LEAFY (LFY; At5g61850) is a plant-specific nuclear FLO/LFY-family DNA-binding transcription factor that commits Arabidopsis primordia to floral fate. Its core activity is sequence-specific binding to cis-regulatory DNA at floral meristem and floral organ identity loci, including AP1, AP3, AG and CAL, followed by transcriptional activation. Recent mechanistic work synthesized in the Falcon research file supports LFY as a pioneer transcription factor: LFY binds nucleosome-occupied AP1 regulatory DNA, displaces linker histone H1, recruits SWI/SNF chromatin remodelers, and licenses chromatin for floral fate reprogramming. Its target selection is modulated by oligomerization through an N-terminal SAM domain and by cofactors such as UFO, LMI2, SYD and BRM.
Definition: A DNA-binding transcription factor activity in which a gene product binds cognate cis-regulatory DNA in nucleosome-occupied or otherwise closed chromatin and initiates local chromatin opening to enable subsequent transcriptional activation.
Justification: Existing LFY annotations capture DNA-binding transcription factor activity and chromatin DNA binding separately, but not the experimentally supported pioneer activity that couples nucleosomal DNA binding to H1 displacement, SWI/SNF recruitment and competence for floral fate reprogramming.
Parent term: DNA-binding transcription factor activity, RNA polymerase II-specific
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009909 regulation of flower development | IBA GO_REF:0000033 | ACCEPT | Summary: The phylogenetic annotation is consistent with LFY membership in the conserved FLO/LFY family and with extensive Arabidopsis evidence that LFY promotes floral fate by activating floral meristem and organ identity genes. Reason: Regulation of flower development is a correct high-level biological process for LFY. The term is broad, but it captures a core developmental output of the LFY transcription-factor program and is supported by both family context and direct Arabidopsis experiments. Supporting Evidence: file:interpro/panther/PTHR36079/PTHR36079-entries.csv Q00958,Protein LEAFY,protein,3702,Arabidopsis thaliana,Arabidopsis thaliana (Mouse-ear cress),LFY,420,PTHR36079:SF1,PROTEIN LEAFY,True PMID:12324613 These data suggest that the LFY gene is required for the development of type 3 metamers and that the transition from type 2 to type 3 metamers is a developmental step distinct from that between vegetative and reproductive growth |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: LFY is clearly a DNA-binding protein, but the generic parent term loses the important functional specificity: LFY binds floral cis-regulatory sequences as a transcription factor. Reason: InterPro domain evidence and experimental literature support a more informative term than generic DNA binding. LFY should be represented as binding transcriptional cis-regulatory DNA, with separate annotations capturing sequence-specific DNA binding and transcription factor activity. Proposed replacements: transcription cis-regulatory region binding Supporting Evidence: PMID:10417387 Use of steroid-inducible activation of LFY demonstrated that early expression of AP1 is a result of transcriptional induction by LFY. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization is consistent with the UniProt subcellular location mapping and with LFY's experimentally supported activity at chromatin-bound regulatory loci. Reason: LFY functions as a DNA-binding transcription factor at nuclear chromatin; the cellular component annotation is appropriate. Supporting Evidence: file:ARATH/LFY/LFY-uniprot.txt SUBCELLULAR LOCATION: Nucleus file:ARATH/LFY/LFY-deep-research-falcon.md LFY's biochemical function is exerted at chromatin, consistent with nuclear localization as a DNA-binding transcription factor. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: LFY regulates transcription, but the existing term is broader than the experimentally demonstrated activator role at floral regulators such as AP1, AP3 and AG. Reason: LFY is best captured as a positive transcriptional regulator of RNA-polymerase-II target genes, rather than the nonspecific parent process. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:10417387 This AP1 induction is independent of protein synthesis and occurs specifically in the tissues and at the developmental stage in which floral fate is assumed. PMID:22323601 The SWI2/SNF2 ATPases are recruited to the regulatory regions of AP3 and AG during flower development and physically interact with two direct transcriptional activators of class B and class C gene expression, LEAFY (LFY) and SEPALLATA3 (SEP3). |
| GO:0010074 maintenance of meristem identity | IEA GO_REF:0000117 | MODIFY | Summary: LFY is a floral meristem identity regulator, but the ARBA term "maintenance of meristem identity" is overly generic and does not distinguish floral meristem fate from other meristem-maintenance processes. Reason: The evidence for LFY supports floral meristem fate/determinacy and regulation of flower development. A floral-meristem-specific term is more accurate than the broad maintenance term. Proposed replacements: floral meristem determinacy regulation of flower development Supporting Evidence: PMID:21750030 LFY is considered to be a central meristem identity regulator because lfy null mutants cause a very dramatic delay in the meristem identity transition PMID:20626659 LEAFY (LFY) and APETALA1 (AP1) are key regulators of this transition and expression of these genes in primordia produced by the inflorescence meristem confers floral fate. |
