EMBO/SourceData huggingface dataset:
Figure legend: " (C) Quantification of Smc5 sumoylated species in pull downs from the indicated smc5-KE mutants, relative to wild-type controls from at least three independent experiments. Boxes, 25-75% data range; whiskers, total data range; black bar, median; grey cross, mean. ****P &lt; 0.0001; ***P&lt;0.001; **P &lt; 0.01; *P&lt;0.05. 1-way ANOVA, n = number of samples analyzed "
NCBI gene IDs:
"smc5: 854123"
Figure legend: " (D) Co-immunoprecipitation analysis of the Smc5-Nse2 interactions. NSE2-6HA cells were transformed with centromeric plasmids expressing the indicated SMC5 alleles, and protein extracts from exponentially growing cells subjected to anti-HA immunoprecipitation. A strain with no HA tag was used as control "
NCBI gene IDs:
"NSE2: 856695
SMC5: 854123"
Figure legend: " (E) Same as in (D), but using SMC6-6HA cells "
NCBI gene IDs:
"SMC6: 851099"
Figure legend: "A, Seedlings  of WT, abs3-1D, FD11-55, and arf2-20 before and after 6 d C-deprivation. B, Seedlings  of WT, abs3-1D, FD18-70, and pif5-10 before and after 6 d C-deprivation."
NCBI gene IDs:
"abs3: 829035
arf2: 836321
pif5: 825075"
Figure legend: "C and D, RT-qPCR  analysis of ABS3  expression levels in 7-d-old seedlings  of the same genotypes as shown in A (C) and B (D). Fold changes were calculated with respect to the expression level in the WT. two-tailed t test, ****, p&lt;0.0001, n.s., not significant. data are means ± standard deviation (s.d.) of 3 biological replicates."
NCBI gene IDs:
"ABS3: 829035"
Figure legend: "G and H, RT-qPCR analysis of ORE1  and SGR1  expression levels in genotypes shown in A (G) and B (H) before and after 4 d C-deprivation. Fold changes were calculated with respect to the expression level in the WT before C-deprivation. data are means ± standard deviation (s.d.) of 3 biological replicates."
NCBI gene IDs:
"ORE1: 833957
SGR1: 824589"
Figure legend: "C, Heatmap of log2FC values of 2,587 ABS3-regulated genes (abs3-1D vs. WT) under C-deprivation  in indicated comparisons."
NCBI gene IDs:
"ABS3: 829035
abs3: 829035"
Figure legend: "F, Heatmap of log2FC values of 1,326 ARF2, PIF5, and C-deprivation co-regulated genes in indicated comparisons. C-deprivation: abs3-1D 4 d C-deprivation  vs. abs3-1D 0 d C-deprivation; ARF2: abs3-1D vs. arf2-20 abs3-1D after 4 d C-deprivation; PIF5: abs3-1D vs. abs3-1D pif5-10 after 4 d  C-deprivation. Enlarged were expression  changes of senescence genes identified in DAVID GO analysis"
NCBI gene IDs:
"abs3: 829035
ARF2: 836321
arf2: 836321
PIF5: 825075
pif5: 825075"
Figure legend: "D,  Co-immunoprecipitation  of ARF2-HA  with PIF5-GFP  in vivo. ARF2-HA  was coexpressed with PIF5-GFP  or GFP  alone in protoplasts. Proteins co-immunoprecipitated  by GFP-Trap beads were immunoblotted  with anti-GFP  and anti-HA  antibodies."
NCBI gene IDs:
"GFP: 
HA: 
ARF2: 836321
PIF5: 825075"
Figure legend: "A, Seedlings  of WT, pARF2:ARF2-GFP  OEs in the WT background, pif4-2 pif5-10, and pARF2:ARF2-GFP  OEs in the pif4-2 pif5-10 background before and after 6 d C-deprivation."
