Arabidopsis autonomous flowering contributions to FLC repression

Arabidopsis autonomous flowering regulators promote floral transition through overlapping mechanisms that reduce FLOWERING LOCUS C (FLC) expression. FCA and FY couple processing of COOLAIR antisense RNA to chromatin-associated and termination machinery involving FLD, LD, SDG26/ASHH1, APRF1 and TOPP4. FPA contributes through a distinct RNA-processing route; FLK recognizes modified FLC sense mRNA; FVE/MSI4 supports chromatin-regulatory associations. These relationships vary with genetic background, dosage and locus. Reduced FLC can release repression of FT and SOC1, while FVE also has a distinct direct regulatory effect at FT. Conserved proteins in other plants share biochemical features without necessarily sharing this native RNA-target and chromatin circuit.

MODULE:autonomous_flowering_pathwayCOMPLETECONCRETEBiological Processmodules/autonomous_flowering_pathway.yaml
PMID:31740502
The review describes reciprocal transcription–chromatin feedback that can reinforce the FLC repressed state, rather than a purely one-way RNA-processing handoff.
The transcriptional output feeds back to influence the chromatin environment, reinforcing and stabilizing that state.
PMID:36035698
The review proposes an NDX-stabilized R-loop at the COOLAIR-producing FLC 3-prime region as one chromatin/RNA interface. This is contextual synthesis; NDX is not added as an unreviewed participant.
NDX stabilizes the R-loop at the FLC 3′-end
PMID:38417841
The review illustrates species-dependent flowering adaptation through weakened rice photoperiod regulators, supporting a distinction between conserved components and a shared native FLC circuit.
natural mutations in Ghd7 and Ghd8/DTH8 with reduced functions that enable rice to be cultivated in temperate regions.
PMID:41840059
The review distinguishes graded FLC expression from ON/OFF control during early development and cold, supporting explicit limits on a qualitative signed graph.
Graded expression and switching to ON/OFF control occur during early development and during long-term cold exposure
PMID:41654258
The current review places FLC alternative splicing and m6A regulation alongside epigenetic regulation, supporting separate sense-RNA and chromatin routes without proving each edge itself.
post-transcriptional, including alternative splicing (AS) and m⁶A RNA methylation

Native mechanistic envelope is Arabidopsis thaliana. All 13 native sampled gene products have complete individual reviews; rice FCA Q6K271 and OsFY Q0R3J2 are reviewed comparative evidence only and are not annoton representatives. Family descriptors document verified classification of exact GENE_PRODUCT selections and do not transfer FLC-specific function across broad families. COOLAIR is a lncRNA, so its processing uses GO:0031123 RNA 3'-end processing rather than an mRNA-specific term. The sampled route is not an exhaustive protein complex or a universal knockout-necessity rule. Quantitative feedback and graded versus Polycomb ON/OFF regulation are not reduced to an unvalidated kinetic simulation. FRIGIDA, photoperiod, cold-triggered vernalization and complete downstream floral identity programs remain outside the boundary. No cached GO-CAM index rows matched the 13 native accessions at audit time. Source-access and provider-failure details, exact logic scope and comparative evidence are in the companion notes.

12Nodes
7Parts
1Variant Sets
4Variants
13Annotons
10Connections

Derived QC

Recommended-field compliance

97.6% recommended fields populated
  • knowledge_gaps[0].provenance[0] · reference_section_type (0/1)

Module deep research

✗ none found

No MODULE:autonomous_flowering_pathway deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

