EMBO/SourceData huggingface dataset:
Figure legend: "E-H. Immunofluorescence  analysis of endogenous LC3  in MEFs  generated from Trim27+/+ or Trim27-/- mice  cultured in fed  (E) or starved  conditions (G). Quantification of LC3B  puncta Fed  conditions (F), starved  conditions (H) (n = 50 cells per condition). Data are mean ± s.d. in F and H. Scale bar, 10 μm. Data information: (F, H, Statistical analysis was performed using two-tailed unpaired Student's t-tests, *P&lt; 0.05,***P&lt;0.001."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "I-J. Western blot analysis of autophagy  markers in the kidneys   of three-month-old Trim27  +/+ and Trim27-/- mice. Each lane represents a different mouse  (I). Quantification of p62,  LC3-II/LC3-I  ratio, and LC3-II/actin  ratio in I (J). Data are mean ± s.e.m. for three mice  per genotype. Data information: J, Statistical analysis was performed using two-tailed unpaired Student's t-tests, *P&lt; 0.05,***P&lt;0.001."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "A. Ubiquitination  analysis of HA-ULK1 in HeLa derivatives co-expressing His-Ub  with or without TRIM27  knockout, the cells were treated with starvation  for the indicated time."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "B. Western blot  analysis of ULK1 levels in HeLa  cells with or without TRIM27  knockout. The cells were treated with starvation  for the indicated time. The lysates were analyzed using anti-ULK1, anti-TRIM27, or anti-Actin."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "C. HA-ULK1, HA-ULK1  K568/K571R were stably expressed in ULK1  knockout HeLa  cells, the cells were treated with starvation, the lysates were analyzed by  western blot using anti-HA, or anti-Actin."
NCBI gene IDs:
"HA: 
ULK1: 22241
ULK1: 8408"
Figure legend: "E. Co-immunoprecipitation of Flag-TRIM27  with HA-ULK1  in HEK293T  cells with or without STK38L  knockdown, the cells were treated with starvation. Flag-TRIM27  was immunoprecipitated  using anti-Flag, the bound HA-ULK1  was detected using anti-HA."
NCBI gene IDs:
"STK38L: 23012"
Figure legend: "G. Co-immunoprecipitation  of Flag-STK38L  with ULK1, or TRIM27  in HEK293T  cells with or without starvation  treatment. Flag-STK38L   was immunoprecipitated  using anti-Flag, the immunoprecipitates  and lysates were analyzed with anti-ULK1, anti-TRIM27."
NCBI gene IDs:
"Flag: 
STK38L: 23012"
Figure legend: "H. Co-immunoprecipitation of endogenous TRIM27  with endogenous ULK1  in HeLa  cells with or without STK38L  knockout. The cells were treated with starvation before lysis."
NCBI gene IDs:
"STK38L: 23012"
Figure legend: "I. Western blot analysis of ULK1  levels in starved HeLa  cells expressing either Myc-STK38L, or Flag-TRIM27, or both. The lysates were analyzed using anti-ULK1, anti-Flag, anti-Myc, or anti-actin."
NCBI gene IDs:
"Flag: 
Myc: 
STK38L: 23012
TRIM27: 5987"
Figure legend: "J. Ubiquitination  analysis of HA-ULK1  in HEK293T  cells co-expressing Flag-TRIM27  and His-Ub, or together with Myc-STK38L."
NCBI gene IDs:
"Flag: 
His: 
Myc: 
STK38L: 23012
TRIM27: 5987
Ub: 7314"
Figure legend: "K. Western blot  analysis of ULK1  levels in HeLa  cells with or without STK38L  knockout, the cells were treated with starvation  for the indicated time."
NCBI gene IDs:
"STK38L: 23012"
Figure legend: "L.  Western blot analysis of p62  or LC3  levels in HeLa  cells with or without STK38L  knockout, the cells were treated with starvation  for the indicated time. Bafilomycin A1 (BAF A1) was used to inhibit the fusion between autophagosomes  and lysosomes."
