LHY (LATE ELONGATED HYPOCOTYL) is a single-MYB (MYB-related, SHAQKYF/SANT-class) sequence-specific DNA-binding transcription factor that forms the morning-expressed arm of the Arabidopsis circadian oscillator together with its close paralog CCA1. LHY transcript and protein peak around one hour after dawn, and the protein is nuclear. It binds the Evening Element (AAATATCT) and related CCA1-binding-site motifs in target promoters and acts predominantly as a transcriptional repressor, directly repressing evening-phased clock genes such as TOC1/APRR1 and TCP21/CHE, repressing CCA1, and autorepressing its own gene. Through these negative feedback loops LHY (acting partly redundantly with CCA1) is required to sustain robust circadian oscillations. LHY also drives clock outputs, including positive circadian and cold regulation of the CBF cold-response regulon (contributing to freezing tolerance) and the photoperiodic control of flowering. LHY can homodimerize and heterodimerize with CCA1 and is found in a large nuclear protein complex.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic DNA binding inferred electronically from the InterPro Myb/SANT domain. True but uninformative relative to the experimentally supported transcription-factor and cis-regulatory-region-binding terms. Reason: LHY is a genuine MYB DNA-binding protein, so the term is correct, but it is a generic parent superseded by GO:0003700 (DNA-binding transcription factor activity, IDA) and GO:0000976 (cis-regulatory region binding, IDA). Retain as supporting, non-core. Supporting Evidence: PMID:9657154 LHY was shown to encode a MYB DNA-binding protein. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization inferred electronically from UniProt subcellular location mapping; consistent with experimental evidence. Reason: Correct location and experimentally corroborated by the EXP nucleus annotation (PMID:19218364); accepted to match the experimentally supported core location. Supporting Evidence: PMID:19218364 they also colocalize in the nucleus and heterodimerize in vitro and in vivo |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Generic ARBA/IEA process term for a transcriptional regulator; true but far less informative than the specific transcription-regulation and circadian terms. Reason: LHY does regulate gene expression, but this is a high-level parent of regulation of DNA-templated transcription and of (negative) regulation of circadian rhythm, which are better supported. Retain as non-core. Supporting Evidence: PMID:19286557 CCA1 and LHY are DNA binding proteins that repress TOC1 expression through direct binding to its promoter region |
| GO:0005634 nucleus | EXP PMID:19218364 CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL fun... | ACCEPT | Summary: Experimentally demonstrated nuclear localization; LHY colocalizes with CCA1 in the nucleus and acts there on target promoters. Reason: Direct experimental evidence for nuclear localization, the correct and expected compartment for a transcription factor that binds clock-gene promoters. Supporting Evidence: PMID:19218364 they also colocalize in the nucleus and heterodimerize in vitro and in vivo |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:30356219 Transcriptional regulation of nitrogen-associated metabolism... | ACCEPT | Summary: LHY recovered as a transcription factor binding a target promoter in a large yeast-one-hybrid nitrogen transcriptional regulatory network. Reason: Reports a genuine, correct molecular capacity (cis-regulatory region binding) for a bona fide DNA-binding TF; accepted consistently with the core IDA cis-regulatory-region-binding term (PMID:19286557). It derives from a high-throughput eY1H screen in a non-clock context, so it is corroborating rather than the primary clock-target evidence. Supporting Evidence: PMID:30356219 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 |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:31806676 A PXY-Mediated Transcriptional Network Integrates Signaling ... | ACCEPT | Summary: LHY recovered as a promoter-binding transcription factor in a large PXY-mediated vascular-development yeast-one-hybrid network (690 TF-promoter interactions). Reason: Correct molecular capacity (cis-regulatory region binding) for a real DNA-binding TF; accepted consistently with the core IDA cis-regulatory-region-binding term (PMID:19286557). It comes from a high-throughput eY1H screen outside the clock context, so it corroborates rather than primarily establishes the function. Supporting Evidence: PMID:31806676 we generated a transcriptional regulatory network (TRN) |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Nuclear localization predicted computationally (AtSubP); consistent with the experimental EXP nucleus annotation. Reason: Correct, predicted, and corroborated by the experimental nucleus annotation (PMID:19218364); accepted to match the core location. Supporting Evidence: PMID:19218364 they also colocalize in the nucleus and heterodimerize in vitro and in vivo |
