EMBO/SourceData huggingface dataset:
Figure legend: "D, E Cumulative fraction for fold change in TE in eIF4A1/A2 dKD or ASCC3 KD cells relative to control cells. Results are shown for all coding transcripts and for transcripts with a decreased (D) or increased (E) SRO. The P values were calculated with the Mann-Whitney U test."
NCBI gene IDs:
"ASCC3: 10973
eIF4A1: 1973
A2: 1974"
Figure legend: "D Cumulative fraction for fold change in TE in eIF4A1/A2 dKD or ASCC3 KD cells relative to control cells. Results are shown for all coding transcripts and skewed transcripts. The P values were calculated with the Mann-Whitney U test."
NCBI gene IDs:
"ASCC3: 10973
eIF4A1: 1973
A2: 1974"
Figure legend: "E Number of transcripts showing significant down-regulation of TE among skewed transcripts in eIF4A1/A2 dKD and ASCC3 KD cells."
NCBI gene IDs:
"ASCC3: 10973
eIF4A1: 1973
A2: 1974"
Figure legend: "Luciferase assays for RADX, DNAJB6, and LDHA constructs (B) in control and ASCC3-depleted HEK293T cells. The results of the luciferase assays (right) and schematic representations of the constructs (left) are shown. Rluc, Renilla luciferase; Fluc, firefly luciferase. Assay data are means ± s.d. for three independent experiments. *P &lt; 0.05, **P &lt; 0.01, *** P &lt; 0.001, NS (two-sided Student's t test)."
NCBI gene IDs:
"Fluc: 
luciferase: 
Rluc: 
ASCC3: 10973
DNAJB6: 10049
LDHA: 3939
RADX: 55086"
Figure legend: "Luciferase assays for corresponding deletion mutants of the RADX and DNAJB6 constructs (C) in control and ASCC3-depleted HEK293T cells. The results of the luciferase assays (right) and schematic representations of the constructs (left) are shown. The deleted regions of the RADX and DNAJB6 constructs are indicated by dashed white boxes. Rluc, Renilla luciferase; Fluc, firefly luciferase. Assay data are means ± s.d. for three independent experiments. *P &lt; 0.05, **P &lt; 0.01, *** P &lt; 0.001"
NCBI gene IDs:
"Fluc: 
luciferase: 
Rluc: 
ASCC3: 10973
DNAJB6: 10049
RADX: 55086"
Figure legend: "C Similar to CSR-1, the majority of small RNAs interacting with CSR-2 in vivo have 5′PPP ends. The RNAs in the immunopurified Argonaute complexes were treated with or without Vaccinia virus capping enzyme followed by an alkaline phosphatase, and finally labeled with [γ-32P]ATP and a polynucleotide kinase. RNA products were resolved by 15% sequencing gels."
NCBI gene IDs:
"CSR-2: 
CSR-1: 177591"
Figure legend: "G Three csr-1 hypomorphic mutants showed a diminished RNAi response to exo-dsRNA. The WT, the csr-1(fj150) mutant, and several strains were injected with dsRNA (1.25 µg/µL) targeting the maternal gene pos-1, essential for embryogenesis. The incidence of lethal embryos in the F1 progeny was examined. The number of F1 progeny counted is indicated by n. Error bars represent 95% confidence intervals (CIs)."
NCBI gene IDs:
"csr-1: 177591
pos-1: 179224"
Figure legend: "E Immunofluorescence images of H3K9me2 and SYP-1 in male nuclei of the WT and the Argonaute mutants. High-resolution fluorescence images, 3D reconstruction images (3D CG), and maximum intensity projection (MIP) images of segmented H3K9me2 signals are presented. In the male nuclei of the csr-1 mutant and the csr-2; csr-1 double mutant, some H3K9me2 segments showed abnormally large volumes (narrow arrow) and/or overlapped partially with SYP-1 signals (arrowhead). In the double mutant, DAPI signals were often detected in an aggregated state (dashed line)."
NCBI gene IDs:
"csr-2: 
csr-1: 177591"
Figure legend: "Immunofluorescence experiments were performed on the pachytene nuclei of X0 males. C H3K9me2 signals at the pachytene region in the males of cec mutants and cohesin mutants. Worms were cultured at 20°C, except for the smc-1(e870) mutant that was cultured at 23°C. The intensity of the H3K9me2 signal in the him-8 mutant male was similar to that in the WT male."
