EMBO/SourceData huggingface dataset:
Figure legend: "(d) EBER1 5'-pppRNA detection using splint-ligation. EBV-WT- or EBV-ΔBRLF1-harboring HNE1 cells were cotransfected with empty vector, BRLF1 or BRLF1 L578A, BRLF1 plus BZLF1, or BRLF1 L578A plus BZLF1 for 48 h. The total RNAs were extracted, and 5 μg of each RNA was subjected to splint-ligation with FAM-labeled probe to quantify the 5′-monophosphorylated EBER1 and total EBER1 RNA. The ligation products were separated using urea-PAGE, visualized by a fluorescent scanner and analyzed using ImageJ software. The ratio of 5'-pRNA density to total RNA density and the relative 5'-pppRNA level were calculated for three independent experiments."
NCBI gene IDs:
"BRLF1: 3783727
BZLF1: 3783744
EBER1: RF01789"
Figure legend: "(e) EBV-WT-harboring HNE1 cells were transfected with control vector, BRLF1 or BRLF1 L578A-expressing plasmid in the presence of GST-tagged RNA polymerase subunit POLR3F for 48 h. The cells were harvested and ChIP assay was performed with anti-GST affinity beads. The POLR3F-binding promoter fragments of BSRF1, BMLF1, EBER1, EBER2, EBNA1, 7SK, RN7SL1 and the GAPDH as negative control in the ChIP samples were detected by real-time PCR assays."
NCBI gene IDs:
"EBER2: 
EBNA1: 
GAPDH: 
GST: 
BRLF1: 3783727
BMLF1: 3783758
BSRF1: 3783731
EBER1: RF01789
POLR3F: 10621
7SK: 125050
RN7SL1: 6029"
Figure legend: "(a) Stable 293T cells in the presence of pro-caspase-1, pro-IL-1β and ASC overexpression were transfected with control vector or BRLF1 with control vector, IFI16, NLRP3, RIG-I or AIM2 for 36 h. After the cells were infected with HSV-1 (MOI=1) for 12 h, the cells were collected, and the cell lysates were analyzed by western blotting to determine the levels of pro-caspase-1, cleaved caspase-1, pro-IL-1β and mature IL-1β as indicated."
NCBI gene IDs:
"AIM2: 9447
BRLF1: 3783727
RIG-I: 23586
IFI16: 3428
NLRP3: 114548
ASC: 29108"
Figure legend: "(b) Scramble (sc) or shRNAs against RIG-I and empty control vector (ctr), BRLF1- or BRLF1 L578A-expressing plasmids were co-transfected into EBV-ΔBRLF1-harboring HNE1 cells. Thirty-six hours after the transfection, cell pellets were collected, after which the cleavage of caspase-1 and IL-1β was measured as indicated."
NCBI gene IDs:
"BRLF1: 3783727
RIG-I: 23586"
Figure legend: "(c) Analysis of ASC oligomerization. ASC-expressing plasmid was transfected into 293T cells or HNE1 cells with empty vector or GFP-BRLF1 in the presence of AIM2- or RIG-I-expressing plasmid. Twelve hours after HSV-1 infection (MOI=1) in 293T cells, or 48 h after EBV-ΔBRLF1 infection (MOI=1000) in HNE1 cells, the cell pellets were collected, and cell lysates were treated with DSS to induce chemical cross-linking and analyzed by western blotting for ASC oligomerization."
NCBI gene IDs:
"GFP: 
AIM2: 9447
BRLF1: 3783727
RIG-I: 23586
ASC: 29108"
Figure legend: "(d) EBV-ΔBRLF1-harboring HNE1 cells were transfected with control vector, BRLF1 or BRLF1 L578A in the absence or presence of BZLF1 for 48 h. The total RNAs were extracted and subjected to real-time PCR analysis."
NCBI gene IDs:
"BRLF1: 3783727
BZLF1: 3783744"
Figure legend: "(e) A549 cells were transfected with control vector, BRLF1 or BRLF1 L578A for 36 h. After the cells were infected with HSV-1 (MOI=1) for 12 h, the total RNAs were extracted and subjected to real-time PCR analysis."