NCBI gene IDs:
"GFP: 
ARF2: 836321
pif4: 818903
pif5: 825075"
Figure legend: "B,  RT-qPCR analysis of ARF2   expression levels in 7-d-old seedlings   of the same genotypes as shown in A. Fold changes were calculated with respect to the expression level in the WT. data are means ± s.d. of 3 biological replicates."
NCBI gene IDs:
"ARF2: 836321"
Figure legend: "D, Seedlings  of WT, pPIF5:PIF5-GFP  OEs in the WT background, arf2-20, and pPIF5:PIF5-GFP  OEs in the arf2-20 background before and after 6 d C-deprivation."
NCBI gene IDs:
"GFP: 
arf2: 836321
PIF5: 825075"
Figure legend: "E,  RT-qPCR analysis of PIF5  expression levels in 7-d-old seedlings  of the same genotypes as shown in D. Fold changes were calculated with respect to the expression level in the WT. data are means ± s.d. of 3 biological replicates."
NCBI gene IDs:
"PIF5: 825075"
Figure legend: "G, Seedlings  of WT, arf2-20, pif5-10, and arf2-20 pif5-10 before and after 12 d C-deprivation."
NCBI gene IDs:
"arf2: 836321
pif5: 825075"
Figure legend: "I, Seedlings of WT, abs3-1D, arf2-20 abs3-1D, pif5-10 abs3-1D, and arf2-20 pif5-10 abs3-1D before and after 8 d C-deprivation."
NCBI gene IDs:
"abs3: 829035
arf2: 836321
pif5: 825075"
Figure legend: "C, ChIP-qPCR  analysis of ARF2-GFP binding  to the promoters of ORE1  and SGR1  in the WT and pif4-2 pif5-10 backgrounds. In C fold enrichments were calculated with respect to the input. PP2A  served as a non-binding  control. Data are means ± s.d. of 3 technical replicates. two-tailed t test, n.s., not significant, ****, p&lt;0.0001. The experiment has been independently repeated with similar results."
NCBI gene IDs:
"ORE1: 833957
pif4: 818903
pif5: 825075
PP2A: 843333
SGR1: 824589"
Figure legend: "D, RT-qPCR analysis of ORE1  and SGR1  expression levels in seedlings  of WT, pARF2:ARF2-GFP  OEs in the WT background, pif4-2 pif5-10, and pARF2:ARF2-GFP  OEs in the pif4-2 pif5-10 background before and after 4 d C-deprivation. Fold changes were calculated with respect to the expression level in the WT before C-deprivation. In D data are means ± s.d. of 3 biological replicates. Data are means ± s.d. of 3 technical replicates. two-tailed t test, n.s., not significant, ****, p&lt;0.0001. The experiment has been independently repeated with similar results."
NCBI gene IDs:
"GFP: 
ARF2: 836321
ORE1: 833957
pif4: 818903
pif5: 825075
SGR1: 824589"
Figure legend: "E, ChIP-qPCR  analysis of PIF5-GFP binding  to the promoters of ORE1  and SGR1  in the WT and arf2-20 backgrounds. In fold enrichments were calculated with respect to the input. PP2A  served as a non-binding  control. Data are means ± s.d. of 3 technical replicates. two-tailed t test, n.s., not significant, ****, p&lt;0.0001. The experiment has been independently repeated with similar results."
NCBI gene IDs:
"arf2: 836321
ORE1: 833957
PP2A: 843333
SGR1: 824589"
Figure legend: "F, RT-qPCR  analysis of ORE1  and SGR1  expression levels in seedlings  of WT, pPIF5:PIF5-GFP  OEs in the WT background, arf2-20, and pPIF5:PIF5-GFP  OEs in the arf2-20 background before and after 4 d C-deprivation. Fold changes were calculated as in D. In F, data are means ± s.d. of 3 biological replicates. Data are means ± s.d. of 3 technical replicates. two-tailed t test, n.s., not significant, ****, p&lt;0.0001. The experiment has been independently repeated with similar results."
