EMBO/SourceData huggingface dataset:
Figure legend: "Representative confocal images of control (CTL-1) and OPA1S545R patient fibroblasts treated with OPA1, DNM1L, PGS1, and non-targeting (NT) siRNAs or indicated combinations for 72 hours. Mitochondria (anti-TOM40, green) and nuclei (DAPI, blue). Scale bar=20μm. Passages number between P10-15. Mitochondrial morphology quantification of (A) using control fibroblasts with fragmented (OPA1 siRNA), normal (non-targeting NT siRNA), and hypertubulated (DNM1L siRNA) mitochondria. Data represent mean ± SD of three independent experiments, One-way ANOVA (905-3695 cells per cell line), (% fragmented); ; ****p &lt; 0.0001, ns; not significant.."
NCBI gene IDs:
"TOM40: 
DNM1L: 10059
OPA1: 4976
PGS1: 9489"
Figure legend: "Representative confocal images of wild type (WT) and Opa1Crispr MEFs treated with NT or Pgs1 siRNA for 72 hours. Live imaging of mitochondria (mitoYFP, green) and nuclei (NucBlue, blue). Scale bar=10μm. Mitochondrial morphology quantification of (C) using WT MEFs treated with Opa1 siRNA (fragmented), NT siRNA (normal), or Dnm1l siRNA (hypertubulated) ground truth training sets. Data represent mean ± SD of three independent experiments, One-way ANOVA (6613-8758 cells per cell line), (% fragmented) ; ****p &lt; 0.0001, ns; not significant."
NCBI gene IDs:
"Dnm1l: 74006
Opa1: 74143
Pgs1: 74451"
Figure legend: "Representative confocal images of WT, Opa1Crispr MEFs complemented with pLenti-Opa1, Opa1CrisprPgs1Crispr MEFs and Pgs1Crispr MEFs complemented with pLenti-Pgs1 by lentiviral delivery. Live imaging of mitochondria (mitoYFP, green) and nuclei (NucBlue, blue). Scale bar=10μm. Supervised ML mitochondrial morphology quantification of (E) using WT MEFs treated with Opa1 siRNA (fragmented), NT siRNA (normal), or Dnm1l siRNA (hypertubulated) training sets. Data represent mean ± SD of three independent experiments, One-way ANOVA (691-3990 cells per cell line), (% fragmented) ; ****p &lt; 0.0001, ns; not significant.."
NCBI gene IDs:
"Crispr: 
Dnm1l: 74006
Opa1: 74143
Pgs1: 74451"
Figure legend: "Representative confocal micrographs of MEFs WT and Opa1Crispr MEFs treated with indicated siRNAs for 72 hours. Mitochondria (anti-TOM40, green) and nuclei (DAPI, blue). Scale bar=10μm. Supervised ML mitochondrial morphology quantification of (B) using WT MEFs with fragmented (Opa1 siRNA), normal (non-targetting NT siRNA), and hypertubular (Dnm1l siRNA) mitochondria. Data represent mean ± SD of three independent experiments, One-way ANOVA (726-4236 cells per cell line), (% fragmented); *** p &lt; 0.001, ****p &lt; 0.0001, ns; not significant."
NCBI gene IDs:
"Crispr: 
Dnm1l: 74006
Opa1: 74143"
Figure legend: "Representative confocal micrographs of MEFs WT, Pgs1Crispr and Dnm1lCrispr MEFs treated with indicated siRNAs for 72 hours. Mitochondria (anti-TOM40, green) and nuclei (DAPI, blue). Scale bar=10μm. Supervised ML mitochondrial morphology quantification of (G) using WT MEFs with fragmented (Opa1 siRNA), normal (non-targetting NT siRNA), and hypertubulated (Dnm1l siRNA) mitochondria. Data represent mean ± SD of &gt;3 independent experiments, (3096-7238 cells per cell line), One-way ANOVA (% fragmented) ; *p &lt; 0.05, ** p &lt; 0.01, ****p &lt; 0.0001, ns; not significant."
NCBI gene IDs:
"Crispr: 
Dnm1l: 74006
Opa1: 74143
Pgs1: 74451"
Figure legend: "Representative transmission electron micrographs of MEFs of the indicated genotypes showing loss of lamellar cristae in Opa1Crispr and Opa1CrisprPgs1Crispr MEFs. Scale bar=200nm. Quantification of (C) of mitochondrial ultrastructure; outer membrane/inner membrane ration (IMM/OMM) and cristae number per mitochondrion. Violin plot of >50 mitochondria per cell line, One-way ANOVA; *p &lt; 0.05, ** p &lt; 0.01, ****p &lt; 0.0001, ns; not significant."