NCBI gene IDs:
"BRLF1: 3783727"
Figure legend: "Jurkat cells (a) were infected with EBV-WT or EBV-ΔBRLF1 virus (MOI=500) for 36 h. Then, the cells were collected, and the total RNAs were extracted, reverse-transcribed and analyzed by real-time PCR. Color gradient depicts the mean mRNA expression normalized to the housekeeping gene GAPDH and compared to the mock group."
NCBI gene IDs:
"GAPDH: 
BRLF1: 3783727"
Figure legend: "NK-92MI cells (b) were infected with EBV-WT or EBV-ΔBRLF1 virus (MOI=500) for 36 h. Then, the cells were collected, and the total RNAs were extracted, reverse-transcribed and analyzed by real-time PCR. Color gradient depicts the mean mRNA expression normalized to the housekeeping gene GAPDH and compared to the mock group."
NCBI gene IDs:
"GAPDH: 
BRLF1: 3783727"
Figure legend: "Jurkat and NK-92MI cells were cultured with conditional medium from EBV-WT or EBV-ΔBRLF1-infected Ramos cells (paracrine), or Jurkat and NK-92MI cells were directly infected with EBV-WT or EBV-ΔBRLF1 viruses (autocrine). (c) The cell pellets were collected and the whole cell extracts were analyzed by western blotting to detect TAK1, IKKα/β and IκB phosphorylation."
NCBI gene IDs:
"BRLF1: 3783727"
Figure legend: "Anti-IL-1β and/or anti-IL-18 neutralizing antibodies (NA), TAT-Flag or TAT-N572 peptide were added into EBV-WT- or EBV-ΔBRLF1-infected Jurkat cells or NK-92MI cells for 24 h. (f) TAK1, IKKα and IκB phosphorylation were detected as indicated."
NCBI gene IDs:
"BRLF1: 3783727"
Figure legend: "(a-d) PBMCs were isolated and infected with EBV-WT or EBV-ΔBRLF1 virus (MOI=500). Thirty-six hours after infection, the cells were harvested and the total RNAs were extracted, reverse-transcribed and subjected to real-time PCR analysis. The differential expression of receptors and cytokines (a), cytotoxic genes (b), T cell-specific genes (c) and NK cell-specific genes (d) are shown. The values are shown as the mean ± standard deviations of five analyses of PBMCs from five different health donors."
NCBI gene IDs:
"BRLF1: 3783727"
Figure legend: "(e-h) FACS analysis of T and NK cell activation in PBMCs in the presence of EBV-WT or EBV-ΔBRLF1 primary infection. The PBMCs were left uninfected or infected with EBV-WT or EBV-ΔBRLF1 virus for 36 h, and the EBV-ΔBRLF1-infected lymphocytes were incubated with additional TAT-Flag or TAT-N572 peptide for 12 h. Immunofluorescent PE-CD3 and APC-CD25 antibodies were used to detect T cell activation (e, g), and PE-CD56 and APC-CD69 were used to detect NK cell activation (f, h). Representative images of the FACS analysis of T cell and NK cell activation are shown (e, f), and the percentages of activated T cells and NK cells were calculated and are shown as the mean ± standard deviation (g, h) for lymphocytes from 5 different health donors;"
NCBI gene IDs:
"BRLF1: 3783727"
Figure legend: "(a) Representative image of a Control (left) and Myo1cKO (right) embryo. Top: max projections of embryos stained with Phalloidin (green) and DAPI (gray). Bottom: magnifications at dashed rectangles of Phalloidin (grey) with white arrows pointing at fragments. Data information: Mann-Whitney test p values are indicated. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(b-c) Number of fragments without DNA (b) per embryo and mean radius (c) in Control (grey) and Myo1cKO (salmon) embryos (left, Control n = 20, Myo1cKO n = 20). Boxplot shows median, upper and lower quartiles, min and max values. Whisker plot shows median, upper and lower quartiles. Data information: Mann-Whitney test p values are indicated. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(d) Representative images of a time-lapse of Myo1cKO embryo undergoing fragmentation outside of division (top) and during division (bottom). Max projections of embryos expressing mTmG (grey) and mCherry-EB3 (grey) imaged with light sheet microscopy are shown. White arrows point at the forming fragments. (e) Ratio of fragmentation events during and outside of division (n = 13 cells from 7 embryos). Data information: Mann-Whitney test p values are indicated. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(a) Representative images of Control (left) and Myo1cKO (right) embryos expressing mTmG and mCherry-EB3 (grey) shown as max projections. White arrows point at the mitotic spindle. (b-c) Spindle persistence in Control (n = 6) and Myo1cKO (n = 9) embryos (b) and in non-fragmenting and fragmenting cells of Myo1cKO embryos (c, n = 42 and 12 cells from 7 Myo1cKO embryos). Spindle persistence measures the time from appearance to disassembly of the spindle. Data information: Mann-Whitney test p values are indicated. Boxplots show median, upper and lower quartiles, min and max values. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(d) Top: Representative images of a time-lapse of a Myo1cKO embryo expressing Myh9-GFP (green) and mTmG (magenta) while labelled with SiRDNA (grey) undergoing fragmentation during mitosis shown as max projections. Bottom: magnifications of Myh9-GFP (grey) at dashed rectangles showing cortical accumulation (middle) followed by fragmentation (right). Data information Boxplots show median, upper and lower quartiles, min and max values. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(e) Control (grey) and Myo1cKO (salmon) embryos Myh9-GFP Ic/Iref values at DNA-cortex distances &lt; 20 µm and &gt; 20 µm (Control embryos n = 10, cells n = 35; Myo1cKO embryos n = 9, cells n = 26) Data information: Kruskal-Wallis and pairwise Mann-Whitney tests (e) p values are indicated. Boxplots show median, upper and lower quartiles, min and max values. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(f) Comparison of the increase in Myh9-GFP intensity in Control and Myo1cKO embryos when DNA is in close proximity to the cortex. The ratio Ic0-20/Ic&gt;20 is calculated from Myh9-GFP intensities at the contact region when DNA-cortex distances are &lt; 20 µm (Ic0-20) divided by intensities when distances are &gt; 20 µm (Ic&gt;20) (Control embryos n = 10, cells n = 33; Myo1cKO n = 9, cells n = 26). Data information: Mann-Whitney test p values are indicated. Boxplots show median, upper and lower quartiles, min and max values. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(a) Representative images of Control (left) and Myo1cKO (right) embryos labelled with SiRDNA (grey) and expressing a reporter of Cdc42 activity (yellow) in one blastomere, which is undergoing mitosis, shown as max projections. The second blastomere is outlined with a dashed line. White arrows point at the accumulation of active Cdc42 at the cortex in close proximity to DNA. (b) The ratio of active Cdc42 Ic/Iref was compared between &lt; 20 µm and &gt; 20 µm DNA-cortex distances for Control (dark yellow) and Myo1cKO (yellow) embryos (Control embryos n = 10; Myo1cKO embryos n = 10). Data information: Kruskal-Wallis and pairwise Mann-Whitney tests (b Boxplots show median, upper and lower quartiles, min and max values. Scale bars, 10 µm."
NCBI gene IDs:
"Myo1c: 17913"
Figure legend: "(c) Representative images of Myo1cKO embryos expressing LifeAct-GFP (green) alone (left) or together with dominant negative Cdc42 (DNCdc42, right) labelled with SiRDNA (grey) shown as max projections. White arrows point at the cortex in close proximity to DNA. (d) LifeAct-GFP Ic/Iref values at DNA-cortex distances &lt; 20 µm and &gt; 20 µm for Myo1cKO (salmon) and Myo1cKO + DNCdc42 (yellow) embryos (Myo1cKO embryos n = 8, cells n = 19; Myo1cKO + DNCdc42 embryos n = 12, cells n = 30). Data information: Kruskal-Wallis and pairwise Mann-Whitney tests d) Boxplots show median, upper and lower quartiles, min and max values. Scale bars, 10 µm."