NCBI gene IDs:
"smc-1: 172116
him-8: 188247"
Figure legend: "C SC formation in the WT and multiple mutants were analyzed by immunostaining against SYP-1 and COH-3/4. The SC formed string-like structures in the csr-2; csr-1 double mutant and the ego-1 mutant, but the superstructure of the SC was often abnormally branched."
NCBI gene IDs:
"csr-2: 
csr-1: 177591
ego-1: 172524"
Figure legend: "A Multicolor FISH for the 5S rRNA region (rDNA, green) of autosome V and the right region of the X chromosome (LGX-R, magenta) in nuclei of the WT strain, coh-3/4 double mutant, csr-1 mutants, csr-2; csr-1 double mutant, and ego-1 mutant. Arrows indicate occasional colocalizations of the 5S rDNA and X-R loci detected in the mutant strains."
NCBI gene IDs:
"csr-2: 
coh-3: 179949
csr-1: 177591
ego-1: 172524"
Figure legend: "E csr-1(fj67) and csr-1(fj126) in-frame mutations reduced the abundance of CSR-1 at the chromosomal regions in pachytene nuclei. The WT strain and the csr-1 mutants were stained by anti-CSR-1 antibodies."
NCBI gene IDs:
"csr-1: 177591"
Figure legend: "A, B ChIP-seq data for CSR-1, SMC-1, COH-3/4, and histone H3K9me2 were compared with sub-populations in CSR-1-interacting small RNAs. Adult worms were used for experiments. ChIP signals on autosome III (A) and the X chromosome (B) from the WT hermaphrodites were visualized by aggregation plots with a bin size of 20 kbp. H3K9me2 ChIP signals derived from the him-8 mutant population rich in X0 males are shown in the lower part. The common ChIP regions computed from the technical duplicates were used for panels A, B, In the adult body, about half of the nuclei correspond to germ cells. Most H3K9me2 ChIP signals from the WT hermaphrodites were likely to originate in somatic cells because staining signals of H3K9me2 in adult hermaphrodites were detected abundantly in somatic cells and very weakly in the germline. Most meiosis-specific COH-3/4 ChIP signals were thought to originate in the germline. For comparison, aggregation plots were also constructed from the following sub-populations of CSR-1-interacting small RNAs: small RNAs mapped in sense orientation to coding genes (exons and introns), and repeat-derived small RNAs. The small RNA data merged from the technical duplicates were used for panels A and B. Densities of protein-coding exons, all non-simple repeats, and five major repeats on the reference genome are attached. The CeRep55 sequences were partially degenerate, and no clear ChIP signal for CSR-1 was detected in CeRep55 cluster #4 on the X chromosome in the ce10 reference genome."
NCBI gene IDs:
"him-8: 188247"
Figure legend: "F The CeRep55 lncRNA signals partially colocalized with those of COH-3/4 in hermaphrodites. Pachytene nuclei in the WT strain and the csr-2; csr-1 double mutant were stained."
NCBI gene IDs:
"csr-2: 
 csr-1: 177591"
Figure legend: "H The CeRep55 lncRNA signal was also detected at a region of the unpaired X chromosome where the CEC-5 and COH-3/4 signals overlapped. The pachytene chromosome showing the strongest CEC-5 enrichment was considered to be the unpaired X chromosome in males. The RNA-directed in situ hybridizations were performed with stringent conditions that detected only long RNAs."
NCBI gene IDs:
"CEC-5: 177537
COH-3: 179949"
Figure legend: "Pachytene nuclei were analyzed. B Multicolor FISH using the 5S rDNA and LGX-R probes in the csr-1(fj150) mutant and the csr-1(fj150); CeRep55_X(Q) mutant."
NCBI gene IDs:
"csr-1: 177591"
Figure legend: "(Ci) The levels of WDR6 were determined and normalized against GAPDH in three groups. Normal, n=21; Noninvasive, n=15; Invasive, n=8. (Cii) The levels of WDR6 in 10 pairs of patients' tissues."
NCBI gene IDs:
"GAPDH: 2597
WDR6: 11180"
Figure legend: "(F) Analysis of WDR6 using TCGA LIHC data. Fi and Fiii were plotted with GEPIA analyzing tool, and Fii were analyzed by UALCAN analyzing tool."
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(A) Western blots confirmed WDR6 knockdown in HCC cells transduced with shWDR6 or shcontrol lentiviral vector."