11 gene-function check(s) reflected in core functions · 0 conflict(s) · 11 evidence or coverage gap(s) (22 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
fca_coolair_binding FCA
UniProtKB:O04425
Gene 		lncRNA binding
GO:0106222 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fld_h3k4_demethylase FLD
UniProtKB:Q9CAE3
Gene 		histone H3K4 demethylase activity
GO:0032453 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sdg26_dna_binding ASHH1
UniProtKB:Q84WW6
Gene 		double-stranded DNA binding
GO:0003690 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
aprf1_chromatin_scaffold APRF1
UniProtKB:Q9LYK6
Gene 		chromatin binding
GO:0003682 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
topp4_phosphatase TOPP4
UniProtKB:P48484
Gene 		protein serine/threonine phosphatase activity
GO:0004722 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fpa_rna_processing FPA
UniProtKB:Q8LPQ9
Gene 		RNA binding
GO:0003723 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
flk_sense_rna_reader FLK
UniProtKB:Q9SR13
Gene 		N6-methyladenosine-containing RNA reader activity
GO:1990247 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fve_chromatin_association FVE
UniProtKB:O22607
Gene 		histone binding
GO:0042393 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
flc_repressor FLC
UniProtKB:Q9S7Q7
Gene 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ft_coactivator FT
UniProtKB:Q9SXZ2
Gene 		transcription coactivator activity
GO:0003713 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
soc1_transcription_factor SOC1
UniProtKB:O64645
Gene 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fca_coolair_binding RNA BINDING PROTEIN
PANTHER:PTHR24012
Family 		lncRNA binding
GO:0106222 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR24012.
fld_h3k4_demethylase PROTEIN FLOWERING LOCUS D
PANTHER:PTHR10742:SF260
Family 		histone H3K4 demethylase activity
GO:0032453 		Family Function Unreviewed
The family review has no applicable adjudication supporting or excluding GO:0032453.
sdg26_dna_binding SET DOMAIN PROTEINS
PANTHER:PTHR22884
Family 		double-stranded DNA binding
GO:0003690 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR22884.
aprf1_chromatin_scaffold PROTEIN ANTHESIS POMOTING FACTOR 1
PANTHER:PTHR19861:SF9
Family 		chromatin binding
GO:0003682 		Family Function Unreviewed
The family review has no applicable adjudication supporting or excluding GO:0003682.
topp4_phosphatase SERINE_THREONINE-PROTEIN PHOSPHATASE PP1 ISOZYME 4
PANTHER:PTHR11668:SF490
Family 		protein serine/threonine phosphatase activity
GO:0004722 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11668:SF490.
fpa_rna_processing RNA RECOGNITION MOTIF-CONTAINING
PANTHER:PTHR23189
Family 		RNA binding
GO:0003723 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR23189.
flk_sense_rna_reader KH DOMAIN CONTAINING RNA BINDING PROTEIN
PANTHER:PTHR10288
Family 		N6-methyladenosine-containing RNA reader activity
GO:1990247 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10288.
fve_chromatin_association WD40 REPEAT FAMILY
PANTHER:PTHR22850
Family 		histone binding
GO:0042393 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR22850.
flc_repressor SERUM RESPONSE FACTOR HOMOLOG
PANTHER:PTHR48019
Family 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR48019.
ft_coactivator PROTEIN FLOWERING LOCUS T-RELATED
PANTHER:PTHR11362:SF9
Family 		transcription coactivator activity
GO:0003713 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11362:SF9.
soc1_transcription_factor SERUM RESPONSE FACTOR HOMOLOG
PANTHER:PTHR48019
Family 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR48019.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

  • flc_chromatin_repression ⊣ flc_output [closed]
    flc_chromatin_repression is regulated by flc_proximal_processing, cpf_termination_bridge: feedback loop closed
  • fpa_processing_route ⊣ flc_output [input]
    fpa_processing_route is a negative regulator with no upstream edge (not described as feedback)
  • flk_sense_rna_route ⊣ flc_output [input]
    flk_sense_rna_route is a negative regulator with no upstream edge (not described as feedback)
  • fve_chromatin_route ⊣ flc_output [input]
    fve_chromatin_route is a negative regulator with no upstream edge (not described as feedback)
  • flc_output ⊣ ft_output [input]
    flc_output is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (13/13 grounded genes reviewed)

7 complete review(s) · 3 with deep research · 0 missing review · 10 reviewed but lacking deep research

Gene Review Complete Deep research
APRF1 Q9LYK6 ✓ 7/11 ✗
ASHH1 Q84WW6 ✓ 15/17 ✗
FCA O04425 ✓ 20/22 ✗
FLC Q9S7Q7 ✓ ✓ ✓
FLD Q9CAE3 ✓ 12/15 ✗
FLK Q9SR13 ✓ ✓ ✗
FPA Q8LPQ9 ✓ 12/13 ✗
FT Q9SXZ2 ✓ ✓ ✓
FVE O22607 ✓ 39/42 ✗
FY Q6NLV4 ✓ ✓ ✗
LD Q38796 ✓ ✓ ✗
SOC1 O64645 ✓ ✓ ✓
TOPP4 P48484 ✓ ✓ ✗

Details

Context
Arabidopsis thalianaNCBITaxon:3702
nucleusGO:0005634
Arabidopsis autonomous contributions to FLC repressionBiological Processautonomous_flowering_pathway

FLC-regulatory contributions are selectable overlapping implementations, not universally interchangeable complete pathways. At least one nonempty upstream route and the FLC target are required to recognize a represented route; FT/SOC1 are optional readouts.