NCBI gene IDs:
"Cdc42: 
Myo1c: 17913"
Figure legend: "F-M Compared with wild-types (F-I), mutants (J-M) completely lost the CM (red) in the gut of 7dpf larva (F, J), as well as in the intestinal bulb (G, K), middle intestine (H, L) and posterior intestine (I, M) of adults. Red, SNAP-CBD stain; blue, DAPI stain; WT, wild-type; MU, chs1-/- mutant."
NCBI gene IDs:
"chs1: 322468"
Figure legend: "B Comparison of 3-month-old wild-types and mutants in the pairwise microbiota compositional dissimilarity (Jaccard distance) between the digesta (niche1) and the epithelia (niche2). This metric represents the radial gradient of the gut bacterial composition. The comparison was done on four taxonomy levels. Data of n=14 individuals were represented in box (interquartile range) and whisker (min to max) plots. Individual data points were plotted as black dots. * P &lt; 0.05, ** P &lt; 0.01 by the conservative, nonparametric Kruskal-Wallis test. Please see Appendix Fig S10 for another way of data presentation, and Dataset EV1 for the details of the sample information and raw statistics. Note that each 16S-rRNA library contains only one sample from one animal."
NCBI gene IDs:
"16S-rRNA: "
Figure legend: "A Luciferase complementation imaging (LCI) assays showing that BIC1 interacts with BZR1. nLUC-BZR1 was co-transformed with cLUC-CCA1, cLUC-TOC1, cLUC-ELF3, cLUC-LUX, cLUC-BIC1, cLUC, respectively, in leaf epidermal cells of Nicotiana benthamiana as indicated."
NCBI gene IDs:
"LUC: 
BIC1: 824440
BZR1: 843845
CCA1: 819296
ELF3: 817134
LUX: 823817
TOC1: 836259"
Figure legend: "B BiFC assays showing the interaction of BIC1 and BZR1 mainly in nucleus. Leaf epidermal cells of Nicotiana benthamiana were co-transformed with nYFP-BZR1 and cYFP-BIC1. BF, bright field. Scale bars represent 20 μm."
NCBI gene IDs:
"YFP: 
BIC1: 824440
BZR1: 843845"
Figure legend: "A, B Hypocotyl elongation phenotypes of the BIC1 overexpression and mutant lines in response to BR treatment. Col-0, 35S:BIC1-YFP, 35S:BIC1-Flag and bic1bic2 seedlings were grown for 6 days on 1/2 MS medium supplemented with 1 μM brassinazole (BRZ) plus different concentrations of epibrassinolide (eBL). Images of the representative seedlings are shown in (A), and the hypocotyl lengths of the indicated genotypes were measured and are shown in (B). Data are means ± SD; n>20. Scale bars, 2 mm."
NCBI gene IDs:
"Flag: 
YFP: 
bic2: 823570
BIC1: 824440
bic1: 824440"
Figure legend: "C RT-qPCR analysis of BZR1-activated gene expression in the bic1bic2 double mutants. The 6-d-old Col-0 and bic1bic2 seedlings grown on 1/2 MS medium supplemented with 1 μM BRZ were treated with 5 μM eBL (+eBL) or not (-eBL) for 1 hour. The PP2A gene served as internal control. Data are means ± SD (n=3)."
NCBI gene IDs:
"bic2: 823570
bic1: 824440
PP2A: 843333"
Figure legend: "D Heat map of BIC1-regulated genes. The Col-0 and 35S:BIC1-YFP seedlings were grown on 1/2 MS medium for 10 days. Three biologic replicates were performed. The colored bar beneath the map indicates fold change (log2 value)."
