PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
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
Organism
Arabidopsis thaliana
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
1HLH49.57.4e-16288334455
                  HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   hn  Er+RRdriN+++  L+el+P +      K +Ka++L +A+eY+ksLq
  AT2G20180.3 288 VHNLSERKRRDRINERMKALQELIPRC-----NKSDKASMLDEAIEYMKSLQ 334
                  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:4.10.280.101.2E-20288343IPR011598Myc-type, 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:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020003anatomyplant ovule
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
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
MHHFVPDFDT DDDYVNNHNS SLNHLPRKSI TTMGEDDDLM ELLWQNGQVV VQNQRLHTKK  60
PSSSPPKLLP SMDPQQQPSS DQNLFIQEDE MTSWLHYPLR DDDFCSDLLF SAAPTATATA  120
TVSQVTAARP PVSSTNESRP PVRNFMNFSR LRGDFNNGRG GESGPLLSKA VVRESTQVSP  180
SATPSAAASE SGLTRRTDGT DSSAVAGGGA YNRKGKAVAM TAPAIEITGT SSSVVSKSEI  240
EPEKTNVDDR KRKEREATTT DETESRSEET KQARVSTTST KRSRAAEVHN LSERKRRDRI  300
NERMKALQEL IPRCNKSDKA SMLDEAIEYM KSLQLQIQMM SMGCGMMPMM YPGMQQYMPH  360
MAMGMGMNQP IPPPSFMPFP NMLAAQRPLP TQTHMAGSGP QYPVHASDPS RVFVPNQQYD  420
PTSGQPQYPA GYTDPYQQFR GLHPTQPPQF QNQATSYPSS SRVSSSKESE DHGNHTTG
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1292297ERKRRD
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.430030.0leaf
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible265584_at0.0
Expression AtlasAT2G20180-
AtGenExpressAT2G20180-
ATTED-IIAT2G20180-
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.[PIF1]
    [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]
  24. COP1 promotes the degradation of HFR1 under shade, thus increasing the ability of PIFs to control gene expression, increase auxin levels and promote stem growth.
    [PMID: 27105120]
  25. Data we show in vivo PIF1 targeting to specific binding sites is determined by its interaction with PTFs and their binding to GCEs.
    [PMID: 27303023]
  26. results indicate that RPGE1 acts downstream of PIF1 in the endodermis to repress photosynthetic genes and regulate plastid development.
    [PMID: 27591813]
  27. Genetic evidence indicated that HDA15 acts downstream of PHYB and represses seed germination in the dark dependent on PIF1.
    [PMID: 28444370]
  28. the transcriptional cascade consisting of PIF1/PIF3, HY5, and BBX23 controls photomorphogenesis.
    [PMID: 28687557]
  29. results reveal a new mechanism for NO signals in modulating PHYB-mediated seed germination by repressing PIF1 expression at the transcriptional level as well as preventing PIF1 activity by stabilizing HFR1 protein.
    [PMID: 29248678]
  30. PIL5 is involved in floral transition interacting with flowering integrators and gibberellic acid.
    [PMID: 29588173]
  31. The genetic, physiological, and biochemical evidence, when taken together, leads us to propose that PIF1 and CTG10 coexist, and even accumulate, in the nucleus in darkness, but that, following illumination, CTG10 assists in reducing PIF1 amounts, thus promoting the completion of seed germination and subsequent seedling development.
    [PMID: 29632208]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00074ChIP-chip26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G20180.3
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
PlantRegMapRetrieveRetrieve
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_001189559.10.0phytochrome interacting factor 3-like 5
RefseqNP_001318252.10.0phytochrome interacting factor 3-like 5
RefseqNP_001323902.10.0phytochrome interacting factor 3-like 5
RefseqNP_001323904.10.0phytochrome interacting factor 3-like 5
SwissprotQ8GZM70.0PIF1_ARATH; Transcription factor PIF1
TrEMBLA0A178VU820.0A0A178VU82_ARATH; PIL5
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
    [PMID:11118137]
  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
    [PMID:12679534]
  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
    [PMID:12826627]
  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
    [PMID:12897250]
  5. Huq E, et al.
    Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis.
    Science, 2004. 305(5692): p. 1937-41
    [PMID:15448264]
  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
    [PMID:15486102]
  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
    [PMID:16303558]
  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
    [PMID:16359394]
  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
    [PMID:16740147]
  10. Dreher K,Callis J
    Ubiquitin, hormones and biotic stress in plants.
    Ann. Bot., 2007. 99(5): p. 787-822
    [PMID:17220175]
  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
    [PMID:17449805]
  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
    [PMID:17933900]
  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
    [PMID:18053005]
  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
    [PMID:18487351]
  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
    [PMID:18539749]
  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
    [PMID:18591656]
  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
    [PMID:18653696]
  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
    [PMID:19062289]
  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
    [PMID:19244139]
  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
    [PMID:19255368]
  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
    [PMID:19291320]
  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
    [PMID:19380720]
  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
    [PMID:19380736]
  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
    [PMID:19619162]
  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
    [PMID:19874540]
  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
    [PMID:19911288]
  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
    [PMID:19920208]
  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
    [PMID:19948955]
  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
    [PMID:20093430]
  30. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  31. 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
    [PMID:20534526]
  32. 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
    [PMID:20736450]
  33. 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
    [PMID:20844019]
  34. 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
    [PMID:21133043]
  35. 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
    [PMID:21220341]
  36. 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
    [PMID:21299564]
  37. 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
    [PMID:21330376]
  38. 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
    [PMID:21467583]
  39. 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
    [PMID:21562334]
  40. 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
    [PMID:21684034]
  41. 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
    [PMID:21884939]
  42. 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
    [PMID:21928113]
  43. 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
    [PMID:22451940]
  44. 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
    [PMID:22492120]
  45. 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
    [PMID:22517317]
  46. 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
    [PMID:22634759]
  47. 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
    [PMID:22820378]
  48. Park E, et al.
    Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters.