Context
Arabidopsis thalianaNCBITaxon:3702
nucleusGO:0005634

Connections

Targeted proximal antisense processing favors the FLD-associated repressive chromatin state; FY-SDG26 provides a physical link.
PMID:19965720
Antisense processing triggers localized demethylase activity.
This targeted processing triggers localized histone demethylase activity and results in reduced FLC sense transcription.
PMID:32541063
FY-SDG26 physically connects processing and chromatin regulation.
APRF1/LD-mediated termination contributes to the repressive chromatin state. The direction is a causal contribution, not identification of a phosphatase substrate.
PMID:38851185
Termination influences subsequent transcription via local chromatin.
This work shows how the APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC.
Chromatin/termination feedback enhances early termination as H3K4me1 is depleted. The edge represents a supported feedback model, not irreversible substrate handoff or Boolean switching kinetics.
Context
FCA-mediated proximal-termination/chromatin feedback model; primary available as abstract
PMID:38851186
Model and experimental tests support H3K4me1-dependent processivity feedback.
H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination
flc_chromatin_repression -> flc_output Negatively Regulates
FLD-associated chromatin regulation lowers FLC transcription and hence repressor output.
PMID:17996704
FCA requires FLD for FLC repression.
FCA requires FLOWERING LOCUS D (FLD)
PMID:32541063
FLD/LD/SDG26 oppose an active FLC chromatin state.
fpa_processing_route -> flc_output Negatively Regulates
FPA-dependent RNA processing reduces FLC expression; its relationship to FLD and FY differs from FCA under tested dosage/genotype contexts.
Context
FPA processing and genotype-dependent repression; no direct COOLAIR-binding or universal FY independence asserted
PMID:20079695
FPA controls alternatively processed FLC antisense RNA.
PMID:18628965
Overexpressed FPA reduces FLC in fca/fy but has much weaker effects in fld.
flk_sense_rna_route -> flc_output Negatively Regulates
FLK recognition reduces FLC sense-RNA stability/splicing and accumulated FLC levels.
PMID:37050878
m6A-dependent FLK binding regulates FLC RNA fate.
reducing its stability and splicing
fve_chromatin_route -> flc_output Negatively Regulates
FVE-associated chromatin regulation reduces FLC transcription; catalytic modification is supplied by partner enzymes.
PMID:14745447
FVE participates in a deacetylation-associated FLC-repressing complex.
PMID:21282611
FVE/MSI4 regulates FLC with CLF-associated machinery.
flc_output -> ft_output Negatively Regulates
FLC directly represses FT via a first-intron region; reducing FLC can relieve this repression without directly activating the target protein.
PMID:16623882
In vivo binding to FT first intron and SOC1 promoter supports the direct target edges.
FLC binds to a region of the first intron of FT that contains a putative CArG box
PMID:16600915
Tissue-specific FLC represses systemic and meristem flowering responses.
flc_output -> soc1_output Negatively Regulates
FLC directly represses SOC1 via its promoter; reducing FLC can relieve this repression without directly activating the target protein.
PMID:16623882
In vivo binding to FT first intron and SOC1 promoter supports the direct target edges.
confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene.
PMID:16600915
Tissue-specific FLC represses systemic and meristem flowering responses.
fve_chromatin_route -> ft_output Negatively Regulates
FVE/MSI4 also contributes directly to repression at FT chromatin. This target-specific branch can oppose the indirect FT derepression caused by lowering FLC; no single net flowering sign is inferred from this edge.
Context
FVE/MSI4-CLF/CUL4-DDB1 study context; not a universal consequence of each FVE-containing complex
PMID:21282611
FVE-associated regulation includes FT as well as FLC.
Part: required nonempty regulatory contribution
Context-dependent autonomous regulatory routesBiological Processautonomous_inputs
Variant set: At least one supported autonomous contribution by RNA substrate, chromatin mechanism and experimental context (One Or More)

ONE_OR_MORE means a represented contribution is present, not that a single factor is sufficient to recreate wild-type flowering or compensate for every other pathway lesion.