NCBI gene IDs:
"YFP: 
BIC1: 824440"
Figure legend: "E BIC1 facilitates the expression of cell elongation genes. RT-qPCR analysis of genes selected in transcriptomic data. The Col-0, 35S:BIC1-YFP and 35S:BIC1-Flag seedlings were grown for 5 days under long-day conditions. The PP2A gene served as internal control. Data are means ± SD (n=3)."
NCBI gene IDs:
"Flag: 
YFP: 
BIC1: 824440
PP2A: 843333"
Figure legend: "A, B BIC1 and BZR1 synergistically promote hypocotyl elongation. The Col-0, 35S:BZR1-MYC, 35S:BIC1-YFP and 35S:BZR1-MYC/35S:BIC1-YFP plants were grown for 5 days under long-day conditions. Images of the representative seedlings are shown in (A), and the hypocotyl lengths of the indicated genotypes were measured and are shown in (B). Data are means ± SD (n&gt;20). **p &lt; 0.01, as determined by Student's t-test. Scale bar, 2 mm."
NCBI gene IDs:
"MYC: 
YFP: 
BIC1: 824440
BZR1: 843845"
Figure legend: "C-E BR signaling is enhanced in the 35S:BZR1-MYC/35S:BIC1-YFP plants. Seedlings were grown for 6 days on medium supplemented with 1 μM brassinazole (BRZ) plus a gradient of concentrations of epibrassinolide (eBL) under long-day conditions. Images of the representative seedlings when grown with 500 nM eBL (+eBL) or not (-eBL) are shown in (C), and the hypocotyl lengths of the indicated genotypes were measured and are shown in (D) and (E). Data are means ± SD (n&gt;20). **p &lt; 0.01, as determined by Student's t-test. Scale bar, 2 mm."
NCBI gene IDs:
"MYC: 
YFP: 
BIC1: 824440
BZR1: 843845"
Figure legend: "F, G BZR1-mediated hypocotyl elongation phenotype is dependent on the function of BIC1 and BIC2. Seedlings were grown for 5 days under long-day conditions. Images of the representative seedlings are shown in (F), and the hypocotyl lengths of the indicated genotypes were measured and are shown in (G). Data are means ± SD (n&gt;20). **p &lt; 0.01, n.s. indicates no significant difference, (Student's t-test). Scale bar, 2 mm."
NCBI gene IDs:
"BIC2: 823570
BIC1: 824440
BZR1: 843845"
Figure legend: "H BZR1-mediated hypocotyl elongation phenotype is dependent on the function of BIC1 and BIC2. The Col-0, 35S:BZR1-MYC, bic1bic2, 35S:BZR1-MYC/bic1bic2 seedlings were grown on medium supplemented with 1 μM BRZ plus different concentrations of eBL for 6 days and then the hypocotyl lengths were measured. Data are means ± SD (n&gt;20)."
NCBI gene IDs:
"MYC: 
bic2: 823570
bic1: 824440
BZR1: 843845"
Figure legend: "A BR enhances the stability of BIC1 proteins. The 5-d-old 35S:BIC1-YFP transgenic plants were treated with 100 μM cycloheximide (CHX) or co-treated with 100 μM CHX and 1 μM epibrassinolide (eBL). Samples were collected at indicated time points and BIC1-YFP protein levels were analyzed by western blots using anti-GFP antibody. Actin was used to verify equal protein loadings. Intensity of the bands was measured using Adobe Photoshop CS3 Extended program. Three independent experiments were performed with similar results."
NCBI gene IDs:
"YFP: 
BIC1: 824440"
Figure legend: "C Transactivation analysis of BIC1 using a yeast assays. The GAL4 DNA-binding domain (BD) alone was used as the negative control. SD-W, synthetic dextrose medium lacking Trp; SD-WH, synthetic dextrose medium lacking both Trp and His."
NCBI gene IDs:
"GAL4: 855828"
Figure legend: "E Transient transcriptional activity analysis in Arabidopsis protoplasts illustrating the transcriptional activation activity of BIC1. The relative luciferase activities were calculated by normalizing the LUC values against REN. Error bars represent SD (n = 3). **p &lt; 0.01, as determined by a Student's t-test."