| GO:0005515 protein binding | IPI PMID:18287201 An Arabidopsis F-box protein acts as a transcriptional co-fa... | MODIFY | Summary: The underlying evidence is a specific LFY interaction with UFO, a transcriptional cofactor that helps recruit the LFY complex to the AP3 promoter. The generic protein binding term is uninformative. Reason: This should not remain as undifferentiated protein binding. The literature supports LFY binding to a transcriptional coregulator in a DNA-associated floral homeotic gene activation complex. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:18287201 Here, we show that UFO physically interacts with LFY both in vitro and in vivo, and this interaction is necessary to recruit UFO to the AP3 promoter. |
| GO:0005515 protein binding | IPI PMID:22323601 SWI2/SNF2 chromatin remodeling ATPases overcome polycomb rep... | MODIFY | Summary: This annotation reflects LFY interaction with the SWI/SNF ATPases SYD and BRM. The interaction is biologically meaningful but should not be represented only as generic protein binding. Reason: The paper supports LFY binding to transcriptional/chromatin coregulators that are recruited to floral homeotic gene loci. A coregulator-binding replacement better captures the function than protein binding. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:22323601 SYD and BRM physically interact with two tissue- and stage-specific activators of AP3 and AG, the plant-specific transcription factor LFY, which is known to play a central role in class B and class C gene induction, and with the MADS box transcription factor SEP3 |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:31806676 A PXY-Mediated Transcriptional Network Integrates Signaling ... | ACCEPT | Summary: The annotation is consistent with LFY's core molecular activity and with the high-throughput transcription-factor/promoter interaction framework used in the cited study. The specific LFY promoter interactions are not described in the main text, so direct LFY/AP1 and LFY/chromatin studies are important additional support. Reason: LFY's function requires binding transcriptional cis-regulatory regions. Although PMID:31806676 is a broad eY1H network paper, independent direct evidence strongly supports this molecular function for LFY. Supporting Evidence: PMID:31806676 Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis file:ARATH/LFY/LFY-deep-research-falcon.md LFY is a sequence-specific DNA-binding transcription factor that recognizes semi-palindromic DNA elements |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: The AtSubP-based prediction agrees with the independently supported nuclear site of action for LFY. Reason: LFY's experimentally supported transcription-factor and chromatin-binding activities occur in the nucleus, so this predicted localization is consistent with the biology. Supporting Evidence: file:ARATH/LFY/LFY-uniprot.txt SUBCELLULAR LOCATION: Nucleus PMID:22323601 SYD and LFY association with the AP3 and AG regulatory loci peaks at the same time during flower patterning |
| GO:0005515 protein binding | IPI PMID:21750030 LATE MERISTEM IDENTITY2 acts together with LEAFY to activate... | MODIFY | Summary: This protein-binding annotation reflects a specific physical interaction between LFY and the MYB transcription factor LMI2 during AP1 activation. Reason: The generic term obscures the more informative biology: LFY binds another DNA-binding transcription factor in a feed-forward floral meristem identity circuit. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:21750030 Like LFY, LMI2 activates AP1 directly; moreover, LMI2 and LFY interact physically. |
| GO:0042803 protein homodimerization activity | IDA PMID:18784751 Structural basis for LEAFY floral switch function and simila... | ACCEPT | Summary: LFY homodimerization on DNA is biologically plausible and is recorded in UniProt from the structural study, but the original PMID is not present in the cached publications for this worktree. Reason: The annotation is consistent with UniProt's curated statement and with the structural description of the LFY DNA-binding domain. Because the source article is not cached locally, this review records the evidence limitation with full_text_unavailable support. Supporting Evidence: file:ARATH/LFY/LFY-uniprot.txt SUBUNIT: Forms homodimer when associated to DNA. |