NCBI gene IDs:
"Crispr: 
Opa1: 74143
Pgs1: 74451"
Figure legend: "mtDNA content in MEFs from (F) was quantified by amplification of MTTL1, 16S and MT-ND1 genes relative to the GAPDH nuclear gene in MEFs. Data represent mean ± SD of three independent experiments, One-way ANOVA; ****p &lt; 0.0001, ns; not significant. mtDNA content in WT and mutant MEFs treated with indicated siRNAs for 72 hours was quantified by amplification of MTTL1, 16S and ND1 genes relative to the GAPDH nuclear gene in MEFs. Data represent mean ± SD of three independent experiments, One-way ANOVA; **p &lt; 0.01, ****p &lt; 0.0001, ns; not significant."
NCBI gene IDs:
"GAPDH: 
16S: 27471
ND1: 17716
MTTL1: 17735"
Figure legend: "B. Distribution of PWWP2B mutations identified in 25 STAD patients. Distribution of PWWP2B mutations identified in the TCGA PanCancer Atlas stomach adenocarcinoma dataset (Network, 2014). Distribution of PWWP2B mutations identified in a large-scale colorectal adenocarcinoma genomic study."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "E. Overall survival curve of 25 gastric cancer patients with and without PWWP2B mutations."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "B. The interaction between exogenous PWWP2B and UHRF1. The indicated plasmids were transfected into 293T cells. After 24 hours, the transfected cell lysates were immunoprecipitated (IP) using an anti-Myc antibody and subjected to Western blotting analysis using the indicated antibodies. The bottom panel shows equal volumes of cell lysates immunoblotted with the indicated antibodies."
NCBI gene IDs:
"PWWP2B: 170394
UHRF1: 29128"
Figure legend: "E. Myc-UHRF1 and either GFP-PWWP2B WT or its serial deletion mutants were co-transfected into 293T cells. The cell lysates were immunoprecipitated with the anti-Myc antibody and then immunoblotted with the indicated antibodies."
NCBI gene IDs:
"GFP: 
Myc: 
PWWP2B: 170394
UHRF1: 29128"
Figure legend: "Cell lysates of 293T expressing Myc-UHRF1 WT or Myc-UHRF1-D4 mutants were incubated with 2 ug of purified GST or GST-PWWP2B-N for 1 h at 4 °C. After pull-down with GST-beads, the bound complex was analyzed by Western blots."
NCBI gene IDs:
"Myc: 
UHRF1: 29128"
Figure legend: "F. HeLa cells were transfected with GFP-PWWP2B WT or deletion mutant expression plasmids, and 24 h later, the cells were treated with laser microirradiation (top panel). The cells with positive GFP expression on the laser stripes are presented in the bar graph (bottom panel). The results represent the average of three independent experiments. The error bars indicate the standard deviation."
NCBI gene IDs:
"GFP: 
PWWP2B: 170394"
Figure legend: "H. GFP-PWWP2B-A2A3 deletion mutant translocates to the DNA damage sites. HeLa cells were transfected with GFP-tagged deletion mutant expression plasmids, and 24 h later, the cells were treated with laser microirradiation (left panel). The cells with positive GFP expression on the laser stripes after 10 minutes were counted and presented in the bar graph (right panel). The results represent the average of three independent experiments. The error bars indicate the standard deviation for the cells transfected with each expression plasmid."
NCBI gene IDs:
"GFP: "
Figure legend: "I-J. HeLa cells depleted with either control or UHRF1 siRNAs were transfected with the GFP-PWWP2B-A2A3 (I) and GFP-PWWP2B WT (J) expression plasmid. After 24 h, the cells were subjected to laser microirradiation. The laser stripes were examined at the indicated time points. The intensity of each laser stripes in each time point was measured by averaging values from indicated number of cells and graphed in the right panel."
