Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
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Genome-wide Arabidopsis transcription factor catalog classifies LHY as a sequence-specific DNA-binding TF based on its MYB-related DNA-binding domain.
"Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants."
Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis.
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CCA1 and LHY are partially redundant; LHY can only partially compensate for loss of CCA1, producing a short-period clock phenotype in cca1-1 plants.
"cca1-1 plants, which lack CCA1 protein, show a short-period phenotype for the expression of several genes when assayed under constant light conditions. This suggests that LHY function is able to only partially compensate for the lack of CCA1 protein, resulting in a clock with a faster pace in cca1-1 plants."
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cca1-1 lhy-R double mutants lacking CCA1 and with strongly reduced LHY cannot maintain sustained circadian oscillations in either constant light or constant darkness, establishing that LHY is required for robust free-running rhythms.
"these plants are unable to maintain sustained oscillations in both constant light and constant darkness"
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Some residual circadian behaviour persists in light/dark cycles in cca1-1 lhy-R plants, indicating the Arabidopsis clock is not entirely dependent on CCA1/LHY when external entrainment is provided.
"these plants exhibit some circadian function in light/dark cycles, showing that the Arabidopsis circadian clock is not entirely dependent on CCA1 and LHY activities"
Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in Arabidopsis.
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LHY and CCA1 repress the floral transition under both short-day and long-day photoperiods, and conversely accelerate flowering under continuous light, placing them upstream of photoperiodic flowering control.
"the circadian clock proteins LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) not only repressed the floral transition under short-day and long-day conditions but also accelerated flowering when the plants were grown under continuous light (LL)"
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LHY/CCA1 regulate the FT-SVP module, modulating accumulation of the flowering repressor SVP and FT expression, implicating them in long-day photoperiodism of flowering as a clock-output (not core oscillator) role.
"Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in Arabidopsis."
CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis.
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LHY localizes to the nucleus and colocalizes with CCA1 there; LHY heterodimerizes with CCA1 and homodimerizes both in vitro and in vivo, providing the experimental (EXP) basis for nuclear localization.
"they also colocalize in the nucleus and heterodimerize in vitro and in vivo"
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CCA1 and LHY are recovered together in the same large (>400 kDa) nuclear protein complex in planta, supporting their joint function as a clock transcriptional module.
"CCA1 and LHY can form homodimers, and they also colocalize in the nucleus and heterodimerize in vitro and in vivo"
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LHY and CCA1 bind to the same region of a Lhcb (CAB) promoter, providing direct evidence that LHY acts as a sequence-specific cis-regulatory region binder at clock-output promoters.
"LHY and CCA1 bind to the same region of the promoter of a Light-harvesting chlorophyll a/b protein (Lhcb, also known as CAB)"
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Single cca1 and lhy mutants each show short-period rhythms, and the cca1 lhy double mutant has a still shorter period than either single mutant, indicating only partial functional redundancy and a synergistic role in the central oscillator.
"cca1 lhy double mutants show an even shorter period phenotype than the cca1 single mutant, suggesting that CCA1 and LHY are only partially functionally redundant"
A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock.
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LHY (with CCA1) directly represses TOC1 transcription by binding the TOC1 promoter region, providing IDA evidence for LHY's core DNA-binding transcription factor activity and cis-regulatory region binding.
"CCA1 and LHY are DNA binding proteins that repress TOC1 expression through direct binding to its promoter region"
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Electrophoretic mobility shift assays (EMSA) demonstrate that LHY specifically binds the CCA1-binding site in the CHE promoter, establishing sequence-specific cis-regulatory binding at a clock-gene target.
"electrophoretic mobility shift assays indicate that CCA1 and LHY specifically bind to the CCA1-binding site in CHE promoter"
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LHY is partially redundant with CHE in repressing CCA1 expression; the che/lhy double mutant has a significantly shorter clock period than the lhy single mutant, supporting LHY's IMP-evidence role in regulating circadian rhythm.
"the pace of the clock in che/lhy double mutant lines exhibited a significantly shorter period length compared to the lhy single mutant"
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LHY inhibits CCA1 expression by binding to a CCA1-binding site (AGATTTTT) located ~479 nt upstream of the TCP-binding site in the CCA1 promoter.
"LHY inhibits CCA1 expression (17) probably through direct binding to a CCA1-binding site (18) (AGATTTTT) located 479 nucleotides upstream of the TCP-binding site"
Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis.
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LHY (with CCA1) directly binds the CBF1-3 promoter region (at EE/CBS and related motifs) and is required for circadian regulation of the CBF cold-response regulon.
"this circadian regulation is caused by the direct action of CCA1 and LHY binding at the CBF1-3 locus—presumably at the EE, CBS, and related motifs"
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The cca1-11/lhy-21 double mutant shows impaired freezing tolerance in both nonacclimated and cold-acclimated plants, demonstrating that LHY contributes to cold tolerance as a clock output.
