PIF3

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003700 DNA-binding transcription factor activity	IEA GO_REF:0000002	ACCEPT	Summary: PIF3 is a bHLH transcription factor that binds DNA (G-box) and regulates transcription of light-responsive genes; this InterPro-based electronic annotation is correct and represents a core molecular function. Reason: Supported by direct experimental evidence (IDA) for DNA-binding transcription factor activity and sequence-specific DNA binding; consistent with the bHLH domain and G-box binding. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Sequence-specific DNA-binding transcription factor; binds the G-box element (5'-CACGTG-3') in target promoters.
GO:0005634 nucleus	IEA GO_REF:0000120	ACCEPT	Summary: PIF3 is a nuclear transcription factor; nuclear localization is experimentally established and is a core part of its function. Reason: Nuclear localization confirmed experimentally (IDA) and consistent with its role as a transcription factor. Supporting Evidence: PMID:9845368 PIF3 localized to the nucleus in transient transfection experiments
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	ACCEPT	Summary: As a DNA-binding transcription factor PIF3 regulates transcription of target genes; this is a core biological process, though somewhat general. Reason: PIF3 directly binds promoters and activates/represses transcription of light-responsive genes; the general transcription-regulation term is correct and supported by more specific experimental annotations. Supporting Evidence: PMID:23548744 HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression
GO:0010017 red or far-red light signaling pathway	IEA GO_REF:0000117	ACCEPT	Summary: PIF3 is a central component of the phytochrome (red/far-red light) signaling pathway, interacting with photoactivated phyA/phyB; this is a core biological process. Reason: Well established by experimental evidence; PIF3 was the first identified phytochrome-interacting factor and functions in phyA and phyB signaling in vivo. Supporting Evidence: PMID:9845368 PIF3 functions in both phyA and phyB signaling pathways in vivo
GO:0046983 protein dimerization activity	IEA GO_REF:0000002	ACCEPT	Summary: The bHLH domain mediates homo- and heterodimerization (e.g. homodimer, heterodimer with PIF4); dimerization activity is correct. Reason: PIF3 forms homodimers and heterodimerizes with other PIFs via its HLH domain, supported by interaction data. Supporting Evidence: PMID:9845368 novel basic helix-loop-helix protein
GO:0005515 protein binding	IPI PMID:10466729 Binding of phytochrome B to its nuclear signalling partner P...	KEEP AS NON CORE	Summary: PIF3 binds the photoactivated Pfr form of phytochrome B (and phyA); this interaction is real but the generic protein binding term is uninformative as a molecular function. Reason: The specific phytochrome interaction is captured by the red/far-red light signaling pathway; bare protein binding is discouraged as a core MF per curation guidelines. Supporting Evidence: PMID:10466729 full-length photoactive phytochrome B binds PIF3 in vitro only upon light-induced conversion to its active form
GO:0005515 protein binding	IPI PMID:10995393 HFR1 encodes an atypical bHLH protein that acts in phytochro...	KEEP AS NON CORE	Summary: PIF3 interaction documented in the context of bHLH PIF-family proteins (HFR1 study); a real interaction but uninformative as a core MF. Reason: Bare protein binding is uninformative; PIF3 dimerization/heterodimerization is better captured by protein dimerization activity. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Many curated IPI partners
GO:0005515 protein binding	IPI PMID:11069292 Phytochrome B binds with greater apparent affinity than phyt...	KEEP AS NON CORE	Summary: PIF3 binds phyA and phyB (phyB with greater apparent affinity), a reaction requiring the PAS domain of PIF3; real interaction, uninformative generic term. Reason: The phytochrome interaction underlies light signaling; the generic protein binding term is not a core MF. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md phyB binds with greater apparent affinity than phyA; reaction requires the PAS domain of PIF3
