Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G09530.2
Common NameBHLH8, EN100, F14J9.19, PAP3, PIF3, POC1
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 bHLH
Protein Properties Length: 524aa    MW: 56990.3 Da    PI: 6.5181
Description phytochrome interacting factor 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G09530.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   hn  ErrRRdriN+++  L+el+P++      K++Ka++L +A+eY+ksLq
                  6*************************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000838.96E-18339397No hitNo description
SuperFamilySSF474591.27E-20340402IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.584343392IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000103.6E-14347393IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.9E-18349398IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009585Biological Processred, far-red light phototransduction
GO:0009704Biological Processde-etiolation
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0010017Biological Processred or far-red light signaling pathway
GO:0031539Biological Processpositive regulation of anthocyanin metabolic process
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042802Molecular Functionidentical protein binding
GO:0046983Molecular Functionprotein dimerization activity
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:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 524 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.109260.0flower| leaf
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G09530-
Functional Description ? help Back to Top
Source Description
TAIRTranscription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes.
UniProtTranscription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3'). {ECO:0000269|PubMed:10466729, ECO:0000269|PubMed:10797009}.
Function -- GeneRIF ? help Back to Top
  1. PIF3 acts transiently, and its major function is to mediate phytochrome-induced signaling during the developmental switch from skotomorphogenesis to photomorphogenesis and/or dark to light transitions
    [PMID: 15155879]
  2. PIF3 may function in early phytochrome signaling at the dark-to-light transition, not only during initial seedling deetiolation, but daily at dawn under diurnal light-dark cycles.
    [PMID: 15505214]
  3. Data suggest that PIF3 may represent the primary intermolecular signaling transaction of the activated photoreceptor, tagging the target protein for proteosomal degradation.
    [PMID: 16885032]
  4. Gibberellins signaling regulates protein stability of HY5, and the activity of PIF3.
    [PMID: 18053005]
  5. Data provide evidence that the mechanism by which PIFs3operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner.
    [PMID: 18252845]
  6. Data show that dephosphorylation of PIF3 is mediated by phytochrome-associated protein phosphatase type 2C.
    [PMID: 18564962]
  7. Results suggest that many type I and type II phytochromes, such as E and C, appear to function through PIF3-mediated pathways.
    [PMID: 19286967]
  8. PIF3 was circadian regulated in dark-grown seedlings.
    [PMID: 19380736]
  9. Studies indicate that phytochromes inhibit hypocotyl negative gravitropism by inhibiting four phytochrome-interacting factors (PIF1, PIF3, PIF4, PIF5), as shown by hypocotyl agravitropism of dark-grown pif1 pif3 pif4 pif5 quadruple mutants.
    [PMID: 21220341]
  10. PIF3 regulates genes misexpressed in the dark, named MIDA genes
    [PMID: 22108407]
  11. The PIF3 protein abundance oscillates under diurnal conditions as a result of a progressive decline in PIF3 protein degradation mediated by photoactivated phyB, and consequent accumulation of the bHLH factor during the dark period.
    [PMID: 22409654]
  12. The nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3).
    [PMID: 22451940]
  13. These results showed an altered response to light in seedlings with an impaired PIF3/MIDA regulatory network.
    [PMID: 22499182]
  14. directly activated by ETHYLENE-INSENSITIVE 3 and indispensible for ethylene-induced hypocotyl elongation in light
    [PMID: 22818915]
  15. The ability of Glc to induce IAA biosynthesis was upregulated in the pif1 pif3 pif4 pif5 quadruple mutant line compared with the wild type.
    [PMID: 23209113]
  16. Data indicate that HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression.
    [PMID: 23548744]
  17. Data indicate that the PIF1/PIF3-HY5/HYH transcriptional modules mediate crosstalk between light and ROS signaling and a mechanism by which plants adapt to the light environments.
    [PMID: 23645630]
  18. Data show that photoreceptor phyB-induced transcription factor PIF3 phosphorylation is required for the known negative feedback modulation of phyB levels in prolonged light, potentially through codegradation of phyB and PIF3.