"the cca1-11/lhy-21 double mutation resulted in impaired freezing tolerance in both nonacclimated and cold-acclimated plants"
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CCA1/LHY-mediated regulation of the CBF cold-response pathway represents an output of the circadian clock that contributes to plant cold tolerance, framing this as circadian regulation of the cold response rather than a direct cold-sensing function.
"CCA1/LHY-mediated output from the circadian clock contributes to plant cold tolerance through regulation of the CBF cold-response pathway"
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LHY (with CCA1) is a core component of the central oscillator and acts upstream of CBF1-3, integrating temporal regulation with cold-stress responses.
"two transcription factors that are core components of the clock, i.e., Circadian Clock-Associated 1 (CCA1) and Late Elongated Hypocotyl (LHY)"
Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
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LHY (with CCA1) directly suppresses ELF4 expression periodically at dawn through physical interactions with the FHY3/FAR1/HY5 transcription-promoting factors at the ELF4 promoter, providing IMP support for negative regulation of circadian rhythm.
"the circadian-controlled CCA1 and LHY proteins directly suppress ELF4 expression periodically at dawn through physical interactions with these transcription-promoting factors"
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A coordinated set of light- and circadian-regulated transcription factors (FHY3, FAR1, HY5 activating; CCA1/LHY repressing) acts at the ELF4 promoter to generate its cyclic expression, linking light input to the central oscillator.
"a set of light- and circadian-regulated transcription factors act directly and coordinately at the ELF4 promoter to regulate its cyclic expression"
Transcriptional regulation of nitrogen-associated metabolism and growth.
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A high-throughput enhanced yeast-one-hybrid screen of nitrogen-responsive root/shoot regulators recovers LHY as a promoter-binding TF, supporting a generic cis-regulatory region binding capacity without implying a nitrogen-specific function.
"a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability"
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Genetic perturbation of TFs in the network revealed coordinated transcriptional regulation of nitrogen metabolism enzymes; LHY appears as a network node rather than a nitrogen-metabolism effector.
"Genetic perturbation of a subset of these transcription factors revealed coordinate transcriptional regulation of enzymes involved in nitrogen metabolism."
A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis.
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LHY is recovered as one of many promoter-binding TFs in a large eY1H-derived vascular-development transcriptional regulatory network (690 TF-promoter interactions), supporting only a generic cis-regulatory region binding capacity rather than a vascular function for LHY.
"we generated a transcriptional regulatory network (TRN)"
The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering.
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LHY encodes a MYB DNA-binding protein, establishing the molecular basis for its DNA-binding transcription factor activity.
"LHY was shown to encode a MYB DNA-binding protein"
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A dominant late elongated hypocotyl mutation that constitutively expresses LHY disrupts circadian regulation of gene expression and leaf movements, demonstrating LHY is required for normal circadian rhythms.
"The dominant late elongated hypocotyl (lhy) mutation of Arabidopsis disrupted circadian clock regulation of gene expression and leaf movements"
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LHY mRNA shows a circadian peak around dawn in wild-type plants but is expressed constitutively in the lhy mutant, indicating circadian regulation of LHY itself.
"the LHY mRNA showed a circadian pattern of expression with a peak around dawn but in the mutant was expressed constantly at high levels"
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Increased LHY expression from a transgene causes the endogenous LHY gene to be expressed at constant high levels, indicating LHY is part of a feedback circuit that regulates its own expression (autorepression).
"Increased LHY expression from a transgene caused the endogenous gene to be expressed at a constant level, suggesting that LHY was part of a feedback circuit that regulated its own expression"
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Constitutive LHY caused flowering to occur independently of photoperiod, identifying LHY as a regulator of the photoperiodic flowering pathway (a clock-output process).
"caused flowering to occur independently of photoperiod"
Falcon/Edison deep research report: LHY
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LHY (with CCA1) forms the core negative feedback architecture of the plant circadian oscillator by directly repressing evening-phase clock genes, summarizing the consensus literature view.
"forming the core negative feedback architecture of the plant oscillator"
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LHY recognizes Evening Element and CCA1-binding-site cis-elements (closely related AAATATCT/AGATTTTT-like motifs) in clock-gene promoters.
"LHY recognizes promoter cis-elements closely related to one another"
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LHY contributes to photoperiodic flowering primarily through control of clock phase rather than direct binding of FT-promoter cis-elements, consistent with reports that LHY (unlike CCA1) does not directly bind the FT promoter.
"LHY affects photoperiodic flowering primarily through **clock phase control**, not necessarily by direct binding to floral integrator promoters"
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LHY's role in cold tolerance is best framed as circadian regulation of the cold response (CBF regulon) rather than general cold tolerance.
"annotate as circadian regulation of cold response rather than general "cold tolerance" unless specifically justified"
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Loss of LHY (and CCA1) abolishes sustained free-running rhythms, establishing essentiality for robust circadian oscillation.
"demonstrating essentiality for robust oscillation"