| GO:0010582 floral meristem determinacy | IGI PMID:20626659 Arabidopsis BLADE-ON-PETIOLE1 and 2 promote floral meristem ... | ACCEPT | Summary: The cited genetic interaction study supports LFY as one of the key floral meristem identity regulators whose activity contributes to floral fate and determinacy, especially in combination with AP1 and BOP1/2. Reason: Floral meristem determinacy is a supported developmental output of LFY. It is not the molecular function, but it is an appropriate core biological process for this developmental regulator. Supporting Evidence: PMID:20626659 Loss-of-function bop1 bop2 mutants show subtle defects in inflorescence and floral architecture but in combination with lfy or ap1, synergistic defects in floral meristem fate and determinacy are revealed. |
| GO:0043565 sequence-specific DNA binding | IDA PMID:18784751 Structural basis for LEAFY floral switch function and simila... | ACCEPT | Summary: LFY has experimentally supported sequence-specific DNA-binding activity through its C-terminal FLO/LFY DNA-binding domain, but the original 2008 structural paper is not cached locally. Reason: The annotation is a core LFY molecular function and is supported by the structural PubMed record, UniProt cross-references, and later mechanistic synthesis. The source limitation is recorded because the cached publication file is unavailable. Supporting Evidence: file:ARATH/LFY/LFY-deep-research-falcon.md LFY is a sequence-specific DNA-binding transcription factor that recognizes semi-palindromic DNA elements |
| GO:0010077 maintenance of inflorescence meristem identity | IGI PMID:18298668 Regulatory networks that function to specify flower meristem... | MODIFY | Summary: The cited paper supports LFY function in flower meristem specification downstream of PNY/PNF, but "maintenance of inflorescence meristem identity" overstates or misdirects the LFY role. Reason: LFY promotes floral meristem specification at the periphery of the inflorescence meristem. The evidence does not support LFY as a maintainer of inflorescence meristem identity; a flower-development term is the better representation. Proposed replacements: regulation of flower development Supporting Evidence: PMID:18298668 floral meristems are specified on the periphery of the inflorescence meristem by the combined activities of the FLOWERING LOCUS T (FT)-FD complex and the flower meristem identity gene, LEAFY (LFY). PMID:18298668 Genetic analysis shows that when mutations in pny and pnf genes are combined with lfy, a synergistic phenotype is displayed that significantly reduces floral specification and alters inflorescence patterning events. |
| GO:0031490 chromatin DNA binding | IDA PMID:18287201 An Arabidopsis F-box protein acts as a transcriptional co-fa... | ACCEPT | Summary: LFY associates with floral homeotic gene regulatory DNA in a chromatin context and recruits or cooperates with cofactors at the AP3 promoter. Later pioneer-factor work strengthens the chromatin-DNA interpretation. Reason: Chromatin DNA binding is a core LFY molecular function, not merely a downstream phenotype. The original UFO/AP3 promoter study and later chromatin studies support LFY action at chromatinized regulatory loci. Supporting Evidence: PMID:18287201 Furthermore, a transcriptional repressor domain fused to UFO reduces endogenous LFY activity in plants, supporting the idea that UFO acts as part of a transcriptional complex at the AP3 promoter. file:ARATH/LFY/LFY-deep-research-falcon.md LFY meets these criteria in plants: it binds nucleosome-occupied DNA at key loci (e.g., AP1), locally unlocks chromatin by displacing linker histone H1 and recruiting SWI/SNF remodelers, and licenses floral fate |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:9596637 Gibberellins promote flowering of arabidopsis by activating ... | MODIFY | Summary: The TAS source primarily discusses GA-dependent LFY promoter activation, but the DNA-binding transcription factor activity itself is strongly supported by direct LFY/AP1 activation and structural DNA-binding work. Reason: DNA-binding transcription factor activity is LFY's core molecular function, but the older GO:0003700 term should be modernized to the more specific RNA polymerase II-specific transcription factor term. The original article is abstract-only in the cache, so this modification relies on the broader body of direct LFY evidence in addition to the TAS annotation. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:10417387 Use of steroid-inducible activation of LFY demonstrated that early expression of AP1 is a result of transcriptional induction by LFY. |
| GO:0005634 nucleus | TAS PMID:9596637 Gibberellins promote flowering of arabidopsis by activating ... | ACCEPT | Summary: The nucleus annotation is consistent with LFY's role as a transcription factor acting at chromatin; the original Plant Cell article is abstract-only in the cache. Reason: LFY's nuclear localization is well supported by UniProt and by chromatin-associated functions in multiple studies. The TAS source is not needed as the sole support. Supporting Evidence: file:ARATH/LFY/LFY-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0009740 gibberellic acid mediated signaling pathway | TAS PMID:9596637 Gibberellins promote flowering of arabidopsis by activating ... | MARK AS OVER ANNOTATED | Summary: The paper shows that gibberellin promotes LFY promoter activity and that constitutive LFY can restore