NCBI gene IDs:
"STK38L: 23012"
Figure legend: "A. Western blot  analysis of ULK1  levels in HeLa cells stably expressing Flag-TRIM27, the cells were transfected with either Myc-vector, Myc-STK38L, or Myc-STK38L-K119A. Then the cells were treated with starvation before lysis."
NCBI gene IDs:
"Flag: 
Myc: 
STK38L: 23012
TRIM27: 5987"
Figure legend: "B. Phosphorylation  of HA-ULK1  in HeLa STK38L  knockout cells with or without expression of Flag-STK38L. HA-ULK1  was immunoprecipitated  and then analyzed by western blot using anti-phosphoserine  or anti-phosphothreonine, and the cell lysates were analyzed using anti-HA  and anti-Myc."
NCBI gene IDs:
"Flag: 
STK38L: 23012"
Figure legend: "C. Co-immunoprecipitation of Flag-TRIM27  with HA-ULK1  or HA-ULK1-S495A in HEK293T  cells. HA-ULK1  or HA-ULK1 S495A was immunoprecipitated  using anti-HA, the immunoprecipitates  and lysates were analyzed with anti-HA  or anti-Flag."
NCBI gene IDs:
"HA: 
ULK1: 22241"
Figure legend: "D. Ubiquitination  analysis of HA-ULK1  WT or HA-ULK1  S495A in HEK293T cells co-expressing Flag-TRIM27  and His-Ub."
NCBI gene IDs:
"Flag: 
HA: 
His: 
TRIM27: 5987
Ub: 7314
ULK1: 22241"
Figure legend: "E. Phosphorylation  of HA-ULK1  in HEK293T  cells co-expressing Myc-STK38L  with or without CIP  treatment. HA-ULK1  was immunoprecipitated  with anti-HA  and analyzed by western blot using a specific antibody against p-ULK1-S495 (Ser495)."
NCBI gene IDs:
"Myc: 
STK38L: 23012"
Figure legend: "F. Phosphorylation  of HA-ULK1 or HA-ULK1  S495A in HEK293T  cells co-expressing Myc-STK38L. HA-ULK1  or HA-ULK1  S495A was immunoprecipitated  with anti-HA  and analyzed by western blot using a specific antibody against p-ULK1-S495 (Ser495)."
NCBI gene IDs:
"HA: 
STK38L: 23012
ULK1: 22241"
Figure legend: "H. Ubiquitination  analysis of Myc-STK38L  in HEK293T  cells co-expressing Flag-TRIM27  and His-Ub."
NCBI gene IDs:
"Flag: 
TRIM27: 5987"
Figure legend: "I. Ubiquitination  analysis of Flag-STK38L  in HEK293T  cells co-expressing His-Ub  with or without TRIM27  knockdown, cells were cultured in fed  or starved  conditions as indicated."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "J. Ubiquitination  analysis of Flag-STK38L  in HEK293T  cells co-expressing Myc-TRIM27  with either His-Ub  (wild-type) or His-Ub  K6R."
NCBI gene IDs:
"Myc: 
TRIM27: 5987
Ub: 7314"
Figure legend: "K. Ubiquitination  analysis of Myc-STK38L  WT, Myc-STK38L-K432R+K434R or Myc-STK38L-K181R+K215R+K224R+K432R+K434R (Myc-STK38L-5KR) mutant in HEK293T  cells co-expressing HA-TRIM27  and His-Ub."
NCBI gene IDs:
"HA: 
Myc: 
STK38L: 23012
TRIM27: 5987"
Figure legend: "L. Ubiquitination  analysis of Myc-STK38L  K1-38R mutant (All lysines  were mutated to arginines), or Myc-STK38L-R181/215/224/432/434K (All lysines were mutated to arginines except the indicated five lysine  residues) mutant in HEK293T  cells co-expressing HA-TRIM27  and His-Ub."
