Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G01060.2
Common NameLHY, LHY1, T25K16.6
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family MYB_related
Protein Properties Length: 645aa    MW: 70438 Da    PI: 6.0252
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G01060.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                     r rWT++E+e++++a +++G   W +I +++g ++t+ q++s+ qk+
                     78******************88.*********.************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129419.9771973IPR017930Myb domain
TIGRFAMsTIGR015572.9E-172271IPR006447Myb domain, plants
SMARTSM007172.4E-122371IPR001005SANT/Myb domain
PfamPF002493.5E-132467IPR001005SANT/Myb domain
CDDcd001672.88E-92669No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009409Biological Processresponse to cold
GO:0009651Biological Processresponse to salt stress
GO:0009723Biological Processresponse to ethylene
GO:0009733Biological Processresponse to auxin
GO:0009737Biological Processresponse to abscisic acid
GO:0009739Biological Processresponse to gibberellin
GO:0009751Biological Processresponse to salicylic acid
GO:0009753Biological Processresponse to jasmonic acid
GO:0042754Biological Processnegative regulation of circadian rhythm
GO:0043433Biological Processnegative regulation of sequence-specific DNA binding transcription factor activity
GO:0046686Biological Processresponse to cadmium ion
GO:0048574Biological Processlong-day photoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 645 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.254660.0flower| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G01060-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers and siliques. {ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364}.
Functional Description ? help Back to Top
Source Description
TAIRLHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1
UniProtTranscription factor involved in the circadian clock. Binds to the promoter region of APRR1/TOC1 and TCP21/CHE to repress their transcription. Represses both CCA1 and itself. {ECO:0000269|PubMed:12015970, ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:9657154}.
Function -- GeneRIF ? help Back to Top
  1. Accumulation of the LHY protein in the lhy-1 mutant was altered by the det1-1 mutation and through the proteasome pathway.
    [PMID: 15988568]
  2. The function of ELF3 and ELF4 in their light-regulated expression associated with CCA1, LHY, and TOC1 as part of the central oscillator of the circadian clock in Arabidopsis is reported.
    [PMID: 16212608]
  3. The linkages of TOC1, CCA1 and LHY genes and the canonical CO-FT flowering pathway were studied.
    [PMID: 17540692]
  4. CCA1 and LHY delay flowering time under continuous light by reducing the accumulation of SVP.
    [PMID: 19011118]
  5. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.
    [PMID: 19218364]
  6. LHY/CCA1 regulates a pathway negatively controlling flowering locus T (FT), possibly via ELF3-SVP/FLC.
    [PMID: 19383102]
  7. A conserved G-Box motif contributes to the rhythmic expression of LHY.
    [PMID: 19789276]
  8. LHY ubiquitination by SINAT5 was inhibited by DET1.
    [PMID: 20599732]
  9. Results reveal a role of PRR7 and PRR9 in regulating CCA1 and LHY activities in response to ambient temperature.
    [PMID: 21098730]
  10. CCA1/LHY-mediated output from the circadian clock contributes to plant cold tolerance through regulation of the CBF cold-response pathway.
    [PMID: 21471455]
  11. Functional interactions between the clock proteins LHY and CCA1 and the photoreceptor PhyB control organ elongation and flowering time.
    [PMID: 21822060]
  12. Interaction of Arabidopsis DET1 with LHY in mediating transcriptional repression in the plant circadian clock
    [PMID: 21884973]
  13. Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived.
    [PMID: 22395476]
  14. Rhythmic expression of LHY under light-dark cycling conditions correlates with histone modification.
    [PMID: 22878891]
  15. Histone 3 activating marks associated with the translational start sites of CCA1/LHY and TOC1 are circadian regulated.