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(B) The effects of WDR6 silencing on the invasive and proliferative ability of HCC cells, respectively. Left panel: HCC-LM3: P=0.912 shControl vs shWDR6-#1, P=0.889 shControl vs shWDR6-#2; HepG2: P=0.826 shControl vs shWDR6-#1, P=0.796 shControl vs shWDR6-#2; right panel: HCC-LM3: P=0.856 shControl vs shWDR6-#1, P=0.814 shControl vs shWDR6-#2; HepG2: P=0.726 shControl vs shWDR6-#1, P=0.745 shControl vs shWDR6-#2."
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(C) The survival plot of Albumin-Cre/+; Wdr6f/f mice with DEN-induced HCC."
NCBI gene IDs:
"Wdr6: 
Albumin: 11657
Cre: 2777477"
Figure legend: "(F) Flow cytometric analysis of MDSC and T cells in tumors from BALB/c mice with H22-WDR6 or empty vector cells orthotopically implantation (n=6/group)."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(G) α-Gr1 antibody injection markedly decreased the tumor volume and lung metastatic nodules' number in BALB/c mice with H22-WDR6 cells orthotopically implantation when compared to IgG control (n=5/group)."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(Ai) ATAC-sequencing showed the effects of WDR6 knockdown on the chromatin accessibility of IL10, IL1β, IL6, and TNFα loci. (Aii) quantitative real-time polymerase chain reaction (qRT-PCR) analyzing cytokines' mRNA levels in Hepa1-6 and H22 cells treated with or without shWDR6 or WDR6, respectively."
NCBI gene IDs:
"IL10: 16153
IL1β: 16176
IL6: 16193
TNFα: 21926
WDR6: 83669"
Figure legend: "(B) TNFα ELISA assays were performed in the conditioned medium from Hepa1-6 and H22 cells with WDR6 knockdown or overexpression, respectively."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(D) The effects of TNFα knockdown in H22-WDR6 cells on MDSC recruitment (Dii), tumor size (Diii), and the ratio of IFN-γ+ CD8+ T cells (Div) in tumors from syngeneic mice (n=5/group)."
NCBI gene IDs:
"TNFα: 21926
WDR6: 83669"
Figure legend: "(E) TNFα supplementation decreased MDSC infiltration induced by WDR6 knockdown in tumor tissues from syngeneic mice (n=6/group)."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(A) The effects of NF‐κB inhibitor IMD0354 or IκBα‐SR on TNFα expression in MHCC-97L cells with or without WDR6 overexpression."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(B) The effects of WDR6 knockdown on the protein levels of p65, RelB, c-Rel, p52, and p50 in HCC cells."
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(Di-ii) The effects of autophagic deficiency using 3-MA on the levels of p65 protein and TNFα secretion in HCC cells with WDR6 knockdown."
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(Ei) WDR6 mRNA levels in Hep3B and MHCC-97L cells treated with or without TNFα in culture media. (Eii) Schematic diagram showing three candidate NF‐κB-binding sites in WDR6 promoter. (Eiii) The impact of IMD0354 on the luciferase reporter of WDR6 proximal promoter in HCC cells. (Eiv-v) ChIP assays using HCC cells or HCC tissues from patients (P#36 and P#54). Da"
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(C) Co-IP analysis indicated the effect of WDR6 mutant (R123A) or (R203A) on the binding of CUL4A to endogenous UVRAG in MHCC-97L cells."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(Di) UVRAG ubiquitination assay in MHCC-97L cells expressing WT-WDR6 or its mutant WDR6-R123A. (Dii) UVRAG ubiquitination in HCC-LM3 cells treated as shown."
NCBI gene IDs:
"WDR6: 11180
WDR6: 83669"
Figure legend: "(Ei) MS assay identified K176 of UVRAG as major ubiquitination site. (Eii) K176R mutant abolished UVRAG ubiquitination promoted by WDR6."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(A) WDR6 or its mutant (Ai) or WDR6 shRNAs (Aii) or WDR6 with CUL4A siRNA (Aiii) affected the levels of endogenous UVRAG in HCC cell lines."
NCBI gene IDs:
"CUL4A: 8451
WDR6: 83669
WDR6: 11180"
Figure legend: "(B) CHX assays of UVRAG stability in HCC-LM3 cells transfected with WDR6 shRNA."
NCBI gene IDs:
"WDR6: 11180"
Figure legend: "(C) The effects of WT-WDR6 or WDR6-R123A mutant on UVRAG levels in MHCC-97L cells in the presence of MG132."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(Di-iii) UVRAG knockdown in Hepa1-6 cells reverted WDR6-deficient-induced chromatin accessibility of TNFα locus and TNFα secretion in culture medium. The cells in (Di) were orthotopically implanted into C57BL/6J mice."
