Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G20180.3
Common NameBHLH15, EN101, PIF1, PIL5, T2G17.2
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: 478aa    MW: 52863.8 Da    PI: 6.7098
Description phytochrome interacting factor 3-like 5
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G20180.3genomeTAIRView 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  Er+RRdriN+++  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
PROSITE profilePS5088818.146284333IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474597.33E-21287362IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000835.35E-17287338No hitNo description
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
PfamPF000101.5E-13288334IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003532.2E-17290339IPR011598Myc-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:0006783Biological Processheme biosynthetic process
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0009959Biological Processnegative gravitropism
GO:0010100Biological Processnegative regulation of photomorphogenesis
GO:0010161Biological Processred light signaling pathway
GO:0010187Biological Processnegative regulation of seed germination
GO:0015995Biological Processchlorophyll biosynthetic process
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0010313Molecular Functionphytochrome 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:0020003anatomyplant ovule
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
PO:0025374developmental stageseed dormant stage
Sequence ? help Back to Top
Protein Sequence    Length: 478 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
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT2G20180-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a novel Myc-related bHLH transcription factor that has transcriptional activation activity in the dark. It is a key negative regulator of phytochrome-mediated seed germination and acts by inhibiting chlorophyll biosynthesis, light-mediated suppression of hypocotyl elongation and far-red light-mediated suppression of seed germination, and promoting negative gravitropism in hypocotyls. Light reduces this activity in a phy-dependent manner. The protein preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB), is physically associated with APRR1/TOC1 and is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis. It also negatively regulates GA3 oxidase expression.
UniProtTranscription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA). {ECO:0000269|PubMed:15448264, ECO:0000269|PubMed:16359394, ECO:0000269|PubMed:18487351, ECO:0000269|PubMed:18539749, ECO:0000269|PubMed:18591656}.
Function -- GeneRIF ? help Back to Top
  1. negatively regulates chlorophyll biosynthesis
    [PMID: 15448264]
  2. PIF1 is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis.
    [PMID: 16359394]
  3. PIL5 binds directly to GAI and RGA promoters but not to Giberellic and Abscisic metabolic gene promoters in arabidopsis.
    [PMID: 17449805]
  4. Data shows that PIL5 activates the expression of SOM by binding directly to its promoter, suggesting that PIL5 regulates ABA and GA metabolic genes partly through SOM.
    [PMID: 18487351]
  5. Data suggest that removal of PIF1 by light-induced proteolytic degradation might be sufficient to promote photomorphogenesis.
    [PMID: 18539749]
  6. These data strongly suggest that PIF1 directly and indirectly regulates key genes involved in chlorophyll biosynthesis to optimize the greening process in Arabidopsis.
    [PMID: 18591656]
  7. PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds.
    [PMID: 19244139]
  8. Data show that AtGA3ox1 is directly regulated by DAG1, and suggest that DAG1 is not a direct regulatory target of PIL5.
    [PMID: 19874540]
  9. PIF1 and other PIFs have roles in transducing light signals to regulate PSY gene expression and carotenoid accumulation during daily cycles of light and dark in mature plants
    [PMID: 20534526]
  10. 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]
  11. Data suggest that CK2-mediated phosphorylation enhances the light-induced degradation of PIF1 to promote photomorphogenesis.
    [PMID: 21330376]
  12. ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter.
    [PMID: 21467583]
  13. Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.
    [PMID: 22634759]
  14. 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]
  15. 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]
  16. HFR1 prevents PIF1 from binding to its target genes and antagonistically regulates PIF1-mediated gene expression. HFR1 and PIF1 are the major transcription regulators responsible for light-directed Transcriptome changes in seed germination.
    [PMID: 24179122]
  17. PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions.
    [PMID: 24420574]
  18. VQ29 is a negative transcriptional regulator of light-mediated inhibition of hypocotyl elongation that likely promotes the transcriptional activity of PIF1 during early seedling development.
    [PMID: 24569844]
  19. EFS is necessary for high-level expression of PIF1 mRNA in imbibed seeds.
    [PMID: 24635727]
  20. DET1 maximizes PIF1's action by both removing PIF1's transcriptional repressor HFR1 and protecting PIF1 from proteasome-mediated degradation.
    [PMID: 25775589]
  21. The results suggest that AtHB1 acts downstream of PIF1 to promote hypocotyl elongation, especially in response to short-day photoperiods.
    [PMID: 25865500]
  22. 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]
  23. Results indicate that LEUNIG_HOMOLOG (LUH) functions with PHYTOCHROME-INTERACTING FACTOR1 (PIF1) as a transcriptional coregulator to inhibit seed germination.