    [PMID: 23128602]
  16. Transcriptional co-regulators PRR9, PRR7 and PRR5 inhibit morning loop LHY and CCA1 expression by binding to their promoters
    [PMID: 24267177]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Circadian-regulation with peak levels occurring around 1 hour after dawn. Up-regulated by APRR1/TOC1 and transiently by light treatment. Down-regulated by APRR5, APRR7 and APRR9. {ECO:0000269|PubMed:12574129, ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:19286557, ECO:0000269|PubMed:20233950, ECO:0000269|PubMed:9657154}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G09530 (A), AT2G46830 (R), AT3G46640 (A), AT5G37260 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G04400(A), AT1G22770(R), AT1G32900(A), AT1G65480(A), AT2G21660(R), AT2G40080(R), AT2G46790(A), AT3G46640(R), AT5G02810(A), AT5G15840(R), AT5G61380(R)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid, auxin, ethylene, gibberellin, jasmonic acid, salicylic acid
Interaction ? help Back to Top
Source Intact With
IntActSearch Q6R0H1
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Shorter circadian oscillations. {ECO:0000269|PubMed:12015970, ECO:0000269|PubMed:19218364}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G01060
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3167280.0AK316728.1 Arabidopsis thaliana AT1G01060 mRNA, complete cds, clone: RAFL04-17-F21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001030924.10.0protein LHY
RefseqNP_171614.10.0protein LHY
RefseqNP_849568.10.0protein LHY
SwissprotQ6R0H10.0LHY_ARATH; Protein LHY
TrEMBLF4HQH30.0F4HQH3_ARATH; Myb-related putative transcription factor
STRINGAT1G01060.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Staiger D,Heintzen C
    The circadian system of Arabidopsis thaliana: forward and reverse genetic approaches.
    Chronobiol. Int., 1999. 16(1): p. 1-16
  2. Green RM,Tobin EM
    Loss of the circadian clock-associated protein 1 in Arabidopsis results in altered clock-regulated gene expression.
    Proc. Natl. Acad. Sci. U.S.A., 1999. 96(7): p. 4176-9
  3. Fowler S, et al.
    GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains.
    EMBO J., 1999. 18(17): p. 4679-88
  4. Park DH, et al.
    Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene.
    Science, 1999. 285(5433): p. 1579-82
  5. Sugano S,Andronis C,Ong MS,Green RM,Tobin EM
    The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 1999. 96(22): p. 12362-6
  6. Coupland G, et al.
    The regulation of flowering time by daylength in Arabidopsis.
    Symp. Soc. Exp. Biol., 1998. 51: p. 105-10
  7. Martínez-García JF,Huq E,Quail PH
    Direct targeting of light signals to a promoter element-bound transcription factor.
    Science, 2000. 288(5467): p. 859-63
  8. Fairchild CD,Schumaker MA,Quail PH
    HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction.
    Genes Dev., 2000. 14(18): p. 2377-91
  9. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  10. Schaffer R, et al.
    Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis.
    Plant Cell, 2001. 13(1): p. 113-23
  11. Hicks KA,Albertson TM,Wagner DR
    EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis.
    Plant Cell, 2001. 13(6): p. 1281-92
  12. Xu Y,Johnson CH
    A clock- and light-regulated gene that links the circadian oscillator to LHCB gene expression.
    Plant Cell, 2001. 13(6): p. 1411-25
  13. Alabadí D, et al.
    Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock.
    Science, 2001. 293(5531): p. 880-3
  14. Makino S,Matsushika A,Kojima M,Yamashino T,Mizuno T
    The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants.
    Plant Cell Physiol., 2002. 43(1): p. 58-69
  15. Alabad
    Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis.
    Curr. Biol., 2002. 12(9): p. 757-61
  16. Mizoguchi T, et al.
    LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis.
    Dev. Cell, 2002. 2(5): p. 629-41
  17. Mouradov A,Cremer F,Coupland G
    Control of flowering time: interacting pathways as a basis for diversity.
    Plant Cell, 2002. 14 Suppl: p. S111-30
  18. Green RM,Tingay S,Wang ZY,Tobin EM
    Circadian rhythms confer a higher level of fitness to Arabidopsis plants.
