KEY RESOURCE TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-FLAG M2 | Sigma | Cat# F1804; RRID:AB_262044 |
| Anti-FLAG-HRP | Sigma | Cat#A8592; RRID:AB_439702 |
| Anti-HA 3F10 | Roche | Cat# 11867423001; RRID:AB_2314622 |
| Anti-HA-HRP | Roche | Cat# 12013819001; RRID: AB_390917 |
| Anti-Actin | Millipore | Cat# MAB1501; RRID:AB_2223041 |
| Anti-Mouse-HRP | BioRad | Cat#1706516 |
| Bacterial and Virus Strains | ||
| E. coli ccdB survival | Invitrogen | A10460 |
| E. coli TOP10 | Invitrogen | C404003 |
| Agrobacterium tumefaciens strain GV3101 | N/A | N/A |
| Agrobacterium tumefaciens strain C58 | N/A | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Hygromycin B | Invitrogen | Cat# 10687010 |
| Glufosinate ammonium (BASTA) | Sigma | Cat#45520 |
| PMSF | Sigma | Cat# P7626 |
| Complete EDTA-free Protease Inhibitor | Roche | Cat# 11836170001 |
| Phosphatase Inhibitor 2 | Sigma | Cat#P5726 |
| Phosphatase Inhibitor 3 | Sigma | Cat#P0044 |
| MG-132 | Peptides International | Cat#3175-v |
| Protein G Dynabeads | Invitrogen | Cat# 10004D |
| GlycoBlue | Invitrogen | Cat# AM9515 |
| D-Luciferin, potassium salt | Biosynth AG | Cat#L-8220 |
| Critical Commercial Assays | ||
| Gateway BP clonase enzyme mix | Invitrogen | Cat#11789020 |
| Gateway LR clonase enzyme mix | Invitrogen | Cat#11791100 |
| ProQuest™ Two-Hybrid System | Invitrogen | Cat#PQ1000101 |
| TnT® SP6 High-Yield Wheat Germ Protein Expression System | Promega | Cat#L3260 |
| DC Protein Assay | BioRad | Cat#5000116 |
| Supersignal West Pico, Dura, and Femto substrates | Pierce | Cat#34577, 34075, 34095 |
| iScript cDNA synthesis kit | BioRad | Cat#1708890 |
| Maxima SYBR Green qPCR Master Mix | Thermo Scientific | Cat#K0253 |
| Ovation® Ultralow V2 kit | NuGEN | Cat# 0344NB-A01 |
| Deposited Data | ||
| ChIP-seq data | This paper | GSEXXXXX |
| Experimental Models: Organisms/Strains | ||
| Col-0 | N/A | N/A |
| gi-2 | Fowler et al., 1999 | N/A |
| GIox | David et al., 2006 | N/A |
| PIF5-HA | Lorrain et al., 2008 | N/A |
| PIF4-Flash | Pedmale et al., 2016 | N/A |
| pif3-1 | Kim et al., 2003 | SALK_030753 |
| pif4-101 | Lorrain et al., 2008 | Garlic_114_G06 |
| pif5-1 | Fujimori et al., 2004 | SALK_087012 |
| pifQ | Leivar et al., 2008 | N/A |
| CCA1::LUC | Salome and McClung, 2005 | N/A |
| gi-2;pif3-1 | This paper | N/A |
| gi-2;pif4-101 | This paper | N/A |
| gi-2;pif5-1 | This paper | N/A |
| gi-2;pif4-101;pif5-1 | This paper | N/A |
| GI-YPET-Flag | This paper | N/A |
| pGI::GI-YPET-Flag | This paper | N/A |
| PIF3-ECFP-HA | This paper | N/A |
| pPIF3::PIF3-ECFP-HA | This paper | N/A |
| PIF3-ECFP-HA;GI-YPET-Flag | This paper | N/A |
| PIF3-ECFP-HA;gi-2 | This paper | N/A |
| pGI::GI-YPET-Flag;pPIF3::PIF3-ECFP-HA | This paper | N/A |
| PIF5-HA;GI-YPET-Flag | This paper | N/A |
| pCCA1::LUC, gi-2;pif3-1 | This paper | N/A |