NCBI gene IDs:
"HA: 
Myc: 
STK38L: 23012
TRIM27: 5987"
Figure legend: "M. Phosphorylation  of HA-ULK1  S495(Ser495) in HEK293T  cells co-expressing Myc-STK38L  WT, or Myc-STK38L-5KR mutant in K. The cells were cultured in fed  or starved  conditions as indicated and HA-ULK1  was immunoprecipitated  using anti-HA, the immunoprecipitates  and lysates were analyzed with a specific antibody against p-ULK1-S495 (Ser495), anti-Myc, anti-HA, or anti-actin."
NCBI gene IDs:
"Myc: 
STK38L: 23012"
Figure legend: "N. Phosphorylation  of HA-ULK1  in HeLa  cells with or without TRIM27-knockout, cells were cultured in fed  or starved  conditions as indicated, HA-ULK1  was immunoprecipitated  using anti-HA, the immunoprecipitates  and lysates were analyzed with a specific antibody against p-ULK1-S495 (Ser495), anti-HA, or anti-actin."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "A. Comparison of the relative mRNA levels of TRIM27  in normal breast  tissues (Normal, n=113) and indicated breast   tumors (Basal，n=143；Her2，n=67；LumA，n=427；LumB，n=190) in the TCGA database. The number of biological replicates are shown as indicated. P &lt; 0.0001 (one-way ANOVA)."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "F. Representative tumors  in MMTV-PyMT mice  of the indicated Trim27  genotypes. Scale bar, 5mm."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "G.  Western blot  analysis of indicated proteins in Trim27-/- PyMT or Trim27+/- PyMT mice  in primary breast  tumors. Actin was used as a loading control."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "H. Kaplan-Meier tumor-free survival curves of Trim27+/- PyMT  (median = 75 d, number = 20), or Trim27  -/- PyMT mice  (median = 95 d, number = 16). P &lt; 0.0001 (Mantel-Cox test)."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "Pulmonary  surface nodules  in Trim27+/- PyMT mice  and Trim27-/- PyMT mice (I Scale bar, 1mm."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "Pulmonary surface nodules   and hematoxylin  and eosin  (H&amp;E) staining  in Trim27+/- PyMT mice  and Trim27-/- PyMT mice  J). Scale bar, 1mm. (K). Bar chart showing quantification for the number of metastatic nodules  per lung lope (Trim27+/-, n=6 mice; Trim27-/- n=6 mice), when compared at the same final timepoint. Each symbol represents a mouse; Data are presented as mean ± s.d. from three independent experiments; ***P&lt;0.001 (unpaired student's t-test)."
NCBI gene IDs:
"Trim27: 19720"
Figure legend: "The number of neoblasts did not change significantly following inhibition of the MTC-gene kiaa1429. Shown is FISH of smedwi-1 (A) in control and kiaa1429 (RNAi) animals (left). smedwi-1+ cells were counted following FISH and showed no significant difference in expression (right; bar represents average normalized cell count; Materials and Methods). Scale = 100 µm."
NCBI gene IDs:
"kiaa1429: 
smedwi-1: "
Figure legend: "The number of neoblasts did not change significantly following inhibition of the MTC-gene kiaa1429. Shown is FISH of h2b (B) in control and kiaa1429 (RNAi) animals (left). h2b+ cells were counted following FISH and showed no significant difference in expression (right; bar represents average normalized cell count; Materials and Methods). Scale = 100 µm."