    Plant Physiol., 2002. 129(2): p. 576-84
  19. Devlin PF
    Signs of the time: environmental input to the circadian clock.
    J. Exp. Bot., 2002. 53(374): p. 1535-50
  20. Carr
    MYB transcription factors in the Arabidopsis circadian clock.
    J. Exp. Bot., 2002. 53(374): p. 1551-7
  21. Matsushika A,Imamura A,Yamashino T,Mizuno T
    Aberrant expression of the light-inducible and circadian-regulated APRR9 gene belonging to the circadian-associated APRR1/TOC1 quintet results in the phenotype of early flowering in Arabidopsis thaliana.
    Plant Cell Physiol., 2002. 43(8): p. 833-43
  22. Hall A,Kozma-Bogn
    Distinct regulation of CAB and PHYB gene expression by similar circadian clocks.
    Plant J., 2002. 32(4): p. 529-37
  23. Sato E,Nakamichi N,Yamashino T,Mizuno T
    Aberrant expression of the Arabidopsis circadian-regulated APRR5 gene belonging to the APRR1/TOC1 quintet results in early flowering and hypersensitiveness to light in early photomorphogenesis.
    Plant Cell Physiol., 2002. 43(11): p. 1374-85
  24. M
    Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis.
    Plant Cell, 2003. 15(1): p. 223-36
  25. Kim JY,Song HR,Taylor BL,Carr
    Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY.
    EMBO J., 2003. 22(4): p. 935-44
  26. Nakamichi N,Matsushika A,Yamashino T,Mizuno T
    Cell autonomous circadian waves of the APRR1/TOC1 quintet in an established cell line of Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(3): p. 360-5
  27. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
  28. Tenorio G,Orea A,Romero JM,M
    Oscillation of mRNA level and activity of granule-bound starch synthase I in Arabidopsis leaves during the day/night cycle.
    Plant Mol. Biol., 2003. 51(6): p. 949-58
  29. Eriksson ME,Millar AJ
    The circadian clock. A plant's best friend in a spinning world.
    Plant Physiol., 2003. 132(2): p. 732-8
  30. Kuno N, et al.
    The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis.
    Plant Cell, 2003. 15(10): p. 2476-88
  31. Hall A, et al.
    The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks.
    Plant Cell, 2003. 15(11): p. 2719-29
  32. Kaldis AD,Kousidis P,Kesanopoulos K,Prombona A
    Light and circadian regulation in the expression of LHY and Lhcb genes in Phaseolus vulgaris.
    Plant Mol. Biol., 2003. 52(5): p. 981-97
  33. Kaczorowski KA,Quail PH
    Arabidopsis PSEUDO-RESPONSE REGULATOR7 is a signaling intermediate in phytochrome-regulated seedling deetiolation and phasing of the circadian clock.
    Plant Cell, 2003. 15(11): p. 2654-65
  34. Khanna R,Kikis EA,Quail PH
    EARLY FLOWERING 4 functions in phytochrome B-regulated seedling de-etiolation.
    Plant Physiol., 2003. 133(4): p. 1530-8
  35. Ito S, et al.
    Characterization of the APRR9 pseudo-response regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(11): p. 1237-45
  36. Oda A,Fujiwara S,Kamada H,Coupland G,Mizoguchi T
    Antisense suppression of the Arabidopsis PIF3 gene does not affect circadian rhythms but causes early flowering and increases FT expression.
    FEBS Lett., 2004. 557(1-3): p. 259-64
  37. Searle I,Coupland G
    Induction of flowering by seasonal changes in photoperiod.
    EMBO J., 2004. 23(6): p. 1217-22
  38. Yasuhara M, et al.
    Identification of ASK and clock-associated proteins as molecular partners of LKP2 (LOV kelch protein 2) in Arabidopsis.
