), so "response to auxin" reflects feedback regulation of PIF4 expression. Reason: Expression-correlation (IEP) evidence; PIF4's core auxin link is as a regulator of auxin biosynthesis/signaling (other annotations), not as a generic auxin-response effector. Supporting Evidence: file:ARATH/PIF4/PIF4-notes.md down-regulated by ethylene (ACC) and auxin (IAA) |
| GO:0140922 positive regulation of thermomorphogenesis | IMP PMID:33824329 RCB initiates Arabidopsis thermomorphogenesis by stabilizing... | ACCEPT | Summary: PIF4 is the central thermoregulator whose stabilization by warm daytime temperature drives thermomorphogenesis; this is a core, experimentally established PIF4 function. Reason: Positive regulation of thermomorphogenesis is a defining, well-supported biological role of PIF4. Supporting Evidence: PMID:33824329 Daytime warm temperature elicits thermomorphogenesis in Arabidopsis by stabilizing the central thermoregulator PHYTOCHROME INTERACTING transcription FACTOR 4 (PIF4) file:ARATH/PIF4/PIF4-deep-research-falcon.md elevated temperature promotes PIF4 accumulation/activity and pif4 complementation assays quantify reduced thermal hypocotyl response in mutants |
| GO:0140922 positive regulation of thermomorphogenesis | IMP PMID:36063057 PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosenso... | ACCEPT | Summary: PIF4, with HMR and MED14, drives thermosensory growth by activating auxin biosynthesis/signaling genes; mutant analyses confirm its central role in thermomorphogenic hypocotyl elongation. Reason: Core, experimentally supported role of PIF4 in positive regulation of thermomorphogenesis. Supporting Evidence: PMID:36063057 PIF4 plays a central role in regulating thermomorphogenetic hypocotyl elongation |
| GO:1902074 response to salt | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | KEEP AS NON CORE | Summary: PIF4 transcript is up-regulated by salt (NaCl) (IEP, expression-pattern evidence). PIF4 is also a target of salt-induced degradation via SSN1/SOS2 condensates, but the IEP term reflects expression regulation. Reason: Expression-correlation (IEP) evidence; salt response is peripheral relative to PIF4's core light/temperature transcriptional functions. Supporting Evidence: file:ARATH/PIF4/PIF4-notes.md up-regulated by salt (NaCl), cold, heat |
| GO:0005515 protein binding | IPI PMID:36063057 PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosenso... | MARK AS OVER ANNOTATED | Summary: PIF4 interacts with the Mediator tail subunit MED14, linking PIF4 to the Pol II Mediator complex for thermoresponsive gene activation. Reason: Bare "protein binding" is uninformative; the MED14 interaction is mechanistically meaningful and is captured in the notes and the thermomorphogenesis core function, not by the generic term. Supporting Evidence: PMID:36063057 the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression |
| GO:0009266 response to temperature stimulus | IMP PMID:36063057 PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosenso... | MODIFY | Summary: PIF4 mediates the warm-temperature growth response; this is correct but is more specifically captured by positive regulation of thermomorphogenesis. Reason: The general response-to-temperature-stimulus term is too broad for PIF4's defined role; the specific thermomorphogenesis term is more informative. Proposed replacements: positive regulation of thermomorphogenesis Supporting Evidence: PMID:36063057 PIF4 plays a central role in regulating thermomorphogenetic hypocotyl elongation |
| GO:1905421 regulation of plant organ morphogenesis | IMP PMID:36063057 PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosenso... | KEEP AS NON CORE | Summary: PIF4 regulates hypocotyl (organ) elongation in response to warm temperature; this broad organ-morphogenesis term overlaps with the more specific thermomorphogenesis annotation. Reason: Correct but general; the specific function (thermomorphogenic hypocotyl growth) is better captured by GO:0140922. Retained as a non-core, broader-process annotation. Supporting Evidence: PMID:36063057 PIF4 plays a central role in regulating thermomorphogenetic hypocotyl elongation |