NCBI gene IDs:
"kiaa1429: 
h2b: "
Figure legend: "(E) Representative FACS plots of cells isolated from control (top) and kiaa1429 (RNAi) animals (bottom) show an increase in cell abundance in the X2 (Fincher et al, 2018) gate (green; Materials and Methods). (F) Quantification of the cells in each FACS gate in control and kiaa1429 (RNAi) animals showed a six-fold increase in the abundance of cells in the X2 gate (Student's t-test *** - p &lt; 0.005. FACS experiments were performed in biological triplicates. Boxes represent the IQR, whiskers represent the 1.5 x IQR, and central band represents the med"
NCBI gene IDs:
"kiaa1429: "
Figure legend: "CAC was induced in control (n = 7) and ColVIcre-Kif3aflx/flx (n = 7) female mice according to the timeline shown in Figure 2A. (E) Representative images of hematoxylin and eosin staining of paraffin-embedded colon sections. Areas with high-grade dysplasia are delimited by black lines."
NCBI gene IDs:
"ColVI: 12834///12833///245026///665033///68553///12835
cre: 2777477
Kif3a: 16568"
Figure legend: "CAC was induced in control (n = 7) and ColVIcre-Kif3aflx/flx (n = 7) female mice according to the timeline shown in Figure 2A. (F,G,H,I) Box-and-whisker plots depicting area (F,G) and number (H,I) of low- and high-grade dysplasia per mouse."
NCBI gene IDs:
"ColVI: 12833///12835///68553///665033///245026///12834
cre: 2777477
Kif3a: 16568"
Figure legend: "(H) Elevated numbers of F4/80+ macrophages in colons of DSS-treated ColVIcre-Kif3aflx/flx mice. Representative images for F4/80 staining in areas with crypt loss are shown. At least 5 fields in the regions of crypt loss were analyzed from each colon of control (n=6) and ColVIcre-Kif3aflx/flx (n=6) mice. Mean cell numbers were scored as low (&lt;500 cells/mm2) or high (&gt;500 cells/mm2)."
NCBI gene IDs:
"ColVI: 12835///12834///12833///245026///665033///68553
cre: 2777477
Kif3a: 16568"
Figure legend: "Elevated numbers of IL-6-expressing F4/80+ macrophages in ColVIcre-Kif3aflx/flx mice treated with DSS as described in Figure 4A. At least 5 fields in the regions of crypt loss were analyzed. Scale bar represent 100 µm. *p&lt;0,05 was calculated by chi-squared test."
NCBI gene IDs:
"ColVI: 12835///12834///12833///245026///665033///68553
cre: 2777477
Kif3a: 16568"
Figure legend: "(E) Quantification of different phenotypes manifesting after RNA interference in comparison to control animals: MN2a axons projecting to the MHE muscle, representing the wild-type (wt) innervation pattern (magenta); MN2a axons projecting to muscles other than the MHE termed abnormal innervation (light grey); abnormal synaptic morphologies at MN2a derived axon terminals termed terminal defects (dark grey). Note, each genetic experiment was performed in parallel to an adequate control experiment using the same driver line crossed to a line that controls expression of either UAS-RFP or UAS-GFPRNAi. Each experiment was performed in triplicates, innervation rates were calculated from n=56 for elav&gt;RFP, n=21 for elav&gt;DfdRNAi, n=10 for elav&gt;hthRNAi and n=7 for elav&gt;mirrRNAi. In the case of Dfd knock-down, two different driver lines were used, the pan-neural elav-GAL4 and the motoneuron-specific OK6-GAL4 drivers, respectively. Both result in similar phenotypes, highlighting that the elav-GAL4 driven effects are specific to MNs. p-values between two genetic conditions were calculated by a two-sided Fisher test. ***: p &lt; 0.005."