    J. Exp. Bot., 2004. 55(405): p. 2015-27
  39. Farré EM,Harmer SL,Harmon FG,Yanovsky MJ,Kay SA
    Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock.
    Curr. Biol., 2005. 15(1): p. 47-54
  40. Fujimori T,Sato E,Yamashino T,Mizuno T
    PRR5 (PSEUDO-RESPONSE REGULATOR 5) plays antagonistic roles to CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2005. 69(2): p. 426-30
  41. Boxall SF, et al.
    Conservation and divergence of circadian clock operation in a stress-inducible Crassulacean acid metabolism species reveals clock compensation against stress.
    Plant Physiol., 2005. 137(3): p. 969-82
  42. Chang WC,Li CW,Chen BS
    Quantitative inference of dynamic regulatory pathways via microarray data.
    BMC Bioinformatics, 2005. 6: p. 44
  43. Nakamichi N,Kita M,Ito S,Yamashino T,Mizuno T
    PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana.
    Plant Cell Physiol., 2005. 46(5): p. 686-98
  44. Harmer SL,Kay SA
    Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis.
    Plant Cell, 2005. 17(7): p. 1926-40
  45. Song HR,Carré IA
    DET1 regulates the proteasomal degradation of LHY, a component of the Arabidopsis circadian clock.
    Plant Mol. Biol., 2005. 57(5): p. 761-71
  46. Hazen SP, et al.
    LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(29): p. 10387-92
  47. Mizoguchi T, et al.
    Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis.
    Plant Cell, 2005. 17(8): p. 2255-70
  48. Lu Y,Gehan JP,Sharkey TD
    Daylength and circadian effects on starch degradation and maltose metabolism.
    Plant Physiol., 2005. 138(4): p. 2280-91
  49. Onai K,Ishiura M
    PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock.
    Genes Cells, 2005. 10(10): p. 963-72
  50. Kikis EA,Khanna R,Quail PH
    ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY.
    Plant J., 2005. 44(2): p. 300-13
  51. Salom
    Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period.
    Plant Cell, 2006. 18(1): p. 55-69
  52. Yanhui C, et al.
    The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family.
    Plant Mol. Biol., 2006. 60(1): p. 107-24
  53. Miwa K,Serikawa M,Suzuki S,Kondo T,Oyama T
    Conserved expression profiles of circadian clock-related genes in two Lemna species showing long-day and short-day photoperiodic flowering responses.
    Plant Cell Physiol., 2006. 47(5): p. 601-12
  54. McClung CR
    Plant circadian rhythms.
    Plant Cell, 2006. 18(4): p. 792-803
  55. Gould PD, et al.
    The molecular basis of temperature compensation in the Arabidopsis circadian clock.
    Plant Cell, 2006. 18(5): p. 1177-87
  56. Chen M,Ni M
    RFI2, a RING-domain zinc finger protein, negatively regulates CONSTANS expression and photoperiodic flowering.
    Plant J., 2006. 46(5): p. 823-33
  57. Locke JC, et al.
    Extension of a genetic network model by iterative experimentation and mathematical analysis.
    Mol. Syst. Biol., 2005. 1: p. 2005.0013
  58. Forger D,Drapeau M,Collins B,Blau J
    A new model for circadian clock research?
    Mol. Syst. Biol., 2005. 1: p. 2005.0014
  59. Martin-Tryon EL,Kreps JA,Harmer SL
    GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation.
    Plant Physiol., 2007. 143(1): p. 473-86
  60. Zeilinger MN,Farr
    A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9.
    Mol. Syst. Biol., 2006. 2: p. 58
  61. Locke JC, et al.
    Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana.
    Mol. Syst. Biol., 2006. 2: p. 59
  62. Loivam
    Circadian rhythms of isoprene biosynthesis in grey poplar leaves.
    Plant Physiol., 2007. 143(1): p. 540-51
  63. Murakami M,Tago Y,Yamashino T,Mizuno T
    Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa.