NCBI gene IDs:
"GFP: 
arf2: 836321
ORE1: 833957
PIF5: 825075
SGR1: 824589"
Figure legend: "G, Hypocotyl  elongation in seedlings  of WT, pPIF5:PIF5-GFP  OEs in the WT background, arf2-20, and pPIF5:PIF5-GFP  OEs in the arf2-20 background. Seedlings  were grown under continuous light for one week."
NCBI gene IDs:
"GFP: 
arf2: 836321
PIF5: 825075"
Figure legend: "H, RT-qPCR  analysis of PIL1  and YUC8  expression levels in seedlings  shown in G. Fold changes were calculated with respect to the expression level in the WT. Color legends in H are the same as in F. In H, data are means ± s.d. of 3 biological replicates. Data are means ± s.d. of 3 technical replicates. two-tailed t test, n.s., not significant, ****, p&lt;0.0001. The experiment has been independently repeated with similar results."
NCBI gene IDs:
"PIL1: 819311
YUC8: 828993"
Figure legend: "J, ChIP-qPCR  analysis of PIF5 binding  to the promoters of PIL1  and YUC8  in the WT and arf2-20 backgrounds. In J, fold enrichments were calculated with respect to the input. PP2A  served as a non-binding  control. Data are means ± s.d. of 3 technical replicates. two-tailed t test, n.s., not significant, ****, p&lt;0.0001. The experiment has been independently repeated with similar results."
NCBI gene IDs:
"arf2: 836321
PIL1: 819311
PP2A: 843333
YUC8: 828993"
Figure legend: "A, RT-qPCR analysis of ARF2  expression levels in 7-d-old seedlings  of WT, pARF2:ARF2-GFP  OEs in the WT background, mateq, and pARF2:ARF2-GFP  OEs in the mateq  background. Fold changes were calculated with respect to the expression level in the WT. B, RT-qPCR analysis of PIF5  expression levels in 7-d-old seedlings  of WT, pPIF5:PIF5-GFP  OEs in the WT background, mateq, and pPIF5:PIF5-GFP  OEs in the mateq  background. Fold changes were calculated as in A. In A, B, data are means ± s.d. of 3 biological replicates."
NCBI gene IDs:
"GFP: 
ARF2: 836321
PIF5: 825075"
Figure legend: "G and H, RT-qPCR analysis of ORE1  and SGR1  expression levels in genotypes shown in A (G) and B (H) before and after 4 d C-deprivation. Fold changes were calculated with respect to the expression level in the WT before  C-deprivation. Color legends in G are the same as in A. Color legends in are the same as in B. data are means ± s.d. of 3 biological replicates."
NCBI gene IDs:
"ORE1: 833957
SGR1: 824589"
Figure legend: "I,  RT-qPCR  analysis of PIL1  and YUC8  expression levels in 7-d-old seedlings  of the same genotypes as shown in B. Fold changes were calculated as in A. Color legends in I are the same as in B. data are means ± s.d. of 3 biological replicates."
NCBI gene IDs:
"PIL1: 819311
YUC8: 828993"
Figure legend: "B, ChIP-qPCR  analysis of ARF2-GFP binding  to the promoters of ABS3. Fold enrichments were calculated with respect to the input. PP2A  served as a non-binding control. Data are means ± s.d. of 4 technical replicates. The experiment has been independently repeated 3 times with similar results."
NCBI gene IDs:
"ABS3: 829035
PP2A: 843333"
Figure legend: "C, pABS3:GFP  or pABS3∆S2:GFP was expressed in WT mesophyll protoplasts with or without p35S:ARF2-HA. p35S:mCherry  was co-transfected and served as a transfection control. Protoplasts  were examined with fluorescence microscopy. Experiments were independently repeated 3 times with similar results. Bars, 100 μm. D, Dot plots of GFP  relative fluorescence intensity in protoplasts  expressing WT and mutant forms of pABS3:GFP  with or without p35S:ARF2-HA. Data are median with interquartile range, n is indicated in parentheses, two-tailed Mann-Whitney test, n.s., not significant, ****, p&lt;0.0001."