GO:0005515 protein binding	IPI PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ...	KEEP AS NON CORE	Summary: Interaction documented in a PIF4 study; real interaction but generic term not informative as core function. Reason: Bare protein binding is discouraged as core; PIF heterodimerization is represented by protein dimerization activity. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md heterodimerizes via the HLH domain
GO:0005515 protein binding	IPI PMID:12897250 The Arabidopsis basic/helix-loop-helix transcription factor ...	KEEP AS NON CORE	Summary: Interaction with PIF4 documented in the Arabidopsis bHLH family study; real interaction, uninformative generic term. Reason: Bare protein binding is not a core MF; dimerization is captured separately. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Can form a heterodimer with REP1 and PIF4
GO:0005515 protein binding	IPI PMID:15155879 Constitutive photomorphogenesis 1 and multiple photoreceptor...	KEEP AS NON CORE	Summary: Interaction documented in a study of light-induced PIF3 degradation; real interaction, uninformative generic term. Reason: Bare protein binding is discouraged as core; the relevant biology is light-induced PIF3 degradation in phytochrome signaling. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIF3 protein is degraded in light
GO:0005515 protein binding	IPI PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato...	KEEP AS NON CORE	Summary: Interaction documented in a PIF1 (chlorophyll biosynthesis regulator) study; real interaction, uninformative generic term. Reason: Bare protein binding is not a core MF; PIF heterodimerization captured separately. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Many curated IPI partners
GO:0005515 protein binding	IPI PMID:15486100 A novel molecular recognition motif necessary for targeting ...	KEEP AS NON CORE	Summary: Interaction documented in a study of the APB phytochrome-recognition motif; real interaction, uninformative generic term. Reason: Bare protein binding is discouraged; phytochrome binding underlies light signaling. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Directly binds photoactivated phytochromes
GO:0005515 protein binding	IPI PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix prote...	KEEP AS NON CORE	Summary: Interaction documented in a PIL5/PIF1 seed-germination study; real interaction, uninformative generic term. Reason: Bare protein binding is not a core MF. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Many curated IPI partners
GO:0005515 protein binding	IPI PMID:18216856 Coordinated regulation of Arabidopsis thaliana development b...	KEEP AS NON CORE	Summary: Interaction documented in a light/gibberellin development study; real interaction, uninformative generic term. Reason: Bare protein binding is discouraged as core; PIF3 interacts with DELLA (RGA) in GA-light crosstalk. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md RGA (Q9SLH3, a DELLA)
GO:0005515 protein binding	IPI PMID:18216857 A molecular framework for light and gibberellin control of c...	KEEP AS NON CORE	Summary: Interaction documented in a light/gibberellin cell-elongation study; real interaction, uninformative generic term. Reason: Bare protein binding is not a core MF. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md RGA (Q9SLH3, a DELLA)
GO:0005515 protein binding	IPI PMID:18728185 Genetically encoded photoswitching of actin assembly through...	KEEP AS NON CORE	Summary: Interaction reported in a study using a photoswitch system; the generic protein binding term is uninformative for PIF3 function. Reason: Bare protein binding is not a core MF; cannot be elevated to a specific function from this generic annotation. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Many curated IPI partners
GO:0005515 protein binding	IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an...	KEEP AS NON CORE	Summary: PIF3 interacts with phytochromes C and E (obligate heterodimers); real interaction, uninformative generic term. Reason: Bare protein binding is discouraged; phytochrome interaction underlies light signaling. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Directly binds photoactivated phytochromes
GO:0005515 protein binding	IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b...	KEEP AS NON CORE	Summary: Interaction documented in a study of PIF1-interacting bHLH dimerization; real interaction, uninformative generic term. Reason: Bare protein binding is not a core MF; dimerization captured separately. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Homodimerizes and heterodimerizes via the HLH domain