    Plant Cell Physiol., 2007. 48(1): p. 110-21
  64. Lee J, et al.
    Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development.
    Plant Cell, 2007. 19(3): p. 731-49
  65. Martini J, et al.
    Multifocal two-photon laser scanning microscopy combined with photo-activatable GFP for in vivo monitoring of intracellular protein dynamics in real time.
    J. Struct. Biol., 2007. 158(3): p. 401-9
  66. Hecht V, et al.
    Pea LATE BLOOMER1 is a GIGANTEA ortholog with roles in photoperiodic flowering, deetiolation, and transcriptional regulation of circadian clock gene homologs.
    Plant Physiol., 2007. 144(2): p. 648-61
  67. Ding Z,Doyle MR,Amasino RM,Davis SJ
    A complex genetic interaction between Arabidopsis thaliana TOC1 and CCA1/LHY in driving the circadian clock and in output regulation.
    Genetics, 2007. 176(3): p. 1501-10
  68. Ding Z,Millar AJ,Davis AM,Davis SJ
    TIME FOR COFFEE encodes a nuclear regulator in the Arabidopsis thaliana circadian clock.
    Plant Cell, 2007. 19(5): p. 1522-36
  69. Nakamichi N, et al.
    Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway.
    Plant Cell Physiol., 2007. 48(6): p. 822-32
  70. Ito S, et al.
    Genetic linkages between circadian clock-associated components and phytochrome-dependent red light signal transduction in Arabidopsis thaliana.
    Plant Cell Physiol., 2007. 48(7): p. 971-83
  71. Niwa Y, et al.
    Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabidopsis thaliana.
    Plant Cell Physiol., 2007. 48(7): p. 925-37
  72. Zhang X, et al.
    Constitutive expression of CIR1 (RVE2) affects several circadian-regulated processes and seed germination in Arabidopsis.
    Plant J., 2007. 51(3): p. 512-25
  73. Perales M,M
    A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock.
    Plant Cell, 2007. 19(7): p. 2111-23
  74. Kevei E, et al.
    Arabidopsis thaliana circadian clock is regulated by the small GTPase LIP1.
    Curr. Biol., 2007. 17(17): p. 1456-64
  75. Farr
    PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis.
    Plant J., 2007. 52(3): p. 548-60
  76. Xu X, et al.
    Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis.
    Plant Cell, 2007. 19(11): p. 3474-90
  77. Ito S, et al.
    Insight into missing genetic links between two evening-expressed pseudo-response regulator genes TOC1 and PRR5 in the circadian clock-controlled circuitry in Arabidopsis thaliana.
    Plant Cell Physiol., 2008. 49(2): p. 201-13
  78. Kant P, et al.
    Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses.
    Plant Cell Environ., 2008. 31(6): p. 697-714
  79. Serikawa M,Miwa K,Kondo T,Oyama T
    Functional conservation of clock-related genes in flowering plants: overexpression and RNA interference analyses of the circadian rhythm in the monocotyledon Lemna gibba.
    Plant Physiol., 2008. 146(4): p. 1952-63
  80. Kim J,Kim Y,Yeom M,Kim JH,Nam HG
    FIONA1 is essential for regulating period length in the Arabidopsis circadian clock.
    Plant Cell, 2008. 20(2): p. 307-19
  81. Abe M,Fujiwara M,Kurotani K,Yokoi S,Shimamoto K
    Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP).
    Plant Cell Physiol., 2008. 49(3): p. 420-32
  82. Bieniawska Z, et al.
    Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
    Plant Physiol., 2008. 147(1): p. 263-79
  83. Kawamura M,Ito S,Nakamichi N,Yamashino T,Mizuno T
    The function of the clock-associated transcriptional regulator CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2008. 72(5): p. 1307-16
  84. Salom
    Circadian timekeeping during early Arabidopsis development.
    Plant Physiol., 2008. 147(3): p. 1110-25
  85. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
  86. Wu JF,Wang Y,Wu SH
    Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering.