NCBI gene IDs:
"LUC: 
REN: 
BIC1: 824440"
Figure legend: "G Transient expression assays in Arabidopsis protoplasts showing that BIC1 and BZR1 synergistically activate PRE5 promoter. The ProPRE5:LUC reporter was co-transformed with the indicated effector constructs. The LUC/REN ratio represents the ProPRE5:LUC activity relative to the internal control (REN driven by the 35S promoter). Error bars represent SD (n = 3)."
NCBI gene IDs:
"LUC: 
REN: 
BIC1: 824440
BZR1: 843845
PRE5: 2745895"
Figure legend: "H, I BIC1-mediated hypocotyl elongation was reduced by the addition of SRDX motif. Seedlings were grown for 5 days under long-day conditions. Images of the representative seedlings are shown in (H), and the hypocotyl lengths of the indicated genotypes were measured and are shown in (I). #1, #2, #3 represent different 35S:BIC1-SRDX-Flag transgenic lines. Data are means ± SD (n>20). **p &lt; 0.01, as determined by Student's t-test. Scale bar, 2 mm."
NCBI gene IDs:
"Flag: 
BIC1: 824440"
Figure legend: "LCI assays showing that BIC1 interacts with PIF4. Leaf epidermal cells of Nicotiana benthamiana were co-transformed with nLUC-BIC1 or nLUC and cLUC-PIF4 or cLUC as indicated."
NCBI gene IDs:
"LUC: 
BIC1: 824440
PIF4: 818903"
Figure legend: "C Co-IP assays showing the interaction between BIC1 and PIF4 in vivo. The 35S:BIC1-YFP, 35S:PIF4-MYC and 35S:PIF4-MYC/35S:BIC1-YFP transgenic plants were grown for 6 days under long-day conditions. The immunoprecipitates were detected using anti-GFP and anti-MYC antibodies, respectively."
NCBI gene IDs:
"MYC: 
YFP: 
BIC1: 824440
PIF4: 818903"
Figure legend: "D, E Phenotypic analyses showing that BIC1 and PIF4 synergistically promote hypocotyl elongation. The Col-0, 35S:BIC1-YFP, 35S:PIF4-MYC and 35S:PIF4-MYC/35S:BIC1-YFP plants were grown for 5 days under long-day conditions. Images of the representative seedlings are shown in (D), and the hypocotyl lengths of the indicated genotypes were measured and are shown in (E). Data are means ± SD (n>20). **p &lt; 0.01, as determined by Student's t-test. Scale bar, 2 mm."
NCBI gene IDs:
"MYC: 
YFP: 
BIC1: 824440
PIF4: 818903"
Figure legend: "F RT-qPCR analysis showing that BIC1 and PIF4 synergistically activate PIF4 target genes. The seedlings growth conditions were same as (D). The PP2A gene was used as an internal control. Data are means ± SD (n=3)."
NCBI gene IDs:
"BIC1: 824440
PIF4: 818903
PP2A: 843333"
Figure legend: "G,H Phenotypic analyses showing that PIF4-induced hypocotyl elongation is partially. dependent on the function of BIC1 and BIC2. The Col-0, bic1bic2, PIF4-MYC and PIF4-MYC/bic1bic2 plants were grown for 5 days under long-day conditions. Images of the representative seedlings are shown in (G) and the hypocotyl lengths of indicated genotypes were measured and are shown in (H). Data are means ± SD (n>20). **p &lt; 0.01, as determined by Student's t-test. Scale bar, 2 mm."
NCBI gene IDs:
"MYC: 
bic2: 823570
bic1: 824440
PIF4: 818903"
Figure legend: "I RT-qPCR analysis showing that PIF4-induced expression of target genes is partially dependent the function of BIC1 and BIC2. The seedlings growth conditions were same as (G). The PP2A gene was analyzed as an internal control. Data are means ± SD (n=3). **p &lt; 0.01, as determined by Student's t-test."