NCBI gene IDs:
"mCherry: 
GFP: 
HA: 
ABS3: 829035
ARF2: 836321"
Figure legend: "E, RT-qPCR  analysis of ABS3  expression levels in 7-d-old seedlings  of WT, pARF2:ARF2-GFP  OEs in the WT background, pif4-2 pif5-10, and pARF2:ARF2-GFP  OEs in the pif4-2 pif5-10 background. Fold changes were calculated with respect to the expression level in the WT. Data are means ± s.d. of 3 biological replicates."
NCBI gene IDs:
"GFP: 
ABS3: 829035
ARF2: 836321
pif4: 818903
pif5: 825075"
Figure legend: "A In-vitro cell survival assay of HGSOC cell lines upon stable RAD51 overexpression. Mean with standard deviation is shown of at least three biological replicates per point. Extra-sum-of-squares F test."
NCBI gene IDs:
"RAD51: 5888"
Figure legend: "B In-vitro colony forming assays comparing RAD51-overexpressing and control HGSOC cell line, Caov-3, after treatment with increasing doses of carboplatin. Mean and SD of four biological replicates (left) a representative experiment (right). P-value for a comparison between cell lines for each drug treatment condition is indicated above the bars. T-test."
NCBI gene IDs:
"RAD51: 5888"
Figure legend: "Whole cell extracts of High Five insect cells individually expressing FLAG-SHLD3, Strep-RIF1, and 6xHis-REV7 through baculovirus infection were combined and subjected to FLAG immunoprecipitation or streptactin pulldown and immunoblotted for REV7 or the Strep or FLAG epitopes. Results are representative of three biologically independent experiments. IB: immunoblot, FL: full-length. For SHLD3, N and C correspond to residues 1-125 and 126-250, respectively."
NCBI gene IDs:
"FLAG: 
His: 
Strep: 
REV7: 10459
RIF1: 55183
SHLD3: 112441434"
Figure legend: "Representative micrographs of the LacR/LacO assay using mCherry-LacR-RIF1N as bait to evaluate chromatin recruitment of eGFP-tagged SHLD3 variants. SHLD3: residues 2-250. SHLD3N: residues 2-125. SHLD3C: residues 126-250. RIF1N: residues 1-967."
NCBI gene IDs:
"mCherry: 
SHLD3: 
RIF1: 55183
SHLD3: 112441434"
Figure legend: "Quantification of LacR/LacO assay measuring chromatin recruitment of eGFP-tagged SHLD3 variants to LacO arrays by mCherry-LacR-RIF1N. GFP intensities are presented as a ratio between the average fluorescence intensity within the mCherry-labeled LacR focus and the average nuclear intensity. Bars represent means (n = 138, 126, 129, 137 for eGFP, eGFP-SHLD3, eGFP-SHLD3N, eGFP-SHLD3C from 3 biologically independent experiments). Analysis was performed by Kruskal-Wallis test followed by Dunn's multiple comparisons against empty vector control or full-length eGFP-SHLD3. ****: P &lt; 0.0001. ns: P &gt; 0.05."
NCBI gene IDs:
"eGFP: 
mCherry: 
SHLD3: 112441434"
Figure legend: "Representative micrographs of the LacR-FokI assay to evaluate DNA damage recruitment of eGFP-tagged SHLD3 variants after induction of LacR-FokI expression."
NCBI gene IDs:
"eGFP: 
FokI: 
SHLD3: 112441434"
Figure legend: "Quantification of LacR-FokI assay evaluating recruitment of eGFP-tagged SHLD3 variants to FokI-induced DSBs at LacO arrays. GFP intensities are presented as a ratio between the average fluorescence intensity within the mCherry-labeled LacR-FokI focus and the average nuclear intensity. Bars represent mean (n = 143, 147, 147, 141 for eGFP, eGFP-SHLD3, eGFP-SHLD3N, eGFP-SHLD3C from 3 biologically independent experiments). Analysis was performed by Kruskal-Wallis test followed by Dunn's multiple comparisons against empty vector control or full-length eGFP-SHLD3. ****: P &lt; 0.0001. ns: P &gt; 0.05."