NCBI gene IDs:
"GFP: 
PWWP2B: 170394
UHRF1: 29128"
Figure legend: "The intensity of each laser stripes in each time point was measured by averaging values from indicated number of cells and graphed in the right panel. K. HeLa cells depleted with either control or PWWP2B siRNA were transfected with GFP-UHRF1 expression plasmids. After 24 h, the cells were subjected to laser microirradiation. The laser stripes were examined at the indicated time points."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "D-G. Quantification of radiation-induced RAD51, BRCA1, and 53BP1 foci formation in HeLa cells treated with the indicated siRNAs. All data were obtained from over cells (open circles), and the mean values are shown as red bars (upper panel). Immunofluorescence analysis of irradiation-induced RAD51, BRCA1, and 53BP1 foci formation. HeLa cells transfected with either control or PWWP2B siRNAs were synchronized in S phase by a double thymidine block and exposed to 0 or 2 Gy of IR. The cells were incubated for 2 h, fixed, and subjected to staining with RAD51 (D and E), BRCA1 (F), or 53BP1 (G) antibodies. The cells in S phase were identified by Cyclin A staining. (E) The siPWWP2B-resistant PWWP2B WT expression vector was transfected into HeLa cells after siRNA-mediated PWWP2B depletion. IR-induced RAD51 foci formation was examined by immunofluorescence."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "A. Immunoblot analysis of RAD51, BRCA1, or 53BP1 protein levels in PWWP2B-depleted HeLa cells."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "C-D. Quantification of radiation-induced RPA2 or S4/S8 phosphorylated RPA foci formation in PWWP2B-depleted HeLa cells. All data were obtained from over 100 cells (open circles), and the mean values are shown as red bars (upper panel).Immunofluorescence analysis of irradiation-induced RPA2 or S4/S8 phosphorylated RPA2 foci formation. HeLa cells treated with either control or PWWP2B siRNAs were exposed to 0 or 2 Gy of IR. The cells were incubated for 2 h, fixed, and subjected to staining with RPA2 (C), or S4/S8 phosphorylation-specific RPA2 (D) antibodies (bottom panel)."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "A. Immunofluorescence analysis for irradiation-induced MRE11 foci formation (left panel). HeLa cells transfected with either control siRNA, siPWWP2B or siUHRF1 were irradiated, fixed and subjected to staining with MRE11 and γH2AX antibodies. More than 100 nuclei per condition were counted.The percentage of MRE11-positive cells is presented as a bar graph (right panel). The results represent the average of three independent experiments. The error bars indicate standard deviation."
NCBI gene IDs:
"PWWP2B: 170394
UHRF1: 29128"
Figure legend: "B. HeLa cells expressing GFP-MRE11 were treated with control siRNA or siRNAs against PWWP2B. After 48 h, the cells were subjected to laser microirradiation. Stripes on the laser were examined at the indicated time points (upper panel).The intensity of the laser stripes at the time points was determined. The average intensity values from 10 cells were graphed in the bottom panel."
NCBI gene IDs:
"PWWP2B: 170394"
Figure legend: "C. The interaction between PWWP2B and MRE11. HA-PWWP2B and Myc-MRE11-expressing vectors were transfected into 293T cells. After 24 h, the cell lysates were immunoprecipitated with anti-HA antibody, followed by immunoblot analysis with the indicated antibodies."
NCBI gene IDs:
"HA: 
PWWP2B: 170394"
Figure legend: "B-C. Comparison of IR-induced foci formation for either RAD51 or BRCA1 in HeLa cells transfected with the indicated siRNAs. Quantification of radiation-induced RAD51 or BRCA1 foci formation in PWWP2B alone, UHRF1 alone or PWWP2B and UHRF1-depleted HeLa cells. All data were obtained from over 100 cells (open circles), and the mean values are shown as red bars (upper panel).Immunofluorescence analysis of irradiation-induced RAD51 or BRCA1 foci formation. HeLa cells treated with the indicated siRNAs were exposed to 0 or 2 Gy of IR. The cells were incubated for 2 h, fixed, and subjected to staining with RAD51 (B), or BRCA1 (C) antibodies (bottom panel)."
NCBI gene IDs:
"PWWP2B: 170394
UHRF1: 29128"
Figure legend: "(A) Northern blot experiments show the expression of RsaI during growth phase in the HG001 strain in MHB medium with or without the addition of 1,5 g/L of D-glucose. Glucose was added either at the beginning of growth (+ glucose, left panel) or after 3h of growth (right panel)."
NCBI gene IDs:
"RsaI: "
Figure legend: "(B) Northern blot experiment shows the expression of RsaI during growth phase in the HG001, ∆ccpA mutant strain, and ∆codY mutant strain, in MHB medium with (+) or without (-) the addition of 1,5 g/L of D-glucose."
NCBI gene IDs:
"RsaI: 
codY: 3920255
ccpA: 3920528"
Figure legend: "(C) Northern blot experiment shows the expression of RsaI in the HG001 and ∆ccpA mutant strains. Total RNA was prepared after 2, 3, 4, 5 and 6h of culture in BHI medium at 37°C."