    Plant Physiol., 2008. 148(2): p. 948-59
  87. Liu H, et al.
    Analysis of clock gene homologs using unifoliolates as target organs in soybean (Glycine max).
    J. Plant Physiol., 2009. 166(3): p. 278-89
  88. Fujiwara S, et al.
    Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in Arabidopsis.
    Plant Cell, 2008. 20(11): p. 2960-71
  89. Ni Z, et al.
    Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids.
    Nature, 2009. 457(7227): p. 327-31
  90. Knowles SM,Lu SX,Tobin EM
    Testing time: can ethanol-induced pulses of proposed oscillator components phase shift rhythms in Arabidopsis?
    J. Biol. Rhythms, 2008. 23(6): p. 463-71
  91. James AB, et al.
    The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots.
    Science, 2008. 322(5909): p. 1832-5
  92. Ito S, et al.
    A genetic study of the Arabidopsis circadian clock with reference to the TIMING OF CAB EXPRESSION 1 (TOC1) gene.
    Plant Cell Physiol., 2009. 50(2): p. 290-303
  93. Takata N, et al.
    Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2.
    New Phytol., 2009. 181(4): p. 808-19
  94. Lu SX,Knowles SM,Andronis C,Ong MS,Tobin EM
    CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis.
    Plant Physiol., 2009. 150(2): p. 834-43
  95. Pruneda-Paz JL,Breton G,Para A,Kay SA
    A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock.
    Science, 2009. 323(5920): p. 1481-5
  96. Proels RK,Roitsch T
    Extracellular invertase LIN6 of tomato: a pivotal enzyme for integration of metabolic, hormonal, and stress signals is regulated by a diurnal rhythm.
    J. Exp. Bot., 2009. 60(6): p. 1555-67
  97. Yakir E, et al.
    Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis.
    Plant Physiol., 2009. 150(2): p. 844-57
  98. Robertson FC,Webb AA
    Revolutionary functional genomics liberates CHE.
    Nat. Chem. Biol., 2009. 5(5): p. 276-7
  99. Stephenson PG,Fankhauser C,Terry MJ
    PIF3 is a repressor of chloroplast development.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(18): p. 7654-9
  100. Yoshida R, et al.
    Possible role of early flowering 3 (ELF3) in clock-dependent floral regulation by short vegetative phase (SVP) in Arabidopsis thaliana.
    New Phytol., 2009. 182(4): p. 838-50
  101. Penfield S,Hall A
    A role for multiple circadian clock genes in the response to signals that break seed dormancy in Arabidopsis.
    Plant Cell, 2009. 21(6): p. 1722-32
  102. Okada R, et al.
    Functional characterization of CCA1/LHY homolog genes, PpCCA1a and PpCCA1b, in the moss Physcomitrella patens.
    Plant J., 2009. 60(3): p. 551-63
  103. Ishida K,Niwa Y,Yamashino T,Mizuno T
    A genome-wide compilation of the two-component systems in Lotus japonicus.
    DNA Res., 2009. 16(4): p. 237-47
  104. Spensley M, et al.
    Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL.
    Plant Cell, 2009. 21(9): p. 2606-23
  105. Rawat R, et al.
    REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(39): p. 16883-8
  106. Nakamichi N, et al.
    Linkage between circadian clock and tricarboxylic acid cycle in Arabidopsis.
    Plant Signal Behav, 2009. 4(7): p. 660-2
  107. Liew LC, et al.
    DIE NEUTRALIS and LATE BLOOMER 1 contribute to regulation of the pea circadian clock.
    Plant Cell, 2009. 21(10): p. 3198-211
  108. Ovadia A,Tabibian-Keissar H,Cohen Y,Kenigsbuch D
    The 5'UTR of CCA1 includes an autoregulatory cis element that segregates between light and circadian regulation of CCA1 and LHY.