    [PMID: 26276832]
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: Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner. {ECO:0000269|PubMed:15448264}.
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 AT1G03430(A), AT1G03630(A), AT1G03790(A), AT1G08980(A), AT1G14920(A), AT1G15550(R), AT1G19180(R), AT1G30040(A), AT1G52920(A), AT1G66350(R), AT1G69010(A), AT1G69720(A), AT1G72770(A), AT1G78390(A), AT1G80340(R), AT2G01570(A), AT2G29090(R), AT2G36270(A), AT2G40220(R), AT3G04730(R), AT3G05120(A), AT3G11540(A), AT3G24220(A), AT3G24650(A), AT3G44310(A), AT3G44320(A), AT3G50660(R), AT3G61830(A), AT4G11140(R), AT4G18710(A), AT4G23750(R), AT4G26080(R), AT4G27440(A), AT4G39920(A), AT5G08130(A), AT5G20960(A), AT5G27320(A), AT5G42750(R), AT5G53290(R), AT5G54190(A), AT5G54510(R), AT5G66880(R), AT5G67030(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid, gibberellin, Gibberellin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT2G20180, AT2G43010, AT3G17609, AT3G03450, AT3G22170, AT3G24650, AT3G59060, AT3G62090, AT5G11260, AT5G61270, AT1G09530, AT1G02340, AT1G75080
IntActSearch Q8GZM7
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants overaccumulate free protochlorophyllide in the darkness and exhibit photooxidative damage (bleaching) in subsequent light, probably caused by the photosensitizing activity of this tetrapyrrole intermediate. {ECO:0000269|PubMed:15448264, ECO:0000269|PubMed:18591656}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G20180
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4885600.0AF488560.2 Arabidopsis thaliana clone bHLH015 putative bHLH transcription factor mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001189559.10.0transcription factor PIF1
RefseqNP_179608.20.0transcription factor PIF1
SwissprotQ8GZM70.0PIF1_ARATH; Transcription factor PIF1
TrEMBLD7L5A80.0D7L5A8_ARALL; Putative uncharacterized protein
STRINGAT2G20180.20.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  2. 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
  3. 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
  4. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  5. Huq E, et al.
    Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis.
    Science, 2004. 305(5692): p. 1937-41
  6. 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
  7. Penfield S, et al.
    Cold and light control seed germination through the bHLH transcription factor SPATULA.
    Curr. Biol., 2005. 15(22): p. 1998-2006
  8. Shen H,Moon J,Huq E
    PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis.
    Plant J., 2005. 44(6): p. 1023-35
  9. Oh E, et al.
    Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis.
    Plant J., 2006. 47(1): p. 124-39
  10. Dreher K,Callis J
    Ubiquitin, hormones and biotic stress in plants.
    Ann. Bot., 2007. 99(5): p. 787-822
  11. Oh E, et al.
    PIL5, a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters in Arabidopsis seeds.
    Plant Cell, 2007. 19(4): p. 1192-208
  12. Zentella R, et al.
    Global analysis of della direct targets in early gibberellin signaling in Arabidopsis.
    Plant Cell, 2007. 19(10): p. 3037-57
  13. 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
  14. Kim DH, et al.
    SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5.
    Plant Cell, 2008. 20(5): p. 1260-77
  15. Shen H, et al.
    Light-induced phosphorylation and degradation of the negative regulator PHYTOCHROME-INTERACTING FACTOR1 from Arabidopsis depend upon its direct physical interactions with photoactivated phytochromes.
    Plant Cell, 2008. 20(6): p. 1586-602
  16. Moon J,Zhu L,Shen H,Huq E
    PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(27): p. 9433-8
  17. Sawada Y, et al.
    Germination of photoblastic lettuce seeds is regulated via the control of endogenous physiologically active gibberellin content, rather than of gibberellin responsiveness.
    J. Exp. Bot., 2008. 59(12): p. 3383-93
  18. Leivar P, et al.
    Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness.
    Curr. Biol., 2008. 18(23): p. 1815-23
  19. Oh E, et al.
    Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis.
    Plant Cell, 2009. 21(2): p. 403-19
  20. Castillon A,Shen H,Huq E
    Blue light induces degradation of the negative regulator phytochrome interacting factor 1 to promote photomorphogenic development of Arabidopsis seedlings.
    Genetics, 2009. 182(1): p. 161-71
  21. Skinner DJ,Gasser CS
    Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants.