NCBI gene IDs:
"GFP: 
RFP: 
Dfd: 40832
elav: 31000
GAL4: 855828
hth: 41273
mirr: 39441"
Figure legend: "(B) Representative confocal images of stage 17 embryonic heads highlighting the expression of Dfd (purple), Myosin in muscles (blue) and FasII in axonal projections (green) in control (elav&gt;RFP) animals and animals mis-expressing the Hox TFs Lab, Dfd and Scr by means of the elav-GAL4 driver. A zoom on the projections (FasII staining) of MN2a and MN3 to the MHE and MHD muscles of an early stage 17 Drosophila embryo are shown. Asterisks highlight the location of MN2a and MN3, respectively. MN2a is identified by the FasII expressing axonal projection emerging from a Dfd expressing MN, which normally innervates the Dfd expressing MHE muscle (as shown in the elav&gt;RFP control), while MN3 is identified as the MN underneath MN2a, which normally innervates the MHD muscle (as shown in the elav&gt;RFP control). The panel on the right side represents a schematic drawing of the confocal image shown on the left side, summarizing the innervation of the anterior muscles (LR, MHE, MHD) by projections emerging from MN2a (magenta) or MN3 (cyan) in control and mis-expression conditions."
NCBI gene IDs:
"RFP: 
Dfd: 40832
elav: 31000
GAL4: 855828
Lab: 40817
Scr: 40833"
Figure legend: "(A) Representative confocal images of stage 17 embryonic heads highlighting the expression of Myosin in muscles (blue) and FasII in axonal projections (green) in control (elav&gt;RFP) animals and in animals with reduced neuronal DIPkappa (elav&gt;DIPkappaRNAi) as well as in animals, which mis-express DIPgamma or dpr1 in neuronal cells (elav&gt;DIPgamma, elav&gt;dpr1). Single channels focusing on the projections (FasII staining) of MN2a and/or MN3 to the MHE, MHD or LR muscles of an early stage 17 Drosophila embryo are shown. Asterisks highlight the location of MN2a and MN3, respectively. MN2a is identified by the FasII expressing axonal projection emerging from a Dfd expressing MN, which normally innervates the Dfd expressing MHE muscle (as shown in the elav&gt;RFP control), while MN3 is identified as the MN underneath MN2a, which normally innervates the MHD muscle (as shown in the elav&gt;RFP control). The panel on the right represents a schematic drawing of the confocal images shown on the left side, summarizing the innervation of the anterior muscles (LR, MHE, MHD) by projections emerging from MN2a (magenta) or MN3 (cyan) in control and mis-expression conditions."
NCBI gene IDs:
"RFP: 
DIPgamma: 43417
DIPkappa: 318958
dpr1: 2768858
elav: 31000"
Figure legend: "(A) Representative confocal images of stage 17 embryonic heads highlighting the expression of Dfd (purple), Myosin in muscles (blue) and FasII in axonal projections (green) in control (elav&gt;RFP) animals and in animals with reduced Dfd expression in neurons (elav&gt;DfdRNAi) or in muscles (Mef2&gt;DfdRNAi) or both in both tissues (elav;Mef2&gt;DfdRNAi). The single channels for the projections (FasII staining) of MN2a and/or MN3 to the MHE, MHD or LR muscles of an early stage 17 Drosophila embryo are shown. Asterisks highlight the location of MN2a and MN3, respectively. MN2a is identified by the FasII expressing axonal projection emerging from a Dfd expressing MN, which normally innervates the Dfd expressing MHE muscle (as shown in the elav&gt;RFP control), while MN3 is identified as the MN underneath MN2a, which normally innervates the MHD muscle (as shown in the elav&gt;RFP control). The panel on the right side represents a schematic drawing of the confocal image shown on the left side, summarizing the innervation of the anterior muscles (LR, MHE, MHD) by projections emerging from MN2a (magenta) or MN3 (cyan) in control and perturbation conditions."
NCBI gene IDs:
"RFP: 
Dfd: 40832
elav: 31000
Mef2: 36032"
Figure legend: "Restoration of glucoseuptake or Akt signaling suppresses the thermogenic defect in AdRiKO mice. (A) HKII mRNA expression level in BAT of AdRiKO and control mice infected with either AAV9-HKII or AAV9-empty (n=8/group)."