    [PMID: 23903316]
  19. PIF3 lies downstream of PHYB and RGL3, and plays an important role in the inhibitory effect of NO on root growth of Arabidopsis seedlings in light.
    [PMID: 24157606]
  20. PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions.
    [PMID: 24420574]
  21. PIF3 phosphorylation induces, and is necessary for, recruitment of LRB
    [PMID: 24904166]
  22. The expression level of PIF3, 4, and 5 was significantly up-regulated during both age-triggered and dark-induced leaf senescence.
    [PMID: 25296857]
  23. Under negative day-night temperature difference, lower auxin biosynthesis activity limits the signaling in this pathway, resulting in low activity of PIF3 and short hypocotyls.
    [PMID: 25516603]
  24. In vivo results support a regulatory mechanism for PIFs in which HMR is a transcriptional coactivator binding directly to PIFs and the 9aaTAD of HMR couples the degradation of PIF1 and PIF3 with the transactivation of PIF target genes.
    [PMID: 25944101]
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: By UV treatment. {ECO:0000269|PubMed:12679534}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G01060(A), AT1G29930(A), AT1G44446(A), AT2G18790(A), AT2G30570(A), AT2G46830(A), AT3G51240(A), AT4G14690(A), AT4G22880(A), AT5G13630(A), AT5G13930(A), AT5G42800(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G09530, AT1G14920, AT1G02340, AT1G66350
IntActSearch O80536
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G09530
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1001660.0AF100166.1 Arabidopsis thaliana phytochrome interacting factor 3 (PIF3) mRNA, complete cds.
GenBankAK1172550.0AK117255.1 Arabidopsis thaliana At1g09530 mRNA for putative transcription factor BHLH8, complete cds, clone: RAFL16-81-C24.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_172424.10.0transcription factor PIF3
RefseqNP_849626.10.0transcription factor PIF3
SwissprotO805360.0PIF3_ARATH; Transcription factor PIF3
TrEMBLD7KJR30.0D7KJR3_ARALL; Putative uncharacterized protein
STRINGAT1G09530.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Halliday KJ,Hudson M,Ni M,Qin M,Quail PH
    poc1: an Arabidopsis mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of PIF3, a gene encoding a phytochrome-interacting bHLH protein.
    Proc. Natl. Acad. Sci. U.S.A., 1999. 96(10): p. 5832-7
  2. Ni M,Tepperman JM,Quail PH
    Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light.
    Nature, 1999. 400(6746): p. 781-4
  3. 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
  4. 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
  5. Zhu Y,Tepperman JM,Fairchild CD,Quail PH
    Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3.
    Proc. Natl. Acad. Sci. U.S.A., 2000. 97(24): p. 13419-24
  6. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  7. Quail PH
    Phytochrome-interacting factors.
    Semin. Cell Dev. Biol., 2000. 11(6): p. 457-66
  8. 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
  9. 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
  10. Matsushika A,Makino S,Kojima M,Yamashino T,Mizuno T
    The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants.
    Plant Cell Physiol., 2002. 43(1): p. 118-22
  11. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
  12. Huq E,Quail PH
    PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis.
    EMBO J., 2002. 21(10): p. 2441-50
  13. Devlin PF
    Signs of the time: environmental input to the circadian clock.
    J. Exp. Bot., 2002. 53(374): p. 1535-50
  14. Kircher S, et al.
    Nucleocytoplasmic partitioning of the plant photoreceptors phytochrome A, B, C, D, and E is regulated differentially by light and exhibits a diurnal rhythm.
    Plant Cell, 2002. 14(7): p. 1541-55
  15. Goda H,Shimada Y,Asami T,Fujioka S,Yoshida S
    Microarray analysis of brassinosteroid-regulated genes in Arabidopsis.
    Plant Physiol., 2002. 130(3): p. 1319-34
  16. M
    Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis.