| pCCA1::LUC; gi-2;pif4-101 | This paper | N/A |
| pCCA1::LUC; gi-2;pif5-1 | This paper | N/A |
| pCCA1::LUC; gi-2;pif4-101;pif5-1 | This paper | N/A |
| pCCA1::LUC; PIF3-ECFP-HA | This paper | N/A |
| pCCA1::LUC; PIF5-HA | This paper | N/A |
| pCCA1::LUC; PIF4-Flash | This paper | N/A |
| Oligonucleotides | ||
| Primers used in this study, see Table S2 | ||
| Recombinant DNA | ||
| pD32-GI | This paper | N/A |
| pD22-PIF1 | Pruneda-Paz et al., 2014 | N/A |
| pD22-PIF3 | Pruneda-Paz et al., 2014 | N/A |
| pD22-PIF4 | Pruneda-Paz et al., 2014 | N/A |
| pD22-PIF5 | Pruneda-Paz et al., 2014 | N/A |
| pTNT-HA | Chory lab | N/A |
| pTNT-Flag | Chory lab | N/A |
| pTNT-HA-GI | This paper | N/A |
| pTNT-Flag-PIF1 | This paper | N/A |
| pTNT-Flag-PIF3 | This paper | N/A |
| pTNT-Flag-PIF4 | This paper | N/A |
| pTNT-Flag-PIF5 | This paper | N/A |
| pTNT-Flag-GFP | This paper | N/A |
| pTNT-Flag-P3-1 | This paper | N/A |
| pTNT-Flag-P3-2 | This paper | N/A |
| pTNT-Flag-P3-3 | This paper | N/A |
| pTNT-Flag-P3-4 | This paper | N/A |
| pB7m34GW | University of Ghent collection | https://gateway.psb.ugent.be |
| pB-35S::GI-YPET-Flag | This paper | N/A |
| pB-pGI::GI-YPET-Flag | This paper | N/A |
| pH7m34GW | University of Ghent collection | https://gateway.psb.ugent.be |
| pH-35S::PIF3-ECFP-HA | This paper | N/A |
| pH-pPIF3::PIF3-ECFP-HA | This paper | N/A |
| pEarleyGate201 | Earley et al., 2006 | N/A |
| pEarleyGate202 | Earley et al., 2006 | N/A |
| pEG201-PIF3 | This paper | N/A |
| pEG201-PIF5 | This paper | N/A |
| pEG201-GFP | This paper | N/A |
| pEG202-PIF1 | This paper | N/A |
| pEG202-PIF3 | This paper | N/A |
| pEG202-PIF4 | This paper | N/A |
| pEG202-PIF5 | This paper | N/A |
| pEG201-GI | This paper | N/A |
| pEG201-GFP | This paper | N/A |
| pGreenII 0800-LUC | Hellens et al., 2005 | N/A |
| pGLUCpPIL1 | This paper | N/A |
| pGLUCpCCA1 | This paper | N/A |
| Software and Algorithms | ||
| VisionWorksLS | UVP, LLC | N/A |
| NIH ImageJ software | Schneider et al., 2012 | https://imagej.nih.gov/ij/ |
| CFX Manager | BioRad | Cat#1845000 |
| LabView | National Instruments | N/A |
| BioDare2 | Moore et al., 2014; Zielinski et al., 2014 | https://www.biodare2.ed.ac.uk |
| Bowtie (v1.0.0) | Langmead et al., 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| MACS2 (v 2.1.1.) | Zhang et al., 2008 | https://pypi.org/project/MACS2/ |
| NGSplot (v 2.41.4) | Shen et al., 2014 | https://github.com/shenlab-sinai/ngsplot |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/download.html |
| Phaser | Mockler et al., 2007 | http://phaser.mocklerlab.org/ |
| PANTHER | Thomas et al., 2003 | http://www.pantherdb.org/ |
| R | RCoreTeam, 2016 | http://www.R-project.org/ |
| ggplot2 plotting package | Wickham, 2009 | https://cran.r-project.org/web/packages/ggplot2/ |