Characterized FCA/FY–chromatin–termination implementationBiological Processfca_fy_chromatin_route

A selected native mechanistic implementation combining the experimentally characterized RNA-processing, AuPC and CPF-like contributions. Requiring its sampled participants defines this implementation, not universal necessity of every participant in every autonomous response.

Context
FCA-associated FLC repression in the Arabidopsis genotypes and seedling contexts of the cited complex/chromatin experiments
Part: antisense RNA processing
FCA/FY-associated proximal RNA processing at FLCBiological Processflc_proximal_processing

The directly characterized antisense substrate is COOLAIR. Its proximal cleavage/polyadenylation uses the RNA-level GO term. The later processivity feedback model concerns productive transcription and early termination at the locus, rather than an exclusively COOLAIR-specific feedback measurement. Constitutive CPSF, CstF64/77 and FLL2 are relevant partners outside the sampled gene panel; FCA and FY are not a complete catalytic machine.

RNA 3'-end processingGO:0031123

Annotons

FCA: COOLAIR binding and recruitment of RNA-processing/chromatin partners
fca_coolair_binding
Participant: Gene Product: FCA
Gene Product:
FCAUniProtKB:O04425
Family:
RNA BINDING PROTEINPANTHER:PTHR24012 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FCAUniProtKB:O04425
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

lncRNA bindingGO:0106222

Processes

RNA 3'-end processingGO:0031123

Locations

nuclear bodyGO:0016604

COOLAIR binding and recruitment of RNA-processing/chromatin partners. Condensate behavior is established separately from RNA-binding assays.

PMID:31032401
FCA binds COOLAIR and interacts with CLF.
FCA physically binds COOLAIR in vitro and in vivo.
PMID:31043738
FLL2 promotes FCA condensate formation and polyadenylation-factor assembly.
FY: Noncatalytic CPSF partner for FCA and SDG26
fy_cpsf_subunit
Participant: Gene Product: FY
Gene Product:
FYUniProtKB:Q6NLV4
Family:
PRE-MRNA 3' END PROCESSING PROTEIN WDR33PANTHER:PTHR22836:SF0 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FYUniProtKB:Q6NLV4
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Processes

RNA 3'-end processingGO:0031123

Locations

nucleusGO:0005634

Noncatalytic CPSF partner for FCA and SDG26. No isolated plant FY RNA-binding or cleavage activity is asserted.

PMID:19439664
Native FY forms stable assemblies with CPSF100 and CPSF160; FCA association is transient.
AtCPSF100 and AtCPSF160, but not FCA, are stably associated with FY in vivo
PMID:12809608
FCA-FY interaction is required for FLC repression; this early paper directly studies FCA pre-mRNA processing, not COOLAIR.
Part: linked chromatin contribution
FLD/LD/SDG26 chromatin-associated repressionBiological Processflc_chromatin_repression

Native association and chromatin changes support this selected complex implementation. ASHH1 conserved-site Y118A rescue argues catalytic dispensability in the tested flowering assay; mutant catalytic inactivity itself was not directly measured. EFL2/EFL4 and PRC2 enzymes are not sampled here.

negative regulation of gene expression, epigeneticGO:0045814

Annotons

FLD: LSD1-family demethylase inference with native H3K4me1/chromatin evidence
fld_h3k4_demethylase
Participant: Gene Product: FLD
Gene Product:
FLDUniProtKB:Q9CAE3
Family:
PROTEIN FLOWERING LOCUS DPANTHER:PTHR10742:SF260 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FLDUniProtKB:Q9CAE3
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

histone H3K4 demethylase activityGO:0032453

Processes

negative regulation of gene expression, epigeneticGO:0045814

Locations

chromatinGO:0000785

LSD1-family demethylase inference with native H3K4me1/chromatin evidence. This is not presented as a purified target-enzyme kinetic assay.