    Plant J., 2012. 72(4): p. 537-46
    [PMID:22849408]
  49. 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
    [PMID:22948663]
  50. Sairanen I, et al.
    Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4907-16
    [PMID:23209113]
  51. Ibarra SE,Auge G,S
    Transcriptional programs related to phytochrome A function in Arabidopsis seed germination.
    Mol Plant, 2013. 6(4): p. 1261-73
    [PMID:23292879]
  52. 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
    [PMID:23382695]
  53. 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
    [PMID:23590427]
  54. 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
    [PMID:23645630]
  55. 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
    [PMID:24179122]
  56. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  57. 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
    [PMID:24420574]
  58. 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
    [PMID:24569844]
  59. 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
    [PMID:24635727]
  60. 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
    [PMID:24858936]
  61. Luo Q, et al.
    COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis.
    Plant Cell, 2014. 26(6): p. 2441-2456
    [PMID:24951480]
  62. Krzymuski M, et al.
    Phytochrome A antagonizes PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis.
    Mol Plant, 2014. 7(9): p. 1415-1428
    [PMID:25009301]
  63. 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
    [PMID:25248553]
  64. Adams E,Diaz C,Hong JP,Shin R
    14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs.
    Int J Mol Sci, 2014. 15(12): p. 22801-14
    [PMID:25501334]
  65. 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
    [PMID:25750178]
  66. 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
    [PMID:25775589]
  67. 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
    [PMID:25865500]
  68. 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
    [PMID:25944101]
  69. Zhu L, et al.
    CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1.
    Nat Commun, 2015. 6: p. 7245
    [PMID:26037329]
  70. Bou-Torrent J, et al.
    Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors.
    Plant Physiol., 2015. 169(3): p. 1584-94
    [PMID:26082398]
  71. 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
    [PMID:26276832]
  72. Galvão VC,Collani S,Horrer D,Schmid M
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana.
    Plant J., 2015. 84(5): p. 949-62
    [PMID:26466761]
  73. Zhu L, et al.
    A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis.
    Plant Cell, 2016. 28(4): p. 855-74
    [PMID:27073231]
  74. Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ
    Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
    New Phytol., 2016. 211(3): p. 967-79
    [PMID:27105120]
  75. Kim J, et al.
    PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1.
    Plant Cell, 2016. 28(6): p. 1388-405
    [PMID:27303023]
  76. Martin G,Soy J,Monte E
    Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.
    Front Plant Sci, 2016. 7: p. 962
    [PMID:27458465]
  77. Zhu L,Xin R,Huq E
    A Protein-Based Genetic Screening Uncovers Mutants Involved in Phytochrome Signaling in Arabidopsis.
    Front Plant Sci, 2016. 7: p. 1086
    [PMID:27499759]
  78. Gangl R,Tenhaken R
    Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark.
    Front Plant Sci, 2016. 7: p. 1115
    [PMID:27507985]
  79. Kim K, et al.
    PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis.
    Mol Plant, 2016. 9(10): p. 1415-1427
    [PMID:27591813]
  80. Kim J, et al.
    Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously.
    Plant Cell, 2016. 28(11): p. 2770-2785
    [PMID:27758895]
  81. Zhang D,Li Y,Zhang X,Zha P,Lin R
    The SWI2/SNF2 Chromatin-Remodeling ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis.
    Mol Plant, 2017. 10(1): p. 155-167
    [PMID:27865928]
  82. Xu X, et al.
    Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis.
    Development, 2017. 144(10): p. 1831-1840
    [PMID:28420710]
  83. Shor E,Paik I,Kangisser S,Green R,Huq E
    PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis.
    New Phytol., 2017. 215(1): p. 217-228
    [PMID:28440582]
  84. Gu D, et al.
    Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark.
    Nucleic Acids Res., 2017. 45(12): p. 7137-7150
    [PMID:28444370]
  85. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
    [PMID:28687557]
  86. Paik I,Kathare PK,Kim JI,Huq E
    Expanding Roles of PIFs in Signal Integration from Multiple Processes.
    Mol Plant, 2017. 10(8): p. 1035-1046
    [PMID:28711729]
  87. Li R, et al.
    Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1.
    Plant Physiol. Biochem., 2018. 123: p. 204-212
    [PMID:29248678]
  88. Wu M, et al.
    PIL5 represses floral transition in Arabidopsis under long day conditions.
    Biochem. Biophys. Res. Commun., 2018. 499(3): p. 513-518
    [PMID:29588173]
  89. Majee M, et al.
    KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1.
    Proc. Natl. Acad. Sci. U.S.A., 2018. 115(17): p. E4120-E4129
    [PMID:29632208]