    BMC Plant Biol., 2009. 9: p. 29
  22. 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
  23. 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
  24. 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
  25. Gabriele S, et al.
    The Dof protein DAG1 mediates PIL5 activity on seed germination by negatively regulating GA biosynthetic gene AtGA3ox1.
    Plant J., 2010. 61(2): p. 312-23
  26. Penfield S,Josse EM,Halliday KJ
    A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy.
    Plant Mol. Biol., 2010. 73(1-2): p. 89-95
  27. 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
  28. Zhong S, et al.
    EIN3/EIL1 cooperate with PIF1 to prevent photo-oxidation and to promote greening of Arabidopsis seedlings.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(50): p. 21431-6
  29. Gallego-Bartolomé J, et al.
    Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis.
    Mol. Biol. Evol., 2010. 27(6): p. 1247-56
  30. Toledo-Ortiz G,Huq E,Rodr
    Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by phytochrome-interacting factors.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(25): p. 11626-31
  31. 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
  32. 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
  33. Kang H,Oh E,Choi G,Lee D
    Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor.
    Int J Data Min Bioinform, 2010. 4(5): p. 588-99
  34. 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
  35. Rizza A,Boccaccini A,Lopez-Vidriero I,Costantino P,Vittorioso P
    Inactivation of the ELIP1 and ELIP2 genes affects Arabidopsis seed germination.
    New Phytol., 2011. 190(4): p. 896-905
  36. Bu Q, et al.
    Phosphorylation by CK2 enhances the rapid light-induced degradation of phytochrome interacting factor 1 in Arabidopsis.
    J. Biol. Chem., 2011. 286(14): p. 12066-74
  37. Park J,Lee N,Kim W,Lim S,Choi G
    ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds.
    Plant Cell, 2011. 23(4): p. 1404-15
  38. 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
  39. Liu Z, et al.
    Phytochrome interacting factors (PIFs) are essential regulators for sucrose-induced hypocotyl elongation in Arabidopsis.
    J. Plant Physiol., 2011. 168(15): p. 1771-9
  40. Rausenberger J, et al.
    Photoconversion and nuclear trafficking cycles determine phytochrome A's response profile to far-red light.
    Cell, 2011. 146(5): p. 813-25
  41. 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
  42. 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
  43. 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
  44. Leivar P, et al.
    Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis.
    Plant Cell, 2012. 24(4): p. 1398-419
  45. Tang W, et al.
    Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.
    Plant Cell, 2012. 24(5): p. 1984-2000
  46. Oh E,Zhu JY,Wang ZY
    Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses.
    Nat. Cell Biol., 2012. 14(8): p. 802-9
  47. Park E, et al.
    Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters.
    Plant J., 2012. 72(4): p. 537-46
  48. Lee KP, et al.
    Spatially and genetically distinct control of seed germination by phytochromes A and B.
    Genes Dev., 2012. 26(17): p. 1984-96
  49. Sairanen I, et al.
    Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4907-16
  50. Ibarra SE,Auge G,S
    Transcriptional programs related to phytochrome A function in Arabidopsis seed germination.
    Mol Plant, 2013. 6(4): p. 1261-73
  51. 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
  52. Footitt S,Huang Z,Clay HA,Mead A,Finch-Savage WE
    Temperature, light and nitrate sensing coordinate Arabidopsis seed dormancy cycling, resulting in winter and summer annual phenotypes.
    Plant J., 2013. 74(6): p. 1003-15
  53. 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
  54. Shi H, et al.
    HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis.
    Plant Cell, 2013. 25(10): p. 3770-84
  55. 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
  56. 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
  57. Lee N,Kang H,Lee D,Choi G
    A histone methyltransferase inhibits seed germination by increasing PIF1
    Plant J., 2014. 78(2): p. 282-93
  58. Xu X, et al.
    PHYTOCHROME INTERACTING FACTOR1 Enhances the E3 Ligase Activity of CONSTITUTIVE PHOTOMORPHOGENIC1 to Synergistically Repress Photomorphogenesis in Arabidopsis.
    Plant Cell, 2014. 26(5): p. 1992-2006
  59. 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
  60. 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
  61. Shi H, et al.
    Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(12): p. 3817-22
  62. Capella M,Ribone PA,Arce AL,Chan RL
    Arabidopsis thaliana HomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation.
    New Phytol., 2015. 207(3): p. 669-82
  63. 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
  64. Lee N,Park J,Kim K,Choi G
    The Transcriptional Coregulator LEUNIG_HOMOLOG Inhibits Light-Dependent Seed Germination in Arabidopsis.
    Plant Cell, 2015. 27(8): p. 2301-13