GO:0005515 protein binding	IPI PMID:22904146 The phytochrome-interacting vascular plant one-zinc finger1 ...	KEEP AS NON CORE	Summary: Interaction with VOZ1/VOZ2 (zinc-finger flowering regulators); real interaction, uninformative generic term. Reason: Bare protein binding is not a core MF. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Many curated IPI partners
GO:0005515 protein binding	IPI PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal ...	KEEP AS NON CORE	Summary: PIF3 binds the C-terminal domains of phyA and phyB (original identification by yeast two-hybrid); real interaction, uninformative generic term. Reason: Bare protein binding is discouraged; the phytochrome interaction is a core part of light signaling, captured by the pathway term. Supporting Evidence: PMID:9845368 PIF3 binds to wild-type C-terminal domains of both phyA and phyB
GO:0042802 identical protein binding	IPI PMID:10995393 HFR1 encodes an atypical bHLH protein that acts in phytochro...	ACCEPT	Summary: PIF3 forms homodimers (self-interaction), consistent with its bHLH fold; this identical protein binding annotation is correct. Reason: Homodimerization is documented (UniProt SUBUNIT and IntAct self-loop); identical protein binding is an informative, correct molecular function. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md GO:0042802 identical protein binding (IPI, self O80536)
GO:0042802 identical protein binding	IPI PMID:12897250 The Arabidopsis basic/helix-loop-helix transcription factor ...	ACCEPT	Summary: PIF3 homodimerization (self-interaction) documented; correct. Reason: Consistent with homodimer formation reported in UniProt and IntAct. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md GO:0042802 identical protein binding (IPI, self O80536)
GO:0042802 identical protein binding	IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b...	ACCEPT	Summary: PIF3 homodimerization (self-interaction) documented in a dimerization study; correct. Reason: Consistent with homodimer formation; informative molecular function. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Homodimerizes and heterodimerizes via the HLH domain
GO:0003700 DNA-binding transcription factor activity	IDA PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Media...	ACCEPT	Summary: Direct experimental evidence that PIF3 binds G-box elements and acts as a transcription factor; a core molecular function. Reason: IDA from a study that assays PIF3 G-box binding and phyA-mediated sequestration; consistent with UniProt FUNCTION. Supporting Evidence: PMID:31732705 They bind to G-box (CACGTG) motifs either alone or together with other transcription factors
GO:0005515 protein binding	IPI PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Media...	KEEP AS NON CORE	Summary: PIF3 binds phyA (used as a comparator in the PIF8 study); real interaction, uninformative generic term. Reason: Bare protein binding is discouraged as core; phytochrome interaction underlies light signaling. Supporting Evidence: PMID:31732705 interacts preferentially with the Pfr form of phyB
GO:0043565 sequence-specific DNA binding	IDA PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Media...	ACCEPT	Summary: PIF3 binds sequence-specific DNA elements (G-box); a core molecular function underlying its transcription factor activity. Reason: Direct experimental evidence of G-box (CACGTG) binding; consistent with the bHLH domain. Supporting Evidence: PMID:31732705 bind to G-box (CACGTG) motifs file:ARATH/PIF3/PIF3-deep-research-falcon.md with strong G-box preference and defined affinity constants (sub-micromolar Kd)
GO:0009408 response to heat	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: This IEP annotation derives from PIF3 mRNA being up-regulated by heat (an expression observation in a gene-family review), not from a demonstrated functional role of PIF3 in heat responses. Reason: IEP expression-induction does not establish process involvement; the annotation reflects transcript induction, captured by UniProt INDUCTION, not a dedicated function. Supporting Evidence: PMID:23708772 developmental gene expression maps, and responses to various stimuli for the various PIF