NCBI gene IDs:
"TNFα: 21926
UVRAG: 78610
WDR6: 83669"
Figure legend: "(F) Heat-map showing the expression of altered genes related to functional signatures in MDSCs after WDR6 alone or with UVRAG knockdown."
NCBI gene IDs:
"UVRAG: 78610
WDR6: 83669"
Figure legend: "(C) BALB/c mice introduced with H22-WDR6 overexpression cells were administered with Pep2-WDxR or Pep2-con with or without anti-PD-L1 antibody. The images and sizes of HCC (Ci), hematoxylin-eosin (H&amp;E) staining and metastasis nodules of lung were presented (Cii). The survival analysis of the mouse after treatment was performed (n = 9/group) (Ciii). In the BALB/c mice from (C), Flow cytometry was performed to analyze PMN-MDSC, M-MDSC, and IFN-γ+ CD8+ T cells in tumors (Civ)."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "(D) The survival test of DEN- and CCl4-induced HCC using WDR6-knockout and WT mice. At twenty-six weeks, mice were administered with or without anti-PD-L1 antibody (n = 6/group)."
NCBI gene IDs:
"WDR6: 83669"
Figure legend: "A,B. 3D views (A) and quantification of variations in the mean tumor volume (B) of HH25 chick embryos engrafted with BRAFwt (OF-MEL-028) or BRAFV600E (OF-MEL-020, OF-MEL-027) patient samples and treated with excipient or a combination of Vemurafenib and Cobimetinib. The number of embryos analyzed for each patient sample is indicated on the graphs. Student t-test for OF-MEL-020; Mann-Whintey test for OF-MEL-028, *: p &lt; 0.05, ns: not significant. Exact p-values are indicated on the graphs."
NCBI gene IDs:
"BRAF: 673"
Figure legend: "Western blot analysis of whole cell lysates from HEK 293 WT and NEDP1 KO cells reveals a loss of free NEDD8 (indicated by asterisk) and an accumulation of NEDD8 reactive species in the NEDP1 KO lysate. The predicted molecular weight sizes of putative, unanchored, poly-NEDD8 chains are denoted by N2 through to N5. Unconjugated NEDD8 is denoted by N1."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "NEDD8 affinity resin shows enrichment of endogenous neddylated proteins in WT and NEDP1 KO cells. Recombinant HALO-NEDP1 C163A (CA) conjugated to HALO-Link beads was used as an affinity resin to enrich for neddylated proteins in lysates from HEK 293 WT and NEDP1 KO cells. Enriched proteins were resolved by SDS-PAGE and processed for Western blot analysis with NEDD8 or Ubiquitin antibodies. HALO-NEDP1 CA specifically enriches for NEDD8-reactive proteins in both WT and NEDP1 KO cells, but does not enrich for Ubiquitin-modified proteins in either cell line."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Components of the NEDD8 conjugation machinery are enriched in HALO-NEDP1 pulldowns from NEDP1 KO lysates. Neddylated proteins from HEK293 KO cells were enriched by HALO-NEDP1 CA pulldown, as in (B) but not by the NEDD8 nonbinder mutant, HALO-NEDP1 DAGC (D29W A98K G99K C163A). The NEDD8 E1s, UBA3 and ULA1, are modified in NEDP1 KO cells, as well as E2 UBE2M, and co-E3s DCNL1 and DCNL2. Cul2 and Cul3 are hyper-neddylated in NEDP1 KO cells. CSN components, CSN5 and CSN8, also co-precipitate in HALO-NEDP1 CA pulldowns."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Western blot analysis from HEK 293 WT and NEDP1 KO cells of the components of the NEDD8 conjugation/de-conjugation pathway shows that similar levels of NEDD8 pathway components are present in both WT and NEDP1 KO cells. Apart from UBA3, there is no detectable amount of NEDD8-modified enzymes in whole-cell lysates from NEDP1 KO cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Neddylated species are NEDD8 E1 dependent. WT and NEDP1 KO HEK 293 cells were treated with NAE inhibitor MLN4924 at 3 μM for the indicated time. Lysed cells were then processed for Western blot analysis. NEDD8 E1 inhibition results in a time-dependent decrease in the amount of Cullin and non-Cullin NEDD8 reactive bands."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Neddylated species are UBE2M dependent. WT and NEDP1 KO HEK 293 cells were left untreated or treated with the indicated siRNA for 48 hours. Lysed cells were then processed for Western blot analysis. Neddylated species are reduced when NEDD8 E2 UBE2M was depleted after siRNA treatment (si2M), but not with control siRNA (siCTRL) or when NEDD8 E2 UBE2F was depleted (si2F). The double knockdown (si2M/2F) does not further reduce NEDD8 modified proteins."