NCBI gene IDs:
"RsaI: 
ccpA: 3920528"
Figure legend: "(D) Northern blot analysis of RsaI in the HG001 strain grown in MHB medium with or without the addition of 1 g/L of glucose, fructose or xylose. For all the experiments, loading controls were done using the expression of 5S rRNA (5S) as revealed after hybridization of the membranes with a specific probe. However for these controls, we used aliquots of the same RNA preparations but the migration of the samples was performed in parallel to the experiments on a separate agarose gel because RsaI and 5S rRNA have very similar sizes."
NCBI gene IDs:
"5S: 
5S rRNA: 
RsaI: "
Figure legend: "(B) Gel retardation assays show the formation of the complex between RsaI and icaR, glcU_2 and fn3K mRNAs. The 5' end-labeled wild-type RsaI (RsaI), RsaI mutant 3 (RsaI mut3, deletion of the two G-track motifs), and RsaI mutant 4 (RsaI mut4, deletion of the C/U rich unpaired interhelical region) were incubated with increasing concentrations of mRNAs: lane 1, 0 nM; lane 2, 25 nM; lane 3, 50 nM; lane 4, 100 nM and lane 5, 200 nM. Below the gels, the predicted interactions between RsaI and its targets are shown. Translation start codons are in green and SD is for Shine Dalgarno sequence. Graphs represented the % of complex formed between either RsaI or its two mutant forms (RsaI mut3 and RsaI mut4) and the target mRNA (icaR, glcU_2, fn3K) as the function of mRNA concentrations."
NCBI gene IDs:
"fn3K: 
glcU_2: 
RsaI: 
icaR: 3921483"
Figure legend: "(C) Gel retardation assays show the formation of the complex between RsaI and RsaG. The 5' end-labeled wild-type RsaI (RsaI), RsaI mutant 2 (RsaI mut2), RsaI mutant 4 (RsaI mut4), and RsaI mutant 1 (RsaI mut1) were incubated with increasing concentrations of RsaG given in nM on the top of the autoradiographies."
NCBI gene IDs:
"RsaG: 
RsaI: "
Figure legend: "(A) Toe-print assays showing the effect of RsaI on the formation of the ribosomal initiation complex of glcU_2 and fn3K mRNAs, respectively. Lane 1 : incubation control of mRNA alone; lane 2 : incubation control of mRNA with 30S subunits; lane 3: incubation control of mRNA with RsaI; lane 4 : formation of the ribosomal initiation complex containing mRNA, 30S and the initiator tRNAfMet (tRNAi); lanes 5 to 9 : formation of the initiation complex in the presence of increasing concentrations of RsaI, respectively : 50 nM (lane 5), 100 nM (lane 6), 150 nM (lane 7), 300 nM (lane 8), and 400 nM (lane 9). Lanes T, A, C, G: sequencing ladders. The Shine and Dalgarno (SD) sequence, the start site of translation (START) and the toe-printing signals (+16) are indicated. At the bottom of the gels are shown the predicted interactions between RsaI and its targets. Translation start codons are in green, and the Shine and Dalgarno (SD) sequence is underlined, the arrowheads depict the toe-printing signals."
NCBI gene IDs:
"fn3K: 
glcU_2: 
RsaI: "
Figure legend: "(B) The β-galactosidase activity (Miller Units) has been measured from various fusions expressed from a plasmid which also carries rsaI gene under its own promoter: PrpoB::glcU::lacZ::rsaI, PrpoB::fn3K::lacZ::rsaI, PrpoB::treB::lacZ::rsaI, PrpoB::HG001_1242::lacZ::rsaI, and PrpoB::HG001_2520::lacZ::rsaI expressed in the mutant strain HG001-∆rsaI. The same constructs were made in the absence of rsaI gene. For the fn3K-lacZ fusion, we also used an additional construct PrpoB::fn3K::lacZ::rsaImut4 expressing both the fusion FN3K-LacZ protein and RsaI mut4. The β-galactosidase activity was normalized for bacterial density and the results represented the mean of four independent experiments. The error bars are standard deviations and the statistical significance was determined using the Student's t-test. * p &lt; 0.05, ** p &lt; 0.005, *** p &lt; 0.0005, **** p &lt; 0.0001, ns is for not significant."