GO:0009409 response to cold	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: IEP annotation derived from cold induction of PIF3 mRNA in a review, not from a functional role in cold response. Reason: Expression-induction evidence (IEP) is insufficient to assert process involvement; reflects transcript induction only. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIF3 mRNA is up-regulated by ABA, ethylene, auxin, salt, cold and heat
GO:0009723 response to ethylene	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: IEP from ethylene induction of PIF3 mRNA in a review. PIF3 does have a genuine functional role downstream of ethylene (MDP60, hypocotyl elongation), but that is established elsewhere by IMP/IDA; this particular expression-based IEP is an over-annotation. Reason: The IEP evidence reflects transcript induction in a gene-family review; the real ethylene-related function is captured by IMP annotations (PMID:31638649, PMID:29167353). Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIF3 mRNA is up-regulated by ABA, ethylene, auxin, salt, cold and heat
GO:0009733 response to auxin	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: IEP from auxin induction of PIF3 mRNA in a review, not a demonstrated functional role. Reason: Expression-induction evidence is insufficient to assert process involvement. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIF3 mRNA is up-regulated by ABA, ethylene, auxin, salt, cold and heat
GO:0009737 response to abscisic acid	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: IEP from ABA induction of PIF3 mRNA in a review, not a demonstrated functional role. Reason: Expression-induction evidence is insufficient to assert process involvement. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIF3 mRNA is up-regulated by ABA, ethylene, auxin, salt, cold and heat
GO:1902074 response to salt	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: IEP from salt induction of PIF3 mRNA in a review, not a demonstrated functional role. Reason: Expression-induction evidence is insufficient to assert process involvement. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIF3 mRNA is up-regulated by ABA, ethylene, auxin, salt, cold and heat
GO:0005515 protein binding	IPI PMID:25944101 HEMERA Couples the Proteolysis and Transcriptional Activity ...	KEEP AS NON CORE	Summary: PIF3 associates with HEMERA (PTAC12/HMR/PAP5), which couples PIF3 proteolysis and transcriptional activity; real interaction, uninformative generic term. Reason: Bare protein binding is discouraged; the interaction relates to light-regulated PIF3 stability/activity captured elsewhere. Supporting Evidence: PMID:25944101 the degradation of PIF1 and PIF3 requires HEMERA (HMR)
GO:0009826 unidimensional cell growth	IMP PMID:31638649 Submergence stress-induced hypocotyl elongation through ethy...	KEEP AS NON CORE	Summary: PIF3 is required for submergence/ethylene-induced underwater hypocotyl (unidimensional cell) elongation; supported by mutant phenotype. Reason: A genuine developmental role established by IMP, but a context-specific downstream function rather than PIF3's core light-signaling/transcription activity. Supporting Evidence: PMID:31638649 Submergence enhanced ethylene signaling, which then activated and stabilized its downstream transcription factor, phytochrome-interacting factor 3 (PIF3), to promote hypocotyl elongation
GO:1905421 regulation of plant organ morphogenesis	IMP PMID:31638649 Submergence stress-induced hypocotyl elongation through ethy...	KEEP AS NON CORE	Summary: PIF3 mutant alters hypocotyl elongation under submergence; the term is general but defensible for the organ-morphogenesis phenotype. Reason: Supported by IMP, but a broad developmental term reflecting a context-specific role, not the core function. Supporting Evidence: PMID:31638649 to promote hypocotyl elongation