flowering in GA-deficient plants, but this positions LFY mainly as a downstream flowering output rather than as a GA signaling component. Reason: Annotating LFY to the gibberellic acid mediated signaling pathway overextends the evidence. The supported biology is that GA activates LFY expression to promote flowering; LFY then executes floral meristem identity transcriptional programs. Supporting Evidence: PMID:9596637 We have found that the failure of gibberellin-deficient ga1-3 mutants to flower in short days was paralleled by the absence of LEAFY promoter induction. PMID:9596637 A causal connection between these two events was confirmed by the ability of a constitutively expressed LEAFY transgene to restore flowering to ga1-3 mutants in short days. |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:10417387 Transcriptional activation of APETALA1 by LEAFY. | MODIFY | Summary: This direct AP1 activation study provides strong evidence that LFY acts as an RNA polymerase II-specific DNA-binding transcription factor during the floral fate transition. Reason: LFY directly induces AP1 without requiring new protein synthesis, supporting direct transcription-factor activity at a protein-coding floral commitment gene. Replace the older, broader GO:0003700 term with the more specific RNA polymerase II DNA-binding transcription factor activity term rather than adding a redundant NEW annotation from the same evidence. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:10417387 Use of steroid-inducible activation of LFY demonstrated that early expression of AP1 is a result of transcriptional induction by LFY. PMID:10417387 This AP1 induction is independent of protein synthesis and occurs specifically in the tissues and at the developmental stage in which floral fate is assumed. |
| GO:0009908 flower development | IMP PMID:12324613 LEAFY, a Homeotic Gene That Regulates Inflorescence Developm... | ACCEPT | Summary: The foundational leafy mutant paper directly supports LFY involvement in flower development and the transition from coflorescence-like metamers to flower-bearing metamers. Reason: Flower development is a broad but appropriate core biological process for LFY, based on mutant phenotypes and downstream floral organ identity effects. Supporting Evidence: PMID:12324613 We describe a mutant of Arabidopsis, Leafy, homozygous for a recessive allele of a nuclear gene LEAFY (LFY), that has an inflorescence composed only of type 2-like metamers. PMID:12324613 Results from double mutant analysis, showing that lfy-1 is epistatic to the floral organ homeotic gene ap2-6, are consistent with the hypothesis that a functional LFY gene is necessary for the expression of downstream genes controlling floral organ identity. |
| GO:0009908 flower development | IMP PMID:11063709 Quantitative trait loci for floral morphology in Arabidopsis... | ACCEPT | Summary: LFY is clearly involved in flower development. The cached abstract for this QTL paper does not provide direct LFY-specific experimental support, so the source-specific limitation is recorded, but the broad term is consistent with independent LFY mutant evidence. Reason: Flower development is an established LFY biological process. The original QTL publication is abstract-only in the cache and does not name LFY in the abstract, so this acceptance should not be treated as strong source-specific support from PMID:11063709 alone. Supporting Evidence: PMID:11063709 We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. PMID:12324613 These data suggest that the LFY gene is required for the development of type 3 metamers and that the transition from type 2 to type 3 metamers is a developmental step distinct from that between vegetative and reproductive growth |
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Download this section (compressed HTML)Q: Which endogenous LFY-UFO-dependent LUBS elements are required in vivo for AP3 and other organ identity targets, and which are redundant?
Suggested experts: Francois Parcy, Doris Wagner
Q: Does LFY pioneer activity require distinct SWI/SNF subunit compositions at AP1, AP3 and AG, or does LFY recruit a common remodeler module to all floral target classes?
Suggested experts: Doris Wagner, Nobutoshi Yamaguchi
Experiment: Introduce precise mutations in the endogenous AP1 LFY binding site and measure LFY occupancy, H1 occupancy, SWI/SNF recruitment, chromatin accessibility and AP1 induction during floral transition using ChIP/CUT&Tag and ATAC-seq in staged inflorescences.
Hypothesis: LFY pioneer activity at AP1 depends on the endogenous LFY binding site and separable recruitment of SWI/SNF remodelers.
Type: genome editing and chromatin profiling
Experiment: CRISPR-mutate candidate LUBS elements near AP3, PI and RBE, then compare LFY and UFO occupancy, reporter expression and floral organ phenotypes against matched LFY-only binding-site mutants.
Hypothesis: UFO-dependent LFY retargeting through LUBS elements is necessary for a defined subset of floral organ identity gene activation in vivo.
Type: cis-regulatory reporter and CRISPR tiling
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