| GO:0009266 response to temperature stimulus | IMP PMID:33824329 RCB initiates Arabidopsis thermomorphogenesis by stabilizing... | MODIFY | Summary: PIF4 acts in the warm-temperature growth response (its stabilization by daytime warmth initiates thermomorphogenesis); more specifically captured by positive regulation of thermomorphogenesis. Reason: The general response-to-temperature-stimulus term is too broad; the specific thermomorphogenesis term is more informative for PIF4. Proposed replacements: positive regulation of thermomorphogenesis Supporting Evidence: PMID:33824329 stabilizing the central thermoregulator PHYTOCHROME INTERACTING transcription FACTOR 4 (PIF4) |
| GO:0005515 protein binding | IPI PMID:30635559 Daytime temperature is sensed by phytochrome B in Arabidopsi... | MARK AS OVER ANNOTATED | Summary: PIF4 interacts directly with the transcriptional activator HEMERA (HMR), which activates thermoresponsive genes and promotes warm-temperature-dependent PIF4 accumulation. Reason: Bare "protein binding" is uninformative; the HMR interaction is a mechanistically important partner captured in the notes and the thermomorphogenesis core function. Supporting Evidence: PMID:30635559 it interacts directly with PIF4, to activate the thermoresponsive growth-relevant genes and promote warm-temperature-dependent PIF4 accumulation |
| GO:0005515 protein binding | IPI PMID:25944101 HEMERA Couples the Proteolysis and Transcriptional Activity ... | MARK AS OVER ANNOTATED | Summary: PIF4 interacts with HEMERA (HMR/PTAC12), a transcriptional coactivator that binds PIFs and couples their proteolysis with transactivation of PIF target genes. Reason: Bare "protein binding" is uninformative; the HMR interaction (via the conserved APB motif) is captured in the notes, not by the generic term. Supporting Evidence: PMID:25944101 We show that HMR interacts with all PIFs. |
| GO:1990841 promoter-specific chromatin binding | IPI PMID:32967288 The PIFs Redundantly Control Plant Defense Response against ... | ACCEPT | Summary: ChIP shows PIF4 (with PIF5) binds directly to the promoter of the ERF1 target gene, supporting promoter-specific chromatin binding as part of its transcription-factor activity. Reason: Direct promoter occupancy (ChIP) is a core aspect of PIF4's sequence-specific DNA-binding transcription-factor function. Supporting Evidence: PMID:32967288 RESPONSE FACTOR1 (ERF1) promoter |
| GO:0005515 protein binding | IPI PMID:31527236 Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to... | MARK AS OVER ANNOTATED | Summary: PIF4 interacts with the PP6 phosphatase catalytic subunits FyPP1 and FyPP3, which dephosphorylate PIF4 (and PIF3) to modulate their stability and repress photomorphogenesis. Reason: Bare "protein binding" is uninformative; the FyPP/PP6 interaction is a specific regulatory partnership documented in the notes, not by the generic term. Supporting Evidence: PMID:31527236 FyPPs directly interacted with PIF3 and PIF4 |
| GO:0009638 phototropism | IMP PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochro... | KEEP AS NON CORE | Summary: Low blue light enhances phototropism by relieving CRY1-mediated repression of PIF4 expression, implicating PIF4 in modulating the phototropic response. Reason: PIF4's contribution to phototropism is a context-specific, light-condition-dependent role downstream of cryptochrome regulation; peripheral relative to its core transcriptional functions. Supporting Evidence: PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Predicted (ISM) nuclear localization, consistent with PIF4's experimentally established role as a nuclear transcription factor. Reason: Nuclear localization is a core, experimentally confirmed cellular component; the computational prediction agrees with direct evidence. Supporting Evidence: PMID:12006496 PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters. |
| GO:0010600 regulation of auxin biosynthetic process | IMP PMID:27827441 Functional roles of Arabidopsis CKRC2/YUCCA8 gene and the in... | ACCEPT | Summary: PIF4 is required for cytokinin-induced upregulation of auxin biosynthesis genes (CKRC1/TAA1 and CKRC2/YUC8) in the IPyA pathway. Reason: Regulation of auxin biosynthesis is a well-supported PIF4 function and a key downstream output of its transcriptional activity. Supporting Evidence: PMID:27827441 the phytochrome-interacting factor 4 (PIF4) is required for this upregulation |