NCBI gene IDs:
"HKII: 15277"
Figure legend: "(B) Cold-induced 2-Deoxyglucose-6-phosphate (2DG6P) accumulation in BAT of AdRiKO and control mice infected with either AAV9-HKII or AAV9-empty housed at 4°C for 4h (n=8/group)."
NCBI gene IDs:
"HKII: 15277"
Figure legend: "(C) Body temperature of AdRiKO and control mice infected with either AAV9-HKII or AAV9-empty housed at 22°C (n=8/group)."
NCBI gene IDs:
"HKII: 15277"
Figure legend: "(D) Body temperature upon cold exposure of AdRiKO and control mice infected with either AAV9-HKII or AAV9-empty. The left panel represents body temperature after each hour of cold exposure while the right panel represents body temperature as a bar graph for the 3h cold exposure time point (n=8/group). a=significant difference between AdRiKO and control mice infected with AAV9-empty, b= significant difference between AdRiKO and control mice infected with AAV9-HKII, d= significant difference between AdRiKO mice infected with AAV9-empty and AAV9-HKII."
NCBI gene IDs:
"HKII: 15277"
Figure legend: "(E) Immunoblot analysis of BAT from AdRiKO and control mice infected with either AAV8-Akt2S474D or AAV8-empty (n=6/group, each lane represents a mix of 3 mice)."
NCBI gene IDs:
"Akt2: 11652"
Figure legend: "(F) Body temperature of AdRiKO and control mice infected with either AAV8-Akt2S474D or AAV8-empty housed at 22°C (n=11/group)."
NCBI gene IDs:
"Akt2: 11652"
Figure legend: "(G) Body temperature upon cold exposure of AdRiKO and control mice infected with either AAV8-Akt2S474D or AAV8-empty. The left panel represents body temperature after each hour of cold exposure while the right panel represents body temperature as a bar graph for the 3h cold exposure time point (n=11/group). a=significant difference between AdRiKO and control mice infected with AAV8-empty, b= significant difference between AdRiKO and control mice infected with AAV8-Akt2S474D, d= significant difference between AdRiKO mice infected with AAV8-empty and AAV8-Akt2S474D."
NCBI gene IDs:
"Akt2: 11652"
Figure legend: "(H) Cold-induced 2-Deoxyglucose-6-phosphate (2DG6P) accumulation in BAT of AdRiKO and control mice infected with either AAV8-Akt2S474D or AAV8-empty housed at 4°C for 4h (n=7 (control AAV8-null), n=6 (AdRiKO AAV8-null), n=6 (control AAV8-AktS474D), n=6 (AdRiKO AAV8-AktS474D)). Data represent mean ± SEM. Statistically significant differences between AdRiKO and control mice were determined with unpaired Student's t-test and are indicated with asterisks (*=p&lt;0.05; **=p&lt;0.01, ***=p&lt;0.001). Statistically significant differences between viruses were determined with unpaired Student's t-test and are indicated with a number sign (#=p&lt;0.05; ##=p&lt;0.01; ###=p&lt;0.001). The exact p-value for each significant difference can be found in Appendix Table S2."
NCBI gene IDs:
"Akt2: 11652"
Figure legend: "A-F Shown are hypocotyl  lengths of cRL-grown 4-day-old seedlings of toc1  complemented with wild-type TOC1 (A), 5X (B), T135A (C), S175A (D) driven by TOC1 native promoter and wild-type TOC1 (E), 5X (F) driven by 35S  promoter at sequential fluent rates. Different letters indicate statistically significant differences between genotypes (p&lt;0.01, one-way ANOVA followed by Tukey-Kramer HSD test), error bars indicate SEM. Data are representative of three biological trials with similar results."