NCBI gene IDs:
"eGFP: 
FokI: 
mCherry: 
SHLD3: 112441434"
Figure legend: "Whole cell extracts of High Five insect cells individually expressing the wild-type (WT) or indicated alanine substitution FLAG-SHLD3C (residues 126-250) variants and Strep-RIF1N (residues 1-980) through baculovirus infection were combined and subjected to FLAG immunoprecipitation or streptactin pulldown and immunoblotted for the Strep or FLAG epitopes. The results are representative of two biologically independent experiments. IB: immunoblot. IP: immunoprecipitation."
NCBI gene IDs:
"FLAG: 
Strep: 
RIF1: 55183
SHLD3: 112441434"
Figure legend: "Quantification of LacR/LacO assay measuring recruitment of eGFP-SHLD3C wild-type (WT) or alanine substitution variants to LacO arrays in U2OS 2-6-3 cells by mCherry-LacR-RIF1N. GFP intensities are presented as a ratio between the average fluorescence intensity within the mCherry-labeled LacR-RIF1N focus and the average nuclear intensity. Bars represent means (n = 134, 125, 120, 130, 104, 129, 117 for EV, WT, S131A, W132A, R166A, N201A, D216A from 3 biologically independent experiments). EV: empty vector. Analysis was performed by Kruskal-Wallis test followed by Dunn's multiple comparisons against empty vector and WT controls. ****: P &lt; 0.0001. ***: P = 0.0004. **: P = 0.002. *: P = 0.02. ns: P &gt; 0.05."
NCBI gene IDs:
"eGFP: 
mCherry: 
RIF1: 55183
SHLD3: 112441434"
Figure legend: "Quantification of LacR-FokI assay measuring recruitment of eGFP-SHLD3C wild-type (WT) or alanine substitution variants to sites of DNA double-strand breaks induced by mCherry-LacR-FokI in U2OS 2-6-3 cells. GFP intensities are presented as a ratio between the average fluorescence intensity within the mCherry-labeled LacR-FokI focus and the average nuclear intensity. Bars represent means (n = 103, 136, 159, 151, 139, 145, 140 for EV, WT, S131A, W132A, R166A, N201A, D216A from 3 biologically independent experiments). Analysis was performed by Kruskal-Wallis test followed by Dunn's multiple comparisons against empty vector and WT controls. ****: P &lt; 0.0001. ns: P &gt; 0.05."
NCBI gene IDs:
"eGFP: 
FokI: 
mCherry: 
SHLD3: 112441434"
Figure legend: "Representative micrographs of immunofluorescence experiments (from 3 biologically independent experiments) analyzing localization of SHLD3 to 53BP1 bodies in RPE SHLD3-KO cells. 3xFLAG-SHLD3-complemented RPE SHLD3-KO cells were treated with 200 nM aphidicolin (Aphi) for 24 h and processed for immunofluorescence microscopy using antibodies against 53BP1, FLAG, and cyclin A. 53BP1 bodies are defined as distinct foci visible in cyclin A-negative cells. Quantification of FLAG and 53BP1 colocalization from A performed in CellProfiler. Pearson's correlation coefficients (PCC) were calculated for pixels within each cyclin A-negative, 53BP1 body-positive nucleus between the 53BP1 and FLAG channels. Each point represents the PCC value of an individual nucleus. Bars represent means. (n = 120, 130 for EV, SHLD3 from three biologically independent experiments). Analysis was performed using two-tailed Mann-Whitney test. ****: P &lt; 0.0001."