    Plant Mol. Biol., 2010. 72(6): p. 659-71
  109. Okada R,Satbhai SB,Aoki S
    Photoperiod-dependent regulation of cell growth by PpCCA1a and PpCCA1b genes encoding single-myb clock proteins in the moss Physcomitrella patens.
    Genes Genet. Syst., 2009. 84(5): p. 379-84
  110. Nakamichi N, et al.
    PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock.
    Plant Cell, 2010. 22(3): p. 594-605
  111. Andr
    Deregulated copper transport affects Arabidopsis development especially in the absence of environmental cycles.
    Plant Physiol., 2010. 153(1): p. 170-84
  112. Baudry A, et al.
    F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression.
    Plant Cell, 2010. 22(3): p. 606-22
  113. Takata N,Saito S,Saito CT,Uemura M
    Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of pseudo-response regulators.
    BMC Evol. Biol., 2010. 10: p. 126
  114. Graf A,Schlereth A,Stitt M,Smith AM
    Circadian control of carbohydrate availability for growth in Arabidopsis plants at night.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(20): p. 9458-63
  115. Park BS, et al.
    Ubiquitination of LHY by SINAT5 regulates flowering time and is inhibited by DET1.
    Biochem. Biophys. Res. Commun., 2010. 398(2): p. 242-6
  116. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
  117. Salom
    The role of the Arabidopsis morning loop components CCA1, LHY, PRR7, and PRR9 in temperature compensation.
    Plant Cell, 2010. 22(11): p. 3650-61
  118. Lu SX, et al.
    The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock.
    Plant Physiol., 2011. 155(2): p. 906-15
  119. Giraud E, et al.
    TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana.
    Plant Cell, 2010. 22(12): p. 3921-34
  120. Barajas-L
    Circadian regulation of chloroplastic f and m thioredoxins through control of the CCA1 transcription factor.
    J. Exp. Bot., 2011. 62(6): p. 2039-51
  121. Farinas B,Mas P
    Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation.
    Plant J., 2011. 66(2): p. 318-29
  122. Dixon LE, et al.
    Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis.
    Curr. Biol., 2011. 21(2): p. 120-5
  123. Nefissi R, et al.
    Double loss-of-function mutation in EARLY FLOWERING 3 and CRYPTOCHROME 2 genes delays flowering under continuous light but accelerates it under long days and short days: an important role for Arabidopsis CRY2 to accelerate flowering time in continuous light.
    J. Exp. Bot., 2011. 62(8): p. 2731-44
  124. Yoo SK,Hong SM,Lee JS,Ahn JH
    A genetic screen for leaf movement mutants identifies a potential role for AGAMOUS-LIKE 6 (AGL6) in circadian-clock control.
    Mol. Cells, 2011. 31(3): p. 281-7
  125. Dai S, et al.
    BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock.
    Plant Cell, 2011. 23(3): p. 961-72
  126. O'Neill JS,van Ooijen G,Le Bihan T,Millar AJ
    Circadian clock parameter measurement: characterization of clock transcription factors using surface plasmon resonance.
    J. Biol. Rhythms, 2011. 26(2): p. 91-8
  127. Dong MA,Farr
    Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(17): p. 7241-6
  128. Farinas B,Mas P
    Histone acetylation and the circadian clock: a role for the MYB transcription factor RVE8/LCL5.
    Plant Signal Behav, 2011. 6(4): p. 541-3
  129. Rawat R, et al.
    REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock.
    PLoS Genet., 2011. 7(3): p. e1001350
  130. Li G, et al.
    Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
    Nat. Cell Biol., 2011. 13(5): p. 616-22
  131. Miyata K,Calvi
    Suppression of late-flowering and semi-dwarf phenotypes in the Arabidopsis clock mutant lhy-12;cca1-101 by phyB under continuous light.