| GO:0048574 long-day photoperiodism, flowering | IGI PMID:19011118 Circadian clock proteins LHY and CCA1 regulate SVP protein a... | KEEP AS NON CORE | Summary: LHY (with CCA1) controls photoperiodic flowering, repressing the floral transition under day/night cycles and modulating FT expression; genetic interaction with SVP. Reason: Flowering-time control is a downstream output of the circadian clock rather than the central oscillator mechanism that defines LHY's core function. The annotation is correct and well supported but should be marked non-core. The Falcon deep-research synthesis adds a useful caveat that LHY appears to act on flowering via clock phase control, and (per Park et al. 2016) LHY does not show direct FT-promoter binding (unlike CCA1), so a direct FT-regulation annotation for LHY would be an over-extension. Supporting Evidence: PMID:19011118 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) file:ARATH/LHY/LHY-deep-research-falcon.md LHY affects photoperiodic flowering primarily through **clock phase control**, not necessarily by direct binding to floral integrator promoters |
| GO:0042754 negative regulation of circadian rhythm | IMP PMID:21499259 Coordinated transcriptional regulation underlying the circad... | ACCEPT | Summary: LHY (with CCA1) directly suppresses expression of the oscillator component ELF4 at dawn, a negative regulatory input to the circadian clock. Reason: Captures the central repressor activity of LHY within the oscillator; directly supported by demonstrated suppression of ELF4 expression at dawn. Supporting Evidence: PMID:21499259 the circadian-controlled CCA1 and LHY proteins directly suppress ELF4 expression periodically at dawn through physical interactions with these transcription-promoting factors file:ARATH/LHY/LHY-deep-research-falcon.md forming the core negative feedback architecture of the plant oscillator |
| GO:0007623 circadian rhythm | IGI PMID:21471455 Circadian clock-associated 1 and late elongated hypocotyl re... | KEEP AS NON CORE | Summary: LHY is a core clock component; the generic circadian rhythm process term applies but is a high-level parent. Reason: True but generic; the more specific (negative) regulation of circadian rhythm terms better capture LHY's role. Retain as non-core parent. Supporting Evidence: PMID:21471455 two transcription factors that are core components of the clock, i.e., Circadian Clock-Associated 1 (CCA1) and Late Elongated Hypocotyl (LHY) |
| GO:0009409 response to cold | IGI PMID:21471455 Circadian clock-associated 1 and late elongated hypocotyl re... | KEEP AS NON CORE | Summary: LHY (with CCA1) positively regulates the CBF cold-response pathway and is required for full freezing tolerance, a clock-output contribution to cold response. Reason: A genuine, well-supported clock-output role in cold acclimation, but it is downstream of LHY's core oscillator function rather than the core function itself. Mark non-core. The Falcon deep-research synthesis concurs, framing this as a clock-controlled output best scoped to circadian regulation of cold response rather than general cold tolerance. Supporting Evidence: PMID:21471455 CCA1/LHY-mediated output from the circadian clock contributes to plant cold tolerance through regulation of the CBF cold-response pathway file:ARATH/LHY/LHY-deep-research-falcon.md annotate as circadian regulation of cold response rather than general “cold tolerance” unless specifically justified |
| GO:0006355 regulation of DNA-templated transcription | TAS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | KEEP AS NON CORE | Summary: Generic transcription-regulation process from a genome-wide Arabidopsis transcription-factor survey; true but high-level. Reason: Correct parent term for LHY's activity but less informative than the specific (negative) regulation of circadian rhythm terms. Retain as non-core. Supporting Evidence: PMID:11118137 Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. |
| GO:0000976 transcription cis-regulatory region binding | IDA PMID:19286557 A functional genomics approach reveals CHE as a component of... | ACCEPT | Summary: Direct experimental demonstration (EMSA) that LHY binds a specific cis-regulatory site in the CHE promoter, and direct binding of clock-gene promoters (CCA1, TOC1). Reason: Core molecular function. LHY is a sequence-specific cis-regulatory region binder at clock-gene promoters; directly demonstrated by EMSA. Supporting Evidence: PMID:19286557 electrophoretic mobility shift assays indicate that CCA1 and LHY specifically bind to the CCA1-binding site in CHE promoter file:ARATH/LHY/LHY-deep-research-falcon.md LHY recognizes promoter cis-elements closely related to one another |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:19286557 A functional genomics approach reveals CHE as a component of... | ACCEPT | Summary: LHY acts as a sequence-specific DNA-binding transcription factor (a repressor) at clock-gene promoters; directly supported by binding and repression data. Reason: This is LHY's core molecular function. Directly demonstrated DNA binding coupled to transcriptional repression of CCA1/TOC1/CHE. Supporting Evidence: PMID:19286557 CCA1 and LHY are DNA binding proteins that repress TOC1 expression through direct binding to its promoter region file:ARATH/LHY/LHY-deep-research-falcon.md LHY recognizes promoter cis-elements closely related to one another |