    Plant Cell, 2003. 15(1): p. 223-36
  17. 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
  18. 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
  19. Eriksson ME,Millar AJ
    The circadian clock. A plant's best friend in a spinning world.
    Plant Physiol., 2003. 132(2): p. 732-8
  20. Yamashino T, et al.
    A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(6): p. 619-29
  21. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  22. Kim J, et al.
    Functional characterization of phytochrome interacting factor 3 in phytochrome-mediated light signal transduction.
    Plant Cell, 2003. 15(10): p. 2399-407
  23. 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
  24. Bauer D, et al.
    Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signaling in Arabidopsis.
    Plant Cell, 2004. 16(6): p. 1433-45
  25. Fujimori T,Yamashino T,Kato T,Mizuno T
    Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana.
    Plant Cell Physiol., 2004. 45(8): p. 1078-86
  26. Huq E, et al.
    Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis.
    Science, 2004. 305(5692): p. 1937-41
  27. Khanna R, et al.
    A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors.
    Plant Cell, 2004. 16(11): p. 3033-44
  28. Oh E, et al.
    PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana.
    Plant Cell, 2004. 16(11): p. 3045-58
  29. Monte E, et al.
    The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development.
    Proc. Natl. Acad. Sci. U.S.A., 2004. 101(46): p. 16091-8
  30. Kevei E, et al.
    Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE.
    Plant Physiol., 2006. 140(3): p. 933-45
  31. Phee BK, et al.
    Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS.
    Proteomics, 2006. 6(12): p. 3671-80
  32. Al-Sady B,Ni W,Kircher S,Schäfer E,Quail PH
    Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation.
    Mol. Cell, 2006. 23(3): p. 439-46
  33. Shin J,Park E,Choi G
    PIF3 regulates anthocyanin biosynthesis in an HY5-dependent manner with both factors directly binding anthocyanin biosynthetic gene promoters in Arabidopsis.
    Plant J., 2007. 49(6): p. 981-94
  34. 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
  35. Brock MT,Tiffin P,Weinig C
    Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana.
    Mol. Ecol., 2007. 16(14): p. 3050-62
  36. Shen Y,Khanna R,Carle CM,Quail PH
    Phytochrome induces rapid PIF5 phosphorylation and degradation in response to red-light activation.
    Plant Physiol., 2007. 145(3): p. 1043-51
  37. Alabadí D, et al.
    Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness.
    Plant J., 2008. 53(2): p. 324-35
  38. Feng S, et al.
    Coordinated regulation of Arabidopsis thaliana development by light and gibberellins.
    Nature, 2008. 451(7177): p. 475-9
  39. de Lucas M, et al.
    A molecular framework for light and gibberellin control of cell elongation.
    Nature, 2008. 451(7177): p. 480-4
  40. Al-Sady B,Kikis EA,Monte E,Quail PH
    Mechanistic duality of transcription factor function in phytochrome signaling.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(6): p. 2232-7
  41. Leivar P, et al.
    The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels.
    Plant Cell, 2008. 20(2): p. 337-52
  42. Phee BK, et al.
    A novel protein phosphatase indirectly regulates phytochrome-interacting factor 3 via phytochrome.
    Biochem. J., 2008. 415(2): p. 247-55
  43. Leung DW,Otomo C,Chory J,Rosen MK
    Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(35): p. 12797-802
  44. Leivar P, et al.
    Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness.
    Curr. Biol., 2008. 18(23): p. 1815-23
  45. Kikis EA,Oka Y,Hudson ME,Nagatani A,Quail PH
    Residues clustered in the light-sensing knot of phytochrome B are necessary for conformer-specific binding to signaling partner PIF3.
    PLoS Genet., 2009. 5(1): p. e1000352
  46. Shen Y, et al.
    Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response.
    Plant Cell, 2009. 21(2): p. 494-506
  47. Clack T, et al.
    Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor.
    Plant Cell, 2009. 21(3): p. 786-99
  48. Waters MT, et al.
    GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis.