NCBI gene IDs:
"FLAG: 
SHLD3: 112441434"
Figure legend: "Representative micrographs of immunofluorescence experiments analyzing localization of FLAG-SHLD3 alanine substitution variants stably expressed in RPE SHLD3-KO cells by lentivirus transduction. Cells were treated with 200 nM Aphi for 24 hours and processed for immunofluorescence microscopy using antibodies raised against 53BP1, FLAG, and cyclin A. 53BP1 bodies are defined as distinct foci visible in cyclin A-negative cells."
NCBI gene IDs:
"FLAG: 
SHLD3: 112441434"
Figure legend: "Quantification of the percentage of cells containing the indicated number of 53BP1 bodies in RPE WT and SHLD3-KO cells with or without 24-hour 200 nM Aphi treatment. Bars represent means ± s.d. (n = 3 biologically independent experiments with ≥ 30 nuclei imaged each)."
NCBI gene IDs:
"SHLD3: 112441434"
Figure legend: "Left: Representation of the region of the RIF1 N-terminal HEAT repeats that is predicted to bind the SHLD3 eIF4E-like domain. Residues 1-173 are highlighted. Right: Quantification of LacR/LacO assay measuring eGFP-SHLD3 recruitment to LacO arrays in U2OS 2-6-3 cells by the indicated truncated mCherry-LacR-RIF1N variants. GFP intensities are presented as a ratio between the average fluorescence intensity within the mCherry-labeled LacR-RIF1N focus and the average nuclear intensity. Bars represent means (n = 148, 123, 122 for EV, 1-567, 174-567 from 3 biologically independent experiments). Analysis was performed using Mann-Whitney two-tailed test. ****: P &lt; 0.001."
NCBI gene IDs:
"GFP: 
mCherry: 
RIF1: 55183"
Figure legend: "Whole cell extracts of High Five insect cells individually expressing the FLAG-SHLD3C (residues 126-250) and the indicated alanine substitution Strep-RIF1 (residues 1-980) variants through baculovirus infection were combined and subjected to FLAG immunoprecipitation or streptactin pulldown and immunoblotted for the Strep or FLAG epitopes. The results are representative of two biologically independent experiments. IB: immunoblot. IP: immunoprecipitation."
NCBI gene IDs:
"FLAG: 
RIF1: 55183
SHLD3: 112441434"
Figure legend: "Representative micrographs of UV laser microirradiation experiments measuring DNA damage recruitment of REV7 in U2OS 2-6-3 cells with endogenously mutated RIF1. DNA damage was induced in U2OS 2-6-3 cells through irradiation in the form of linear stripes and analyzed by immunofluorescence microscopy with RIF1 and REV7 antibodies. Quantification of UV laser microirradiation immunofluorescence experiment measuring DNA damage recruitment of REV7 in U2OS 2-6-3 cells with endogenously mutated RIF1. REV7 immunofluorescence intensities are presented as a ratio between the average fluorescence intensity within the RIF1-labeled irradiation stripe and the average nuclear intensity. Only nuclei containing RIF1 stripes are quantified. Bars represent means (n = 206, 215 for RIF1WT, RIF1D28N from 2 biologically independent experiments). Analysis was performed using Welch's t-test. ****: P &lt; 0.0001."
NCBI gene IDs:
"RIF1: 55183"
Figure legend: "Quantification of class switch recombination in stimulated CH12F3 Shld3-/- cells stably expressing the indicated FLAG-SHLD3 variants through lentiviral transduction. Bars represent means ± s.d., n = 3 biologically independent experiments. Analysis was performed using one-way ANOVA followed by Dunnett's multiple comparisons test against Shld3-/- cells complemented with wild-type SHLD3. **: P &lt; 0.01, *: P &lt; 0.05, ns: P &gt; 0.05."
NCBI gene IDs:
"FLAG: 
Shld3: 113002583
SHLD3: 112441434"
Figure legend: "Competitive growth assay of RPE BRCA1-KO SHLD3-KO cells complemented with 3xFLAG-SHLD3 variants. Growth of the indicated eGFP-expressing cells were compared to mCherry-expressing RPE BRCA1-KO SHLD3-KO cells transduced with empty vector after mixing 1:1 in 24-well plates. Plates were imaged 1, 5, 9, and 13 days after plating. Dotted black lines represent an eGFP:mCherry ratio of 1. Points represent means ± s.d. (n = 3 biologically independent experiments). Analysis was performed using a one sample t-test against a hypothetical eGFP:mCherry ratio value of 1 for the day 13 time point. **: P &lt; 0.01, ns: P &gt; 0.05."