NCBI gene IDs:
"BIC2: 823570
BIC1: 824440
PIF4: 818903
PP2A: 843333"
Figure legend: "J, K Phenotypic analyses showing that BIC1-induced hypocotyl elongation is largely dependent on the function of PIFs. The Col-0, pifQ, 35S:BIC1-Flag, 35S:BIC1-flag/pifQ #7 and BIC1-flag/pifQ #8 plants were grown for 5 days under long-day conditions. Images of the representative seedlings are shown in (J) and the hypocotyl lengths of indicated genotypes were measured and are shown in (K). Data are means ± SD (n>20). **p &lt; 0.01, as determined by Student's t-test. Scale bar, 2 mm."
NCBI gene IDs:
"Flag: 
flag: 
BIC1: 824440"
Figure legend: "B ChIP-qPCR analysis showing the association of BIC1 with the promoter regions of BZR1/PIF4 target genes. The 6-d-old Col-0 and 35S:BIC1-Flag seedlings were used for ChIP assays."
NCBI gene IDs:
"Flag: 
BIC1: 824440"
Figure legend: "C ChIP-qPCR analysis showing that the association of BIC1 with the promoter regions of BZR1/PIF4 target genes is dependent on PIFs. The 6-d-old 35S:BIC1-Flag and 35S:BIC1-Flag/pifQ seedlings were used for ChIP assays."
NCBI gene IDs:
"Flag: 
BIC1: 824440"
Figure legend: "D ChIP-qPCR analysis showing that the enrichment of BZR1 in the promoter regions of its target genes is dependent on BICs. The 10-d-old 35S:BZR1-MYC and 35S:BZR1-MYC/bic1bic2 seedlings were treated with 1 μM epibrassinolide (eBL) for 3 h and then collected for ChIP assays."
NCBI gene IDs:
"MYC: 
bic2: 823570
bic1: 824440
BZR1: 843845"
Figure legend: "E ChIP-qPCR analysis showing that the enrichment of PIF4 in the promoter regions of its target genes is dependent on BICs. The 6-d-old 35S:PIF4-MYC and 35S:PIF4-MYC/bic1bic2 seedlings were used for ChIP assays."
NCBI gene IDs:
"MYC: 
bic2: 823570
bic1: 824440
PIF4: 818903"
Figure legend: "A RT-qPCR analysis showing that BIC1 upregulates the transcriptional expression of PIF4. The Col-0, 35S:BIC1-YFP, 35S:BIC1-Flag and bic1bic2 plants were grown for 5 days under long-day conditions. The PP2A gene served as internal control. Data are means ± SD (n=3). Different letters indicate significant differences (Fisher's LSD, P&lt; 0.05)."
NCBI gene IDs:
"Flag: 
YFP: 
bic2: 823570
BIC1: 824440
bic1: 824440
PIF4: 818903
PP2A: 843333"
Figure legend: "B Transcript levels of BIC1 and PIF4 in transgenic plants containing a chemical-inducible construct pERGW-BIC1. 8-d-old pERGW-BIC1 seedlings were treated with 10 μM estradiol for indicated time points before harvest for RNA extraction and RT-qPCR analysis. The PP2A gene served as internal control. Data are means ± SD (n=3)."
NCBI gene IDs:
"BIC1: 824440
PIF4: 818903
PP2A: 843333"
Figure legend: "C ChIP-qPCR analysis showing the association of BIC1 with the promoter regions of PIF4. The top panel shows the diagram of the promoter structure of PIF4. Arrows indicate the primer positions for ChIP-qPCR. G-box, CACGTG. The 6-d-old Col-0 and 35S:BIC1-Flag seedlings were used for ChIP assays. The chromatin of each sample was immunoprecipitated (IP) using an anti-Flag or not (Mock). Precipitated DNA was quantified by qPCR, and DNA enrichment is displayed as the ratio between IP and Mock, normalized to that of PP2A as an internal control. Data are means ± SD (n=3). *p &lt; 0.05, as determined by Student's t-test."
NCBI gene IDs:
"Flag: 
BIC1: 824440
PIF4: 818903
PP2A: 843333"