GO:1990785 response to water-immersion restraint stress	IEP PMID:31638649 Submergence stress-induced hypocotyl elongation through ethy...	MARK AS OVER ANNOTATED	Summary: The underlying experiment concerns plant submergence (underwater hypocotyl elongation), but this GO term denotes the animal water-immersion restraint-stress model; this appears to be a term mis-mapping of submergence/water immersion. Reason: The genuine biology (submergence/ethylene-induced hypocotyl elongation) is captured by the IMP unidimensional cell growth and organ morphogenesis annotations; the water-immersion-restraint-stress term is not appropriate for a plant submergence study. Marked as over-annotated rather than removed since the underlying experiment is real and the mapping decision is a curator call. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md applying it to Arabidopsis submergence (PMID:31638649) is a mis-mapping
GO:0005515 protein binding	IPI PMID:23548744 PHYTOCHROME INTERACTING FACTOR3 associates with the histone ...	KEEP AS NON CORE	Summary: PIF3 directly interacts with histone deacetylase HDA15; real interaction, but the generic protein binding term is uninformative. Reason: Bare protein binding is discouraged; the functionally relevant HDA15 interaction underlies repression of photosynthesis genes (captured below). Supporting Evidence: PMID:23548744 HDA15 directly interacted with PIF3 in vivo and in vitro
GO:0005634 nucleus	IDA PMID:23548744 PHYTOCHROME INTERACTING FACTOR3 associates with the histone ...	ACCEPT	Summary: PIF3 nuclear localization confirmed by direct assay; a core cellular location for this transcription factor. Reason: Direct experimental evidence; consistent with transcription factor function. Supporting Evidence: PMID:23548744 PIF3 associates with HDA15 to repress chlorophyll biosynthetic and photosynthetic genes in etiolated seedlings file:ARATH/PIF3/PIF3-deep-research-falcon.md PIF3 associates with promoters by ChIP, supporting nuclear/chromatin function
GO:0042548 regulation of photosynthesis, light reaction	IDA PMID:23548744 PHYTOCHROME INTERACTING FACTOR3 associates with the histone ...	ACCEPT	Summary: PIF3 represses photosynthesis (light-reaction) genes in etiolated seedlings by recruiting HDA15; a core, mechanistically defined function. Reason: Directly demonstrated; PIF3 and HDA15 co-target and repress photosynthesis gene expression in the dark. Supporting Evidence: PMID:23548744 negatively regulates chlorophyll biosynthesis and photosynthesis gene expression in etiolated seedlings file:ARATH/PIF3/PIF3-deep-research-falcon.md PIF3 and HDA15 co-target chlorophyll biosynthetic and photosynthesis-associated genes in darkness and repress transcription through histone deacetylation
GO:0000976 transcription cis-regulatory region binding	IPI PMID:27923776 Establishment of Expression in the SHORTROOT-SCARECROW Trans...	ACCEPT	Summary: PIF3 binds the SCARECROW (SCR) promoter and acts as a repressor in the SHR/SCR root transcriptional cascade (eY1H plus pifq genetic validation); consistent with its sequence-specific DNA binding. Reason: Supported by eY1H promoter binding and genetic validation; an informative DNA-binding molecular function. Supporting Evidence: PMID:27923776 The activity of a repressor, PHYTOCHROME INTERACTING FACTOR 3 (PIF3), was inferred by an increase in SCR expression in the quadruple PIF mutant
GO:0000976 transcription cis-regulatory region binding	IPI PMID:29167353 Coordinated Regulation of Hypocotyl Cell Elongation by Light...	ACCEPT	Summary: PIF3 binds the MDP60 promoter to up-regulate it under light/ethylene signaling; supports cis-regulatory region binding. Reason: Direct promoter binding demonstrated; an informative DNA-binding MF. Supporting Evidence: PMID:29167353 Ethylene signaling up-regulates MDP60 expression via PIF3 binding to the MDP60 promoter
GO:0007623 circadian rhythm	IMP NOT PMID:16055924 Functional characterization of phytochrome interacting facto...	ACCEPT	Summary: A NOT annotation correctly recording that PIF3 does not have a significant role in the circadian clock; over/under-expression does not affect period length or light resetting. Reason: The negation is supported by IMP evidence and is informative (corrects a previously hypothesized clock role). Supporting Evidence: PMID:16055924 overexpression or lack of biologically functional PIF3 does not affect period length of rhythmic gene expression or red-light-induced resetting of the circadian clock
GO:0005515 protein binding	IPI PMID:31527236 Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to...	KEEP AS NON CORE	Summary: PIF3 interacts with FYPP1/FYPP3 (PP6 phosphatase subunits) that dephosphorylate PIFs; real interaction, uninformative generic term. Reason: Bare protein binding is discouraged; the interaction relates to light-regulated PIF3 phosphorylation/stability. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md FYPP1/FYPP3 (Q9LHE7/Q9SX52)