NCBI gene IDs:
"fn3K: 
glcU: 
lacZ: 
rsaI: 
treB: 
FN3K: 
HG001_1242: 
HG001_2520: 
LacZ: 
PrpoB: 
RsaI: 
β-galactosidase: "
Figure legend: "(B) Gel retardation assays show the formation of the complex between RsaI and icaR full length, icaR SUBST, icaR-5'UTR, and icaR-3'UTR. The 5' end-labeled of RsaI was incubated with increasing concentrations of the various mRNAs. UTR is for untranslated region, SUBST stands for the substitution of UCCCCUG sequence by AGGGGAC. This mutation, which is located in the 3'UTR of icaR, significantly destabilizes the long-range interaction, and enhances icaR translation. Lane C represents binding between radiolabelled RsaI and full-length icaR mRNA (50 nM). Due to the rather short migration of the gel, the full-length mRNA is still observed in the pocket."
NCBI gene IDs:
"RsaI: 
icaR: 3921483"
Figure legend: "(C) In vivo effect of RsaI on PIA-PNAG synthesis in the S. aureus wild-type (WT) 132 strain, the ∆rsaI mutant, and the strain carrying a deletion of icaR 3'UTR (∆3'UTR). This last mutant strain has been transformed with the pES plasmids expressing rsaI or rsaI mut5. The PIA-PNAG exopolysaccharide biosynthesis was quantified using dot-blot assays. Serial dilutions (1/5) of the samples were spotted onto nitrocellulose membranes and PIA-PNAG production was detected with specific anti-PIA-PNAG antibodies. RsaI was detected in the same samples by Northern blot using a probe directed against RsaI. Ethidium bromide staining of rRNA was used as loading controls of the same gel."
NCBI gene IDs:
"rsaI: 
RsaI: 
icaR: 3921483"
Figure legend: "(A) Ternary complex formation between RsaI, various mRNAs (glcU_2, HG001_00942 and HG001_1242), and RsaG. The 5'-end labeled RsaI was incubated with increasing concentrations of the target mRNA alone or in the presence of 50 nM of RsaG. The various complexes are notified on the sides of the autoradiographies."
NCBI gene IDs:
"glcU_2: 
HG001_00942: 
HG001_1242: 
RsaG: 
RsaI: "
Figure legend: "(B) RsaG does not form stable complexes with glcU_2 and HG001_01242. Binding assays were done in the presence of 5' end-labeled RsaG and either cold RsaI (300 nM) or increasing concentrations of glcU_2 and HG001_01242."
NCBI gene IDs:
"glcU_2: 
HG001_01242: 
RsaG: 
RsaI: "
Figure legend: "(C) Measurements of the half-lives of RsaI and RsaG in HG001-∆rsaG or HG001-∆rsaI mutant strains using Northern blot experiments. The cells were treated with rifampicin at 4h of growth and total RNAs were extracted after 2, 4, 8, 15, 30 and 60 min at 37°C in BHI. 5S rRNA was probed to quantify the yield of RNAs in each lane using the same samples, which were however run on two different gels. Calculated half-lives are shown beneath the autoradiographies and are the average of 2 experiments. The data were normalized to 5S rRNA."
NCBI gene IDs:
"rsaG: 
rsaI: 
RsaG: 
RsaI: "
Figure legend: "E Influence of mutations in CSPα (ΔL116, L115R) on the interactions with ZDHHC17 in primary hippocampal neurons. BRET and LuC ratios were systematically quantified for interactions with wild-type and mutant CSPα fusion proteins."
NCBI gene IDs:
"CSPα: 80331"
Figure legend: "E. Ectopic expression of CG14044   in the  wing pouch (GFP  area indicated by the dotted line) induces caspase  activation and DNA  fragmentation (TUNEL) in the  larval disc, melanization in the  pupal wing    (arrow head) and a structure defect in the adult wing. Data information: Scale bars, 100 μm in E (cleaved caspase) and 20 μm in E (TUNEL) and 500 μm in E (pupae and adult wing)."