NCBI gene IDs:
"toc1: 836259
TOC1: 836259"
Figure legend: "Hypocotyl lengths in SD condition of Col-0, toc1-101 and two independent native or 35S promoter lines of wild-type  TOC1 and each phosphosite mutants. The middle line of the box represents the median, the x in the box represents the mean. The bottom line and the top line of the box represent 1st and 3rd quartile, respectively. The whiskers extend from the ends of the box to the minimum value and maximum value. Data information: 18 to 27 seedlings  per line were entrained in 12h/12h light/dark cycles for 7 d and next transferred to constant red light at ZT2 for image acquisition with 2-h intervals for 1 week."
NCBI gene IDs:
"toc1: 836259
TOC1: 836259"
Figure legend: "C-E, Average CCA1:LUC bioluminescence traces of indicated plant lines. Data information: 18 to 27 seedlings per line were entrained in 12h/12h  light/dark cycles for 7 d and next transferred to constant red light at ZT2 for image acquisition with 2-h intervals for 1 week. White and gray regions indicate subjective  light and  dark  period. Data are representative of at least two independent trials with similar results. Different letters indicate statistically significant differences in period between genotypes (p&lt;0.01, one-way ANOVA followed by Tukey-Kramer HSD test)."
NCBI gene IDs:
"LUC: 
CCA1: 819296"
Figure legend: "A-C, PIL1, AT5G02580 and CDF5 expression pattern in 3-d-old SD-grown seedlings from indicated plant lines at night. Data is representative of 3 biological trials."
NCBI gene IDs:
"CDF5: 843293
AT5G02580: 831095
PIL1: 819311"
Figure legend: "C,  ChIP-qPCR assay of TOC1 binding  to promoter of pre-dawn-phased PIF3 target genes at ZT14 in  Col-0, native promoter TOC1 and 5X lines. D, ChIP-qPCR  assay of the chromatin residence of native promoter TOC1-GFP at target promoters in  toc1 vs. pif3/4/5 toc1 (pif345t1) mutant backgrounds. Data information: 3-d-old SD-grown  seedlings were harvested at ZT14, TOC1-GFP was  immunoprecipitated by α-GFP and magnetic protein G beads. Data from 3 independent trials were averaged, error bars indicate SEM. Asterisks indicates significant differences (** p&lt;0.001, *** p&lt;0.0001, Student's t test), n.s=not significant."
NCBI gene IDs:
"PIF3: 837479
pif3: 837479
toc1: 836259
TOC1: 836259"
Figure legend: "B, Measurement of TOC1-GFP protein turn-over in  TOC1, 5X, T135A, S175A native promoter lines by cycloheximide  (CHX) treatment. 10-d-old seedlings grown in 12h/12h light/dark cycles were subject to cycloheximide (CHX) or  ethanol (Mock) treatment for indicated  time length. Data from 3 independent trials were fitted to non-linear Weibull regression curves. Data information: TOC1  protein was detected by α-GFP, ADK  was used as loading control. TOC1/ADK ratio was calculated by the intensities of TOC1-GFP bands normalized by the intensities of ADK  bands using ImageJ."
NCBI gene IDs:
"TOC1: 836259"
Figure legend: "C, ChIP-qPCR assay of native promoter driven  TOC1-GFP and 5X-GFP's residence at target promoters in toc1 vs. nf-yc3/4/9 toc1 (c349t1) mutants. 3-d-old SD-grown  seedlings were harvested at ZT14, TOC1  and 5X were immunoprecipitated by α-GFP  and magnetic protein G beads. Data from 3 independent trials were averaged. Error bars indicate SEM, asterisks indicate significant differences (* p&lt;0.05, *** p&lt;0.0001, Student's t test), n.s= not significant."
NCBI gene IDs:
"nf-yc3: 841922
toc1: 836259"
Figure legend: "E, Expression of  PIL1, AT5G02580 and CDF5 in 3-d-old SD-grown  seedlings at ZT18. Data from 3 independent experiments were averaged. Error bars indicate SEM. Different letters denote statistically significant differences based on Wilcoxon test (p&lt;0.05)."
NCBI gene IDs:
"CDF5: 843293
AT5G02580: 831095
PIL1: 819311"