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: Predicted nuclear localization (AtSubP); consistent with experimental nuclear localization of this transcription factor. Reason: Concordant with IDA nuclear localization; correct. Supporting Evidence: PMID:9845368 PIF3 localized to the nucleus in transient transfection experiments
GO:0000976 transcription cis-regulatory region binding	IPI PMID:28174592 Integration of Ethylene and Light Signaling Affects Hypocoty...	KEEP AS NON CORE	Summary: PMID:28174592 is a review of ethylene-light integration; while PIF3 cis-regulatory binding is well established, attributing an IPI binding annotation to this review is weakly supported. Reason: The cis-regulatory region binding function is real and accepted from primary IPI evidence (PMID:27923776, PMID:29167353); this duplicate from a review adds nothing and is not the strongest support. Supporting Evidence: PMID:28174592 ethylene stimulates hypocotyl elongation via transcriptional activation of PIF3
GO:0005515 protein binding	IPI PMID:27143545 Phytochrome-interacting ankyrin repeat protein 2 modulates p...	KEEP AS NON CORE	Summary: PIF3 interacts with PIA2 (phytochrome-interacting ankyrin repeat protein 2), which modulates phyA-mediated PIF3 phosphorylation; real interaction, uninformative generic term. Reason: Bare protein binding is discouraged; relates to light-regulated PIF3 phosphorylation. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md PIA2 (Q9FNP4)
GO:0006355 regulation of DNA-templated transcription	TAS PMID:12897250 The Arabidopsis basic/helix-loop-helix transcription factor ...	ACCEPT	Summary: PIF3 regulates transcription as a bHLH transcription factor; correct core process (general term). Reason: Consistent with established transcription-factor function; TAS from the bHLH family review. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Sequence-specific DNA-binding transcription factor
GO:0006355 regulation of DNA-templated transcription	TAS PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal ...	ACCEPT	Summary: PIF3 regulates transcription of light-responsive genes; correct core process (general term). Reason: PIF3 was characterized as a transcriptional regulator acting in phytochrome signaling. Supporting Evidence: PMID:9845368 a potential role in controlling gene expression
GO:0005515 protein binding	IPI PMID:12826627 A Link between circadian-controlled bHLH factors and the APR...	KEEP AS NON CORE	Summary: PIF3 interacts with APRR1/TOC1; real interaction documented by Y2H/in vitro binding, uninformative generic term. Reason: Bare protein binding is discouraged as core; the interaction is documented but PIF3 has no significant clock role (see negated circadian annotation). Supporting Evidence: PMID:12826627 APRR1/TOC1 interacts with certain bHLH factors (i.e. PIF3 and PIL1
GO:0009704 de-etiolation	IMP PMID:18252845 The Arabidopsis phytochrome-interacting factor PIF7, togethe...	ACCEPT	Summary: PIF3 acts (with PIF4/PIF7) in phyB-mediated seedling de-etiolation under prolonged red light; supported by mutant analysis. Reason: IMP evidence; de-etiolation/photomorphogenesis is a core light-signaling output of PIF3. Supporting Evidence: PMID:18252845 PIF7 acts similarly to PIF3 in prolonged red light as a weak negative regulator of phyB-mediated seedling deetiolation
GO:0009740 gibberellic acid mediated signaling pathway	IMP PMID:18053005 Gibberellins modulate light signaling pathways to prevent Ar...	KEEP AS NON CORE	Summary: PIF3 activity is regulated within GA-light crosstalk preventing dark de-etiolation; supported but a context-specific role. Reason: Supported by genetic analysis, but represents PIF3 as a node in GA-light crosstalk rather than its core function. Supporting Evidence: PMID:18053005 stabilization of transcription factors that promote skotomorphogenesis, such as PIF3
GO:0003677 DNA binding	IDA PMID:17319847 PIF3 regulates anthocyanin biosynthesis in an HY5-dependent ...	ACCEPT	Summary: PIF3 directly binds anthocyanin biosynthetic gene promoters (ChIP); supports DNA binding, a core molecular activity. Reason: Direct in vivo promoter binding; consistent with sequence-specific DNA binding and TF activity. Supporting Evidence: PMID:17319847 both PIF3 and HY5 regulate anthocyanin biosynthetic gene expression by directly binding to different regions of the gene promoters in vivo