NCBI gene IDs:
"CG14044: 33702"
Figure legend: "H. Deletion of the BH3 motif suppresses Sayonara-induced caspase  activation, which was detected by the caspase  sensor GC3Ai. I. Quantification of GC3Ai  positive areas with Synr  WT and the BH3 motif deletion mutant. Data information: Statistical significance was determined using one-way ANOVA with Dunnett's post hoc test. Scale bars, 100 μm in"
NCBI gene IDs:
"Sayonara: 33702
Synr: 33702"
Figure legend: "A-D. The Synr-induced wing  structural defect is suppressed by knockdown of Debcl, Buffy  or DCP1. Data information: Scale bars, 500 μm in A"
NCBI gene IDs:
"Buffy: 36251
Synr: 33702
DCP1: 37790
Debcl: 53585"
Figure legend: "F. Synr-induced caspase  activation is suppressed by knockdown of Debcl. G. GC3Ai signals are suppressed by knockdown of Debcl  or Buffy  Data information: Scale bars, 50 μm in F and G"
NCBI gene IDs:
"Buffy: 36251
Synr: 33702
Debcl: 53585"
Figure legend: "H-I. Lysates from HEK293T  cells that express Flag-Debcl  or Flag-Buffy  were incubated with GST  or GST-Synr   bound to glutathione-Sepharose. Flag-Debcl  or Flag-Buffy  is pulled down  with GST-Synr   but not with GST."
NCBI gene IDs:
"Flag: 
Buffy: 36251
Debcl: 53585"
Figure legend: "A. Ectopic expression of Synr   induces autolysosome  accumulation, which was detected by Lysotracker, in the wing disc. B. Ectopic expression of Synr   also induces autophagosome  accumulation, which was detected by mCherry-atg8a. The dotted square regions are magnified in the right pictures. Data information: Scale bars, 100 μm in A and H, 50 μm in B"
NCBI gene IDs:
"Synr: 33702"
Figure legend: "D-F. Knockdown of Atg2  or Atg8a  suppresses the wing  structural defect that is induced by Synr. Data information: Scale bars, 500 μm in D."
NCBI gene IDs:
"Atg2: 38344
Atg8a: 32001
Synr: 33702"
Figure legend: "Synr-induced caspase  activation is suppressed by inhibition of autophagy  (atg2, atg8a  RNAis) in a similar manner to apoptosis  inhibition (Debcl, Dcp-1 RNAis). Data information: Scale bars, 100 μm in"
NCBI gene IDs:
"atg2: 38344
atg8a: 32001
Synr: 33702
Dcp-1: 37729
Debcl: 53585"
Figure legend: "A. Inhibition of Synr  suppresses the wing  defect that is induced by p53, a potent apoptosis inducer. B. Inhibition of Synr  suppresses p53-induced caspase activation. Data information: Statistical significance was determined using a two-tailed unpaired t-test (B), Scale bar, 500 μm in A"
NCBI gene IDs:
"Synr: 33702
p53: 2768677"
Figure legend: "D. Inhibition of Synr  in the midgut enterocytes  enhances resistance to starvation. E. The synr  mutant also exhibits enhanced resistance to starvation. Data information: Statistical significance was determined using a log-rank (Mantel-Cox) test (D-E)."
NCBI gene IDs:
"synr: 33702
Synr: 33702"
Figure legend: "(b) TR3 mutant Flag-ΔNLS but not Flag-NLS promotes the induction of autophagy in response to THPN treatment. The siRNA-resistant versions of Flag-ΔNLS and Flag-NLS were transfected into TR3-knockdown A375 cells. Top, the cells cotransfected with GFP-LC3 were further treated with THPN for 24 h before microscopic analysis (scale bars, 10 μm). Middle, the conversion of LC3-I to LC3-II was analyzed by western blotting. The rate of cell survival was determined after THPN treatment for 48 h (bottom). '-' represents vehicle treatment only."
NCBI gene IDs:
"LC3: Q9GZQ8///Q9BXW4///Q9H492///440738///81631///84557
TR3: 3164"
Figure legend: "(c) Nix assists the TR3 mitochondrial targeting. Cells with Nix, Pink1 and Bnip3 knockdown were treated with THPN (20 μM, 6 h). Top, mitochondrial TR3 was assayed by western blotting. Nix knockdown abolishes the THPN-induced (20 μM, 24 h) formation of LC3 foci (middle and bottom; scale bars, 10 μm). Images of full blots are shown in Supplementary Figure 7. All of the data are presented as the mean ± s.e.m. of three independent experiments. **P 0.01; NS, not significant; ctrl, control."
NCBI gene IDs:
"Bnip3: 664
Nix: 665
Pink1: 65018"
Figure legend: "(b) Site C of LBD is critical for Nix binding, as determined by the in vitro pull-down assay. The purified bead-bound GST or GST-Nix proteins were incubated with different mutants as indicated and THPN (20 μM) for 3 h; the proteins were then analyzed by western blotting. IB, immunoblotting."
NCBI gene IDs:
"Nix: 665"