PMID:32541063
FLD, LD and SDG26 together prevent H3K4me1 accumulation over FLC.
they prevent accumulation of monomethylated H3K4 (H3K4me1) over the FLC gene body
LD: Noncatalytic scaffold connecting FLD-associated chromatin and APRF1/TOPP4 termination assemblies
ld_scaffold
Participant: Gene Product: LD
Gene Product:
LDUniProtKB:Q38796
Family:
HOMEOBOX PROTEIN LUMINIDEPENDENSPANTHER:PTHR33400:SF6 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: LDUniProtKB:Q38796
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Processes

negative regulation of gene expression, epigeneticGO:0045814

Locations

nucleusGO:0005634

Noncatalytic scaffold connecting FLD-associated chromatin and APRF1/TOPP4 termination assemblies. No DNA binding or phosphatase activity is assigned from its historical protein/family name.

PMID:38851185
LD associates with APRF1 and has Ref2/PNUTS-like structural features.
PMID:32541063
LD tightly associates with FLD and SDG26 in vivo.
ASHH1: SDG26/ASHH1 contributes DNA association and contacts FY
sdg26_dna_binding
Participant: Gene Product: ASHH1
Gene Product:
ASHH1UniProtKB:Q84WW6
Family:
SET DOMAIN PROTEINSPANTHER:PTHR22884 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: ASHH1UniProtKB:Q84WW6
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

double-stranded DNA bindingGO:0003690

Processes

negative regulation of gene expression, epigeneticGO:0045814

Locations

chromatinGO:0000785

SDG26/ASHH1 contributes DNA association and contacts FY. Its C-terminal region binds FLC-derived dsDNA in vitro; it is not assigned the FLD demethylase reaction. Older methyltransferase evidence is retained in its gene review.

PMID:35766439
SDG26 C-terminal fragment directly binds FLC-derived dsDNA.
the C-terminal uncharacterized region (320–492 aa) of SDG26 bound to the double-stranded DNA from the FLC sequence (FLC-2)
PMID:32541063
SDG26 contacts FY to link processing and chromatin regulation.
SDG26 interacts with the RNA 3' processing factor FY (WDR33)
Part: termination-associated contribution
APRF1/TOPP4 termination-associated contributionBiological Processcpf_termination_bridge

LD is represented once in the linked chromatin part and also participates in this assembly. RNA Pol II phosphorylation changes do not distinguish a CTD substrate from an elongation-factor substrate. These sampled subassemblies need not form one obligatory stoichiometric supercomplex.

RNA 3'-end processingGO:0031123

Annotons

APRF1: Noncatalytic chromatin-associated scaffold of the APRF1/LD/TOPP4 termination module; no COMPASS methyltransferase activity is inferred from Swd2 homology
aprf1_chromatin_scaffold
Participant: Gene Product: APRF1
Gene Product:
APRF1UniProtKB:Q9LYK6
Family:
PROTEIN ANTHESIS POMOTING FACTOR 1PANTHER:PTHR19861:SF9 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: APRF1UniProtKB:Q9LYK6
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

chromatin bindingGO:0003682

Processes

RNA 3'-end processingGO:0031123

Locations

chromatinGO:0000785

Noncatalytic chromatin-associated scaffold of the APRF1/LD/TOPP4 termination module; no COMPASS methyltransferase activity is inferred from Swd2 homology.

PMID:35766439
APRF1 association with FLC chromatin was tested by native ChIP-PCR.
determined the association of EFL2, APRF1 and SDG26 with FLC chromatin by ChIP-PCR
PMID:38851185
APRF1 associates with LD and TOPP4 in a CPF-like phosphatase assembly.
TOPP4: PP1-type catalytic phosphatase associated with the CPF-like module
topp4_phosphatase
Participant: Gene Product: TOPP4
Gene Product:
TOPP4UniProtKB:P48484
Family:
SERINE_THREONINE-PROTEIN PHOSPHATASE PP1 ISOZYME 4PANTHER:PTHR11668:SF490 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: TOPP4UniProtKB:P48484
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

protein serine/threonine phosphatase activityGO:0004722

Locations

nucleusGO:0005634

PP1-type catalytic phosphatase associated with the CPF-like module. Direct target activity is established on other substrates; its substrate in FLC regulation remains unknown, so no Pol II CTD phosphatase term or direct CTD edge is asserted.