GO:0031539 positive regulation of anthocyanin metabolic process	IMP PMID:17319847 PIF3 regulates anthocyanin biosynthesis in an HY5-dependent ...	KEEP AS NON CORE	Summary: PIF3 positively regulates anthocyanin biosynthesis in an HY5-dependent manner; supported by mutant analysis and direct promoter binding. Reason: A genuine, well-supported downstream output of PIF3, but a specialized/process-specific role rather than its core light-signaling transcription function. Supporting Evidence: PMID:17319847 both PIF3 and HY5 positively regulate anthocyanin biosynthesis by activating the transcription of the same anthocyanin biosynthetic genes
GO:0005634 nucleus	IDA PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal ...	ACCEPT	Summary: PIF3 localizes to the nucleus (transient transfection); core cellular location. Reason: Direct experimental evidence in the founding PIF3 paper. Supporting Evidence: PMID:9845368 PIF3 localized to the nucleus in transient transfection experiments
GO:0009639 response to red or far red light	IMP PMID:10318970 poc1: an Arabidopsis mutant perturbed in phytochrome signali...	ACCEPT	Summary: PIF3 is required for normal responses to red/far-red light; the poc1 mutant (PIF3 promoter T-DNA causing overexpression) alters phyB responsiveness. Reason: IMP evidence; central to PIF3's role in phytochrome light responses. Supporting Evidence: PMID:10318970 the poc1 mutation enhances phyB signal transduction
GO:0010017 red or far-red light signaling pathway	IMP PMID:10318970 poc1: an Arabidopsis mutant perturbed in phytochrome signali...	ACCEPT	Summary: PIF3 functions within the phytochrome red/far-red signaling pathway; supported by genetic evidence (poc1). Reason: Core biological process; IMP-supported and concordant with the founding-paper functional data. Supporting Evidence: PMID:10318970 a component involved in phyB signal transduction
GO:0003700 DNA-binding transcription factor activity	ISS PMID:12679534 The basic helix-loop-helix transcription factor family in pl...	ACCEPT	Summary: Sequence-based assignment of bHLH transcription factor activity; concordant with direct experimental evidence. Reason: Correct and consistent with IDA evidence and the bHLH domain. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Basic helix-loop-helix (bHLH) transcription factor
GO:0003700 DNA-binding transcription factor activity	ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a...	ACCEPT	Summary: Sequence-based assignment of transcription factor activity from a genome-wide TF comparison; concordant with experimental evidence. Reason: Correct and consistent with IDA evidence; core molecular function. Supporting Evidence: file:ARATH/PIF3/PIF3-notes.md Basic helix-loop-helix (bHLH) transcription factor
GO:0007165 signal transduction	TAS PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal ...	MARK AS OVER ANNOTATED	Summary: PIF3 acts in signal transduction (phytochrome signaling); the term is very general and is better represented by the red/far-red light signaling pathway term. Reason: Generic parent term; PIF3 signaling role is more precisely captured by GO:0010017 (red or far-red light signaling pathway), which is already annotated. Supporting Evidence: PMID:9845368 necessary for normal photoinduced signal transduction

Gene Description

Existing Annotations Review

Core Functions

Functions as a sequence-specific bHLH transcription factor that binds G-box (CACGTG) cis-regulatory elements in promoters of light-responsive genes, acting in the nucleus to regulate (activate or repress) their transcription.

Represses chlorophyll biosynthesis and photosynthesis (light-reaction) genes in etiolated (dark-grown) seedlings by binding their promoters and recruiting the histone deacetylase HDA15, decreasing histone acetylation and transcription; PIF3 and HDA15 dissociate from targets upon red light.

References

Suggested Questions for Experts

Suggested Experiments

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📚 Additional Documentation

Notes

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