    Plant Cell, 2009. 21(4): p. 1109-28
  49. Shin J, et al.
    Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(18): p. 7660-5
  50. 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
  51. Lorrain S,Trevisan M,Pradervand S,Fankhauser C
    Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.
    Plant J., 2009. 60(3): p. 449-61
  52. Gong W, et al.
    The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.
    Mol Plant, 2008. 1(1): p. 27-41
  53. Leivar P, et al.
    Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings.
    Plant Cell, 2009. 21(11): p. 3535-53
  54. Wang FF,Lian HL,Kang CY,Yang HQ
    Phytochrome B is involved in mediating red light-induced stomatal opening in Arabidopsis thaliana.
    Mol Plant, 2010. 3(1): p. 246-59
  55. Jang IC,Henriques R,Seo HS,Nagatani A,Chua NH
    Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus.
    Plant Cell, 2010. 22(7): p. 2370-83
  56. Richter R,Behringer C,M
    The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS.
    Genes Dev., 2010. 24(18): p. 2093-104
  57. Shin R,Jez JM,Basra A,Zhang B,Schachtman DP
    14-3-3 proteins fine-tune plant nutrient metabolism.
    FEBS Lett., 2011. 585(1): p. 143-7
  58. 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
  59. Kim K, et al.
    Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(4): p. 1729-34
  60. Josse EM, et al.
    A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling.
    Plant Cell, 2011. 23(4): p. 1337-51
  61. Lozano-Juste J,Le
    Nitric oxide regulates DELLA content and PIF expression to promote photomorphogenesis in Arabidopsis.
    Plant Physiol., 2011. 156(3): p. 1410-23
  62. Bu Q,Castillon A,Chen F,Zhu L,Huq E
    Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis.
    Plant Mol. Biol., 2011. 77(4-5): p. 501-11
  63. Oka Y,Kong SG,Matsushita T
    A non-covalently attached chromophore can mediate phytochrome B signaling in Arabidopsis.
    Plant Cell Physiol., 2011. 52(12): p. 2088-102
  64. Sentandreu M, et al.
    Functional profiling identifies genes involved in organ-specific branches of the PIF3 regulatory network in Arabidopsis.
    Plant Cell, 2011. 23(11): p. 3974-91
  65. Sun TP
    Gibberellin metabolism, perception and signaling pathways in Arabidopsis.
    Arabidopsis Book, 2008. 6: p. e0103
  66. Soy J, et al.
    Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis.
    Plant J., 2012. 71(3): p. 390-401
  67. Pfeiffer A, et al.
    Interaction with plant transcription factors can mediate nuclear import of phytochrome B.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(15): p. 5892-7
  68. Leivar P,Monte E,Cohn MM,Quail PH
    Phytochrome signaling in green Arabidopsis seedlings: impact assessment of a mutually negative phyB-PIF feedback loop.
    Mol Plant, 2012. 5(3): p. 734-49
  69. Sentandreu M,Leivar P,Mart
    Branching of the PIF3 regulatory network in Arabidopsis: roles of PIF3-regulated MIDAs in seedling development in the dark and in response to light.
    Plant Signal Behav, 2012. 7(4): p. 510-3
  70. Yang DL, et al.
    Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(19): p. E1192-200
  71. Hughes RM,Vrana JD,Song J,Tucker CL
    Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins.
    J. Biol. Chem., 2012. 287(26): p. 22165-72
  72. Chen F, et al.
    Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 is a key mechanism defining signaling dynamics of phytochrome A under red and far-red light in Arabidopsis.
    Plant Cell, 2012. 24(5): p. 1907-20
  73. Jang IC,Niu QW,Deng S,Zhao P,Chua NH
    Enhancing protein stability with retained biological function in transgenic plants.
    Plant J., 2012. 72(2): p. 345-54
  74. Jung CH,Wong CE,Singh MB,Bhalla PL
    Comparative genomic analysis of soybean flowering genes.