| GO:0042752 regulation of circadian rhythm | IMP PMID:19286557 A functional genomics approach reveals CHE as a component of... | ACCEPT | Summary: Loss/perturbation of LHY (and the lhy/che, cca1/lhy combinations) alters clock period, demonstrating involvement in regulating circadian rhythm. Reason: Core process. LHY is a central oscillator component whose perturbation changes clock pace; supported by genetic clock-period phenotypes. Supporting Evidence: PMID:19286557 the pace of the clock in che/lhy double mutant lines exhibited a significantly shorter period length compared to the lhy single mutant |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:9657154 The late elongated hypocotyl mutation of Arabidopsis disrupt... | ACCEPT | Summary: Sequence-similarity-based assignment of DNA-binding transcription factor activity based on the MYB domain; later confirmed experimentally. Reason: Correct core molecular function, corroborated by the IDA evidence (PMID:19286557); accepted consistently with the experimentally supported term. Supporting Evidence: PMID:9657154 LHY was shown to encode a MYB DNA-binding protein. |
| GO:0042752 regulation of circadian rhythm | IMP PMID:12007421 Critical role for CCA1 and LHY in maintaining circadian rhyt... | ACCEPT | Summary: Plants lacking CCA1 with strongly reduced LHY cannot maintain sustained circadian oscillations, demonstrating LHY's role in regulating circadian rhythm. Reason: Core process directly supported by the loss-of-rhythmicity phenotype of cca1 lhy plants. Supporting Evidence: PMID:12007421 these plants are unable to maintain sustained oscillations in both constant light and constant darkness file:ARATH/LHY/LHY-deep-research-falcon.md demonstrating essentiality for robust oscillation |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Sequence-similarity-based assignment of DNA-binding transcription factor activity from the genome-wide TF classification; corroborated by the IDA. Reason: Correct core molecular function, corroborated by the IDA evidence (PMID:19286557); accepted consistently with the experimentally supported term. Supporting Evidence: PMID:11118137 Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. |
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Download this section (compressed HTML)Q: How does LHY achieve target specificity at clock-gene promoters when CCA1 and LHY recognize overlapping (Evening Element / CCA1-binding-site) motifs, and to what extent are their in vivo binding repertoires shared versus distinct?
Q: Is LHY-mediated repression of clock-gene promoters direct (recruitment of a corepressor) or indirect (e.g., competition with TCP21/CHE or activator displacement), and which chromatin-modifying complexes interact with LHY at target promoters?
Q: Does LHY directly bind any floral integrator promoters in vivo (the deep research suggests it may not, unlike CCA1), or is its photoperiodic-flowering effect entirely mediated by clock-phase control?
Experiment: Genome-wide LHY ChIP-seq under matched circadian time points in wild-type and lhy mutant backgrounds, compared with parallel CCA1 ChIP-seq, to map shared versus distinct in vivo binding sites and quantify the LHY/CCA1 cis-regulome.
Hypothesis: LHY and CCA1 share most binding sites but each has a distinct subset, accounting for their non-redundant short-period phenotypes.
Type: ChIP-seq
Experiment: Affinity purification of LHY (TAP-tag or proximity labeling such as TurboID) followed by mass spectrometry across day/night time points to define LHY-containing complexes and identify candidate corepressors and chromatin modifiers.
Hypothesis: LHY operates through stable interactions with TPL/TPR-type corepressors and SWI/SNF-related chromatin remodelers to repress evening-phase clock genes.
Type: Affinity-purification mass spectrometry
Experiment: Inducible (e.g. estradiol-driven) LHY expression in cca1 lhy double mutants, with high-resolution circadian assays and time-resolved RNA-seq, to define which clock-output rhythms LHY can rescue and on what timescale.
Hypothesis: Transient pulses of LHY at subjective dawn are sufficient to restore robust oscillator function and clock-output rhythms in cca1 lhy plants.
Type: Inducible complementation with circadian phenotyping and RNA-seq
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