| GO:0005515 protein binding | IPI PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | MARK AS OVER ANNOTATED | Summary: PIF4 physically interacts with the blue-light photoreceptors CRY1 and CRY2 (and with phyB), linking cryptochrome signaling to PIF4-driven growth in low blue light. Reason: Bare "protein binding" is uninformative; the CRY1/CRY2 (and phyB) interactions are documented in the notes and the light-signaling core function. Supporting Evidence: PMID:26724867 CRY1 and CRY2 physically interact with PIF4 and PIF5 |
| GO:0010244 response to low fluence blue light stimulus by blue low-fluence system | IDA PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | KEEP AS NON CORE | Summary: PIF4 (with PIF5) is necessary for low-blue-light-induced hypocotyl growth, acting downstream of CRY1/CRY2 and binding chromatin at E-box variant sites to stimulate gene expression. Reason: This is a specific, condition-dependent light-response role of PIF4; well-supported but peripheral relative to its core phyB/red-light and thermomorphogenesis functions. Supporting Evidence: PMID:26724867 the bHLH transcription factors (TFs) PIF4 and PIF5 are necessary for LBL-induced hypocotyl growth, and that they act downstream of CRY1 and CRY2 |
| GO:0005634 nucleus | IDA PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | ACCEPT | Summary: Direct evidence places PIF4 in the nucleus, where it interacts with CRY1/CRY2 in response to low blue light. Reason: Nuclear localization is a core, directly observed cellular component for this transcription factor. Supporting Evidence: PMID:26724867 CRY1 and CRY2 physically interact with PIF4 and PIF5 |
| GO:0010600 regulation of auxin biosynthetic process | IDA PMID:22536829 Phytochrome interacting factors 4 and 5 control seedling gro... | ACCEPT | Summary: PIF4 (with PIF5) directly controls expression of auxin biosynthesis genes to promote elongation growth under changing light conditions. Reason: Direct regulation of auxin biosynthesis is a well-supported core output of PIF4 transcriptional activity driving cell elongation. Supporting Evidence: PMID:22536829 auxin biosynthesis and auxin signaling components. file:ARATH/PIF4/PIF4-deep-research-falcon.md PIF4 directly or functionally activates auxin-related genes such as YUC8, IAA19, IAA29 to drive elongation under warm conditions |
| GO:0010928 regulation of auxin mediated signaling pathway | IDA PMID:22536829 Phytochrome interacting factors 4 and 5 control seedling gro... | ACCEPT | Summary: PIF4 (with PIF5) directly controls expression of auxin-signaling components, regulating the auxin signaling pathway during elongation growth. Reason: Direct regulation of auxin signaling is a well-supported PIF4 function linking light/temperature cues to growth. Supporting Evidence: PMID:22536829 auxin biosynthesis and auxin signaling components. |
| GO:0005515 protein binding | IPI PMID:20093430 Transcriptional diversification and functional conservation ... | MARK AS OVER ANNOTATED | Summary: PIF4 interacts with the DELLA proteins RGA and RGL2, the basis for gibberellin/DELLA control of PIF4 transcriptional activity. Reason: Bare "protein binding" is uninformative; the DELLA (RGA/RGL2) interaction is documented in the notes, not by the generic term. Supporting Evidence: PMID:20093430 both DELLA proteins display equivalent abilities to interact with PIF4 |
| GO:0005515 protein binding | IPI PMID:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote... | MARK AS OVER ANNOTATED | Summary: PIF4 was identified as a putative 14-3-3 client in a high-throughput tandem-affinity-purification proteomic screen for 14-3-3 interactors. Reason: Bare "protein binding" from a high-throughput screen is uninformative and the 14-3-3 interaction is putative/indirect; not a core function. Supporting Evidence: PMID:19452453 The identification here of 121 putative clients provides support for in vivo 14-3-3 interactions with a diverse array of proteins |