    Plant Signal Behav, 2011. 6(8): p. 1162-71
  132. Sellaro R,Yanovsky MJ,Casal JJ
    Repression of shade-avoidance reactions by sunfleck induction of HY5 expression in Arabidopsis.
    Plant J., 2011. 68(5): p. 919-28
  133. McClung CR
    The photomorphogenic protein, DE-ETIOLATED 1, is a critical transcriptional corepressor in the central loop of the Arabidopsis circadian clock.
    Mol. Cell, 2011. 43(5): p. 693-4
  134. Lau OS, et al.
    Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock.
    Mol. Cell, 2011. 43(5): p. 703-12
  135. Sellaro R,Pac
    Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling.
    Mol Plant, 2012. 5(3): p. 619-28
  136. Gendron JM, et al.
    Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(8): p. 3167-72
  137. Mulekar JJ,Huq E
    Does CK2 affect flowering time by modulating the autonomous pathway in Arabidopsis?
    Plant Signal Behav, 2012. 7(2): p. 292-4
  138. Pokhilko A, et al.
    The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.
    Mol. Syst. Biol., 2012. 8: p. 574
  139. James AB, et al.
    Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes.
    Plant Cell, 2012. 24(3): p. 961-81
  140. Seo PJ, et al.
    Targeted inactivation of transcription factors by overexpression of their truncated forms in plants.
    Plant J., 2012. 72(1): p. 162-72
  141. Seo PJ, et al.
    A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis.
    Plant Cell, 2012. 24(6): p. 2427-42
  142. Song HR,Noh YS
    Rhythmic oscillation of histone acetylation and methylation at the Arabidopsis central clock loci.
    Mol. Cells, 2012. 34(3): p. 279-87
  143. Park MJ,Seo PJ,Park CM
    CCA1 alternative splicing as a way of linking the circadian clock to temperature response in Arabidopsis.
    Plant Signal Behav, 2012. 7(9): p. 1194-6
  144. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
  145. Yon F, et al.
    Identification and characterization of circadian clock genes in a native tobacco, Nicotiana attenuata.
    BMC Plant Biol., 2012. 12: p. 172
  146. Kim MY,Shin JH,Kang YJ,Shim SR,Lee SH
    Divergence of flowering genes in soybean.
    J. Biosci., 2012. 37(5): p. 857-70
  147. Hemmes H,Henriques R,Jang IC,Kim S,Chua NH
    Circadian clock regulates dynamic chromatin modifications associated with Arabidopsis CCA1/LHY and TOC1 transcriptional rhythms.
    Plant Cell Physiol., 2012. 53(12): p. 2016-29
  148. Chen C, et al.
    PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants.
    PLoS ONE, 2012. 7(11): p. e46596
  149. Chen YY, et al.
    Iron is involved in the maintenance of circadian period length in Arabidopsis.
    Plant Physiol., 2013. 161(3): p. 1409-20
  150. Gould PD, et al.
    Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.
    Mol. Syst. Biol., 2013. 9: p. 650
  151. Schmal C,Reimann P,Staiger D
    A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana.
    PLoS Comput. Biol., 2013. 9(3): p. e1002986
  152. Cui X, et al.
    Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis.
    Plant Physiol., 2013. 162(2): p. 897-906
  153. Zhang C, et al.
    Crosstalk between the circadian clock and innate immunity in Arabidopsis.
    PLoS Pathog., 2013. 9(6): p. e1003370
  154. Kusakina J,Gould PD,Hall A
    A fast circadian clock at high temperatures is a conserved feature across Arabidopsis accessions and likely to be important for vegetative yield.
    Plant Cell Environ., 2014. 37(2): p. 327-40
  155. Xie Q, et al.
    LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator.
    Plant Cell, 2014. 26(7): p. 2843-57
  156. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  157. Wang ZY,Tobin EM
    Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression.
    Cell, 1998. 93(7): p. 1207-17
  158. Schaffer R, et al.
    The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering.
    Cell, 1998. 93(7): p. 1219-29