PMID:25010794
TOPP4 directly dephosphorylates DELLA proteins, establishing its catalytic class.
TOPP4 is able to directly bind and dephosphorylate RGA and GAI
PMID:38851185
The flowering-related CPF substrate is unresolved.
Finally, the substrate of the CPF phosphatase module remains to be established.
FPA-associated RNA-processing contributionBiological Processfpa_processing_route

This variant tracks a distinct documented contribution, not an assertion that FPA alone reconstructs wild-type repression without cofactors. Genetic bypass evidence is 35S overexpression; native necessity and dosage are context-dependent.

RNA 3'-end processingGO:0031123
Context
Native FPA RNA-processing phenotypes and separately identified 35S::FPA bypass experiments; these contexts are not treated as identical

Annotons

FPA: Distinct RNA-processing regulator affecting FLC antisense poly(A)-site usage
fpa_rna_processing
Participant: Gene Product: FPA
Gene Product:
FPAUniProtKB:Q8LPQ9
Family:
RNA RECOGNITION MOTIF-CONTAININGPANTHER:PTHR23189 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FPAUniProtKB:Q8LPQ9
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

RNA bindingGO:0003723

Processes

RNA 3'-end processingGO:0031123

Locations

nucleusGO:0005634

Distinct RNA-processing regulator affecting FLC antisense poly(A)-site usage. FPA need not bind COOLAIR or assemble with FCA/FY to reproduce every effect; gene-silencing and direct RNA-contact mechanisms are not equated.

PMID:20079695
FPA and FCA overlap in control of alternatively polyadenylated FLC antisense RNAs.
We show that FPA functions redundantly with FCA
PMID:18628965
Overexpressed FPA bypasses fca/fy in tested backgrounds but depends partly on FLD.
FPA overexpression reduced flowering time and FLC levels in fca, flk, fve and fy mutant backgrounds to the wild type level
FLK-mediated FLC sense-RNA regulationBiological Processflk_sense_rna_route

The m6A reader mechanism requires a modified target transcript and other RNA machinery. It does not establish an interchangeable FCA/FY pathway or a generic activity of all KH proteins.

Context
FLC sense transcripts with the m6A-dependent recognition context tested in Arabidopsis FLK and writer mutants

Annotons

FLK: m6A-dependent recognition of FLC sense mRNA affecting its stability and splicing
flk_sense_rna_reader
Participant: Gene Product: FLK
Gene Product:
FLKUniProtKB:Q9SR13
Family:
KH DOMAIN CONTAINING RNA BINDING PROTEINPANTHER:PTHR10288 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FLKUniProtKB:Q9SR13
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

N6-methyladenosine-containing RNA reader activityGO:1990247

Locations

nucleusGO:0005634

m6A-dependent recognition of FLC sense mRNA affecting its stability and splicing. This is distinct from antisense COOLAIR processing.

PMID:37050878
FLK directly recognizes an m6A site in FLC sense mRNA.
directly binds the m6A site in the 3'-untranslated region of FLC transcripts
FVE/MSI4-associated chromatin contributionBiological Processfve_chromatin_route

This route records the FVE-dependent contribution with associated catalytic partners outside the sampled selector. FVE also affects FT chromatin directly, so its entire biological effect is not forced through FLC.

negative regulation of gene expression, epigeneticGO:0045814
Context
Arabidopsis FVE/MSI4 chromatin contexts; CLF/CUL4-DDB1 and HDAC associations are source-specific, not one invariant complex

Annotons

FVE: MSI4/FVE contributes to chromatin complexes associated with deacetylation and CLF-dependent regulation
fve_chromatin_association
Participant: Gene Product: FVE
Gene Product:
FVEUniProtKB:O22607
Family:
WD40 REPEAT FAMILYPANTHER:PTHR22850 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FVEUniProtKB:O22607
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

histone bindingGO:0042393

Processes

negative regulation of gene expression, epigeneticGO:0045814

Locations

nucleusGO:0005634

MSI4/FVE contributes to chromatin complexes associated with deacetylation and CLF-dependent regulation. It is not a catalytic HDAC or a demonstrated universal stoichiometric PRC2 core subunit.