| GO:0005515 protein binding | IPI PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | MARK AS OVER ANNOTATED | Summary: PIF4 binds selectively to the Pfr (active) form of phytochrome B, the founding interaction defining it as a phytochrome-interacting factor. Reason: Bare "protein binding" is uninformative; the phyB(Pfr) interaction is captured in the notes and the red/far-red light-signaling annotations. Supporting Evidence: PMID:12006496 which binds selectively to the biologically active Pfr form of phyB, but has little affinity for phyA |
| GO:0010161 red light signaling pathway | IGI PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | ACCEPT | Summary: Genetic interaction (srl2/phyB epistasis) shows PIF4 acts specifically and negatively in the phyB red-light signaling pathway. Reason: Participation in red-light (phyB) signaling is a core, genetically-established function of PIF4. Supporting Evidence: PMID:12006496 indicating that this locus functions selectively and negatively in phyB signaling |
| GO:0009704 de-etiolation | IMP PMID:18252845 The Arabidopsis phytochrome-interacting factor PIF7, togethe... | ACCEPT | Summary: PIF4, together with PIF3 and PIF7, acts as a negative regulator of phyB-mediated seedling de-etiolation under prolonged red light, in part by maintaining low phyB levels. Reason: Modulation of seedling de-etiolation is a well-supported, genetically-demonstrated role of PIF4 in light signaling. Supporting Evidence: PMID:18252845 regulates responses to prolonged red light by modulating phyB levels |
| GO:0003677 DNA binding | IDA PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | MODIFY | Summary: PIF4 directly binds a G-box DNA sequence motif found in light-regulated promoters, demonstrating sequence-specific DNA binding. Reason: PIF4 binds a specific cis-element (G-box); the generic DNA binding term is better represented by sequence-specific DNA binding. Proposed replacements: sequence-specific DNA binding Supporting Evidence: PMID:12006496 can bind to a G-box DNA sequence motif found in various light-regulated promoters |
| GO:0005634 nucleus | IDA PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | ACCEPT | Summary: PIF4 directly localizes to the nucleus, consistent with its function as a DNA-binding transcription factor. Reason: Nuclear localization is a core, directly observed cellular component. Supporting Evidence: PMID:12006496 PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters. |
| GO:0010017 red or far-red light signaling pathway | IMP PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | ACCEPT | Summary: The srl2/PIF4 mutant confers selective hypersensitivity to red light acting in phyB signaling, demonstrating PIF4's role in red light signaling. Reason: Core, experimentally (mutant) established role of PIF4 in red/far-red (phytochrome) light signaling. Supporting Evidence: PMID:12006496 which confers selective hypersensitivity to continuous red, but not far-red, light |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12679534 The basic helix-loop-helix transcription factor family in pl... | ACCEPT | Summary: PIF4 (AtbHLH009) is classified as a bHLH transcription factor in the genome-wide bHLH family analysis; TF activity inferred by sequence/family similarity is corroborated by direct evidence. Reason: DNA-binding transcription factor activity is the core molecular function; the ISS family assignment agrees with experimental data. Supporting Evidence: PMID:12679534 Basic helix-loop-helix (bHLH) transcription factors (TFs) belong to a family of transcriptional regulators |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: PIF4 is annotated as a transcription factor in the Arabidopsis genome-wide transcription factor inventory; sequence-based assignment is corroborated by direct evidence. Reason: DNA-binding transcription factor activity is the core molecular function; the ISS genome-wide TF inventory assignment agrees with experimental data. Supporting Evidence: PMID:11118137 Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors |
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