    PLoS ONE, 2012. 7(6): p. e38250
  75. Zhong S, et al.
    A molecular framework of light-controlled phytohormone action in Arabidopsis.
    Curr. Biol., 2012. 22(16): p. 1530-5
  76. Park E, et al.
    Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters.
    Plant J., 2012. 72(4): p. 537-46
  77. Galv
    Photoactivated phytochromes interact with HEMERA and promote its accumulation to establish photomorphogenesis in Arabidopsis.
    Genes Dev., 2012. 26(16): p. 1851-63
  78. Yasui Y, et al.
    The phytochrome-interacting vascular plant one-zinc finger1 and VOZ2 redundantly regulate flowering in Arabidopsis.
    Plant Cell, 2012. 24(8): p. 3248-63
  79. Sairanen I, et al.
    Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4907-16
  80. Zhang Y, et al.
    A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis.
    PLoS Genet., 2013. 9(1): p. e1003244
  81. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  82. Liu X, et al.
    PHYTOCHROME INTERACTING FACTOR3 Associates with the Histone Deacetylase HDA15 in Repression of Chlorophyll Biosynthesis and Photosynthesis in Etiolated Arabidopsis Seedlings.
    Plant Cell, 2013. 25(4): p. 1258-73
  83. Chen D, et al.
    Antagonistic basic helix-loop-helix/bZIP transcription factors form transcriptional modules that integrate light and reactive oxygen species signaling in Arabidopsis.
    Plant Cell, 2013. 25(5): p. 1657-73
  84. Eprintsev AT,Fedorin DN,Igamberdiev AU
    Ca²⁺ is involved in phytochrome A-dependent regulation of the succinate dehydrogenase gene sdh1-2 in Arabidopsis.
    J. Plant Physiol., 2013. 170(15): p. 1349-52
  85. Nito K,Wong CC,Yates JR,Chory J
    Tyrosine phosphorylation regulates the activity of phytochrome photoreceptors.
    Cell Rep, 2013. 3(6): p. 1970-9
  86. Ni W, et al.
    Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis.
    Plant Cell, 2013. 25(7): p. 2679-98
  87. Bai S, et al.
    PIF3 is involved in the primary root growth inhibition of Arabidopsis induced by nitric oxide in the light.
    Mol Plant, 2014. 7(4): p. 616-25
  88. Soy J,Leivar P,Monte E
    PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in Arabidopsis together with PIF3, PIF4, and PIF5.
    J. Exp. Bot., 2014. 65(11): p. 2925-36
  89. Li Y,Jing Y,Li J,Xu G,Lin R
    Arabidopsis VQ MOTIF-CONTAINING PROTEIN29 represses seedling deetiolation by interacting with PHYTOCHROME-INTERACTING FACTOR1.
    Plant Physiol., 2014. 164(4): p. 2068-80
  90. Ni W, et al.
    A mutually assured destruction mechanism attenuates light signaling in Arabidopsis.
    Science, 2014. 344(6188): p. 1160-4
  91. Mar
    Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners.
    Plant Physiol., 2014. 166(2): p. 1022-32
  92. Dong J, et al.
    Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark.
    Plant Cell, 2014. 26(9): p. 3630-45
  93. Song Y, et al.
    Age-triggered and dark-induced leaf senescence require the bHLH transcription factors PIF3, 4, and 5.
    Mol Plant, 2014. 7(12): p. 1776-87
  94. Bours R,Kohlen W,Bouwmeester HJ,van der Krol A
    Thermoperiodic control of hypocotyl elongation depends on auxin-induced ethylene signaling that controls downstream PHYTOCHROME INTERACTING FACTOR3 activity.
    Plant Physiol., 2015. 167(2): p. 517-30
  95. 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
  96. Qiu Y, et al.
    HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.
    Plant Cell, 2015. 27(5): p. 1409-27
  97. Huang H, et al.
    PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis.
    Elife, 2016. 5: p. e13292
  98. Ni M,Tepperman JM,Quail PH
    PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein.
    Cell, 1998. 95(5): p. 657-67