NCBI gene IDs:
"eGFP: 
FLAG: 
mCherry: 
BRCA1: 672
SHLD3: 112441434"
Figure legend: "D Recombinant ALFY (aa 2981-3526) was incubated with GST‐Atg8 proteins conjugated to glutathione Sepharose. The pulled‐down complexes were subjected to SDS-PAGE and anti‐ALFY and anti‐GST immunoblotting. 5% of the recombinant ALFY protein used was loaded as input. Data are representative of three independent experiments."
NCBI gene IDs:
"ALFY: 23001"
Figure legend: "B 35S−labelled in vitro−translated GFP−ALFY (aa 2981-3526) wild−type and different LIR mutants were incubated with GST−GABARAP or −LC3C and binding evaluated by ARG. 10 and 2% of the in vitro−translated proteins used were loaded to illustrate binding affinity. CBB staining shows equal amounts of GST proteins used. Data are representative of three independent experiments."
NCBI gene IDs:
"ALFY: 23001"
Figure legend: "C MBP, MBP−ALFY (aa 3255-3526) or the ALFY−LIR mutant (F3346A) conjugated to amylose resins was incubated in the absence or presence of purified GABARAP. The pulled−down complexes were subjected to SDS-PAGE and visualized by CBB staining. Data are representative of three independent experiments."
NCBI gene IDs:
"ALFY: 23001"
Figure legend: "D GFP−LC3B and GFP−LC3B (Q26K/H27Y/H57D) were immunoprecipitated with GFP−TRAP® from total cell lysate of stably transfected HeLa FlpIn cells, followed by SDS-PAGE and immunoblotting with the indicated antibodies. Data are representative of three independent experiments."
NCBI gene IDs:
"TRAP: 
LC3B: 81631"
Figure legend: "E MBP‐ALFY3255-3526 conjugated to amylose resin was incubated with GST or the indicated GABARAP mutants. The pulled‐down complexes were subjected to SDS-PAGE and visualized by immunoblotting with anti‐MBP and anti‐GABARAP antibodies. Data are representative of three independent experiments."
NCBI gene IDs:
"GABARAP: 11337"
Figure legend: "F MBP−tagged ALFY3255-3526 and p62168-391 or their corresponding LIR mutants (F3346A and W340A, respectively) were conjugated to amylose resin and incubated with purified GST, GABARAP, GABARAP mutant (K24Q/Y25H/D54H), LC3B or LC3B mutant (Q26K/H27Y/H57D). The bound proteins were visualized by immunoblotting with anti−GABARAP, anti−LC3 and anti−MBP antibodies. Data are representative of three independent experiments."
NCBI gene IDs:
"GABARAP: 11337
LC3B: 81631
p62: 8878"
Figure legend: "B GFP−tagged full−length ALFY wild−type or LC3−interacting region (LIR)−mutant was expressed into Alfy−deficient MEFs using an adenovirus system. At 48 h after infection, the MEFs were cultured in normal media or EBSS for 1.5 h before staining with anti−LC3B or anti−GABARAP antibodies. Scale bars 10 μm."
NCBI gene IDs:
"LC3: 67443///66734
ALFY: 72145
Alfy: 72145"
Figure legend: "C HeLa cells were treated with control or siRNA targeting GABARAP, GABARAPL1 and GABARAPL2. 72 h after transfection cells were immunostained with anti−LC3B, anti−ALFY and anti−p62 antibodies. Scale bars, 10 μm."
NCBI gene IDs:
"GABARAP: 11337
GABARAPL1: 23710
GABARAPL2: 11345"