PMID:21282611
FVE/MSI4 associates with CLF-containing chromatin regulatory machinery.
represses FLC expression through its association with a CLF-Polycomb Repressive Complex 2 (PRC2) in Arabidopsis
PMID:25922987
HDA5 associates with FVE, FLD and HDA6; pairwise associations do not define invariant stoichiometry.
HDA5 interacts with FVE, FLD and HDA6
PMID:14745447
FVE-dependent FLC repression involves histone deacetylation.
FVE participates in a protein complex repressing FLC transcription through a histone deacetylation mechanism
Part: shared regulated target
FLC expression and target-specific repressor outputBiological Processflc_output

RNA/chromatin edges decrease FLC expression, thereby reducing availability of its repressor activity. This coarse causal node does not claim direct inhibition of FLC protein by RNA-processing factors.

Annotons

FLC: FLC expression supplies a DNA-binding repressor of FT and SOC1 in the modeled branch
flc_repressor
Participant: Gene Product: FLC
Gene Product:
FLCUniProtKB:Q9S7Q7
Family:
SERUM RESPONSE FACTOR HOMOLOGPANTHER:PTHR48019 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FLCUniProtKB:Q9S7Q7
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

DNA-binding transcription factor activity, RNA polymerase II-specificGO:0000981

Locations

nucleusGO:0005634

FLC expression supplies a DNA-binding repressor of FT and SOC1 in the modeled branch. Other FLC targets can be activated, so a universally negative transcriptional function is not asserted.

PMID:16623882
FLC binds FT first-intron and SOC1 promoter regulatory regions.
FLC binds to a region of the first intron of FT that contains a putative CArG box
PMID:16600915
Meristem FLC directly represses SOC1.
directly repressing expression of the SOC1 MADS-box transcription factor
Part: downstream FT readout (optional)
FT expression and downstream coactivationBiological Processft_output

Output readout; other photoperiod inputs and FD-mediated activation machinery are not modeled.

Context
FT transcription in leaves; FT/FD coactivation at the shoot apex are distinct tissue stages

Annotons

FT: Downstream florigen/coactivator whose expression in leaves is repressed by FLC and whose partnership with FD acts at the shoot apex
ft_coactivator
Participant: Gene Product: FT
Gene Product:
FTUniProtKB:Q9SXZ2
Family:
PROTEIN FLOWERING LOCUS T-RELATEDPANTHER:PTHR11362:SF9 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: FTUniProtKB:Q9SXZ2
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

transcription coactivator activityGO:0003713

Processes

positive regulation of flower developmentGO:0009911

Locations

nucleusGO:0005634

Downstream florigen/coactivator whose expression in leaves is repressed by FLC and whose partnership with FD acts at the shoot apex. Transport and complete meristem activation machinery are outside scope.

PMID:16099980
FT-FD complexes activate floral identity genes.
A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1).
PMID:16099979
FT and FD cooperate at the shoot apex.
Part: downstream SOC1 readout (optional)
SOC1 expression and meristem-transition outputBiological Processsoc1_output

Output readout integrating multiple pathways, not an obligate serial step after FT in every tissue.

Context
SOC1 transcriptional regulation and activity at the shoot apex

Annotons

SOC1: Downstream MADS transcription factor contributing to meristem transition with partners such as AGL24
soc1_transcription_factor
Participant: Gene Product: SOC1
Gene Product:
SOC1UniProtKB:O64645
Family:
SERUM RESPONSE FACTOR HOMOLOGPANTHER:PTHR48019 Verified classification of the selected Arabidopsis protein; this broad family is not a selector for its FLC-specific role.
Representative Members: SOC1UniProtKB:O64645
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product, not every classified family member, is selected.

Function

DNA-binding transcription factor activity, RNA polymerase II-specificGO:0000981

Processes

vegetative to reproductive phase transition of meristemGO:0010228

Locations

nucleusGO:0005634

Downstream MADS transcription factor contributing to meristem transition with partners such as AGL24. Its nuclear DNA-binding role is distinct from FLC binding to the SOC1 promoter.

PMID:18466303
SOC1 directly binds LFY regulatory DNA.
SOC1 directly binds to the distal and proximal region of the LFY promoter
PMID:16600915
SOC1 expression is directly repressed by meristem FLC.