NCBI gene IDs:
"NEDP1: 123228
UBE2F: 140739
UBE2M: 9040"
Figure legend: "(Left) Western blot analysis of large scale HALO-NEDP1 pulldowns from HEK 293 NEDP1 KO lysates. (Right) Diagram of mass spectrometry sample preparation."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Scatterplot of proteins identified by mass spectrometry analysis identifies NEDD8 and components of the NEDD8 conjugation pathway as being the most abundant proteins in HEK 293 NEDP1 KO lysates following NEDP1-CA pulldown. iBAQ analysis of proteins identified in A) are plotted as the log2 value of the enrichment ratio (mass spectrometry intensity of the HALO-NEDP1 CA pulldown over HALO-NEDP1 DAGC pulldown) versus the log10 value of the iBAQ intensity from the HALO-NEDP1 CA pulldown. Blue markers indicate known components of the NEDD8 pathway and red markers indicate proteins that have been identified as substrates of PARP-1 in the database of ADP-ribosylated proteins, ADPriboDB (Vivelo et al., 2017)."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "(Left) The 25-kDa neddylated species induced by oxidative stress increases with time in WT U2OS cells. U2OS WT or NEDP1 KO cells were treated with 600 μM H2O2 for the indicated time and then lysed in LDS sample loading buffer and processed for Western blot analysis. (Right) The same 25 kDa NEDD8 species, which is strongly induced in WT cells, is present in untreated NEDP1 KO cells and does not further increase after oxidative stress induced by H2O2 (as indicated by the arrow)."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "U2OS NEDP1 KO cells are resistant to the PARP-1 inducer, H2O2. WT and NEDP1 U2OS cells were plated in 96-well plates and after 24 hours were treated with the indicated concentration of H2O2. They were assessed for viability 24 hours later by the CellTiter-Glo assay. Graphs represent the mean ± S.E.M. of the percent survival compared to untreated cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "NEDP1 KO cells are re-sensitized to H2O2, following re-expression of NEDP1 by transient transfection. U2OS cells were plated in 96 well plates and reversed transfected with NEDP1 or an empty vector. 48 hours after plating, cells were challenged with the indicated amount of H2O2 and cell viability was assessed 24 hours later by the CellTiter-Glo assay. Graphs represent the mean ± S.E.M. of the percent survival compared to untreated cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Neddylation of cullins is decreased in NEDP1 KO cells and is rescued by re-expression of NEDP1 by transient transfection. Western blot analysis from HEK 293 WT, NEDP1 KO cells and NEDP1 KO cells rescued with transient transfection of NEDP1 reveals that upon NEDP1 re-expression, the intensity of the NEDD8 reactive bands is reduced and the levels of free NEDD8 are increased. NEDP1 re-expression also increased the neddylation of each Cullin. The neddylated band of each Cullin is denoted with a star. Quantification and graph of the mean ± S.E.M. of the percentage neddylation of each Cullin in (E)."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Deletion of Nedp1 does not lead to induction Nrf2 response genes. RNA was harvested from WT and NEDP1 KO U2OS cells, reversed transcribed to cDNA, and analysed by qPCR for Nrf2 and NQO1 expression."
NCBI gene IDs:
"Nrf2: 4780
NQO1: 1728
Nedp1: 123228
NEDP1: 123228"
Figure legend: "Deletion of Nedp1 but not of Cand1 in HEK 293 cells results in resistance to cell death from H2O2. WT, NEDP1 KO, and CAND1 KO cells were plated in 96 wells plates and treated with the indicated amount of H2O2. 24 hours after treatment, cell viability was measured using the CellTiter-Glo assay. Graphs represent the mean ± S.E.M. of the percent survival compared to untreated cells."
NCBI gene IDs:
"Cand1: 55832
CAND1: 55832
Nedp1: 123228
NEDP1: 123228"
Figure legend: "PARP-1 activity is reduced in NEDP1 KO cells. Western blot analysis of whole cell lysates from WT and NEDP1 KO U2OS cells after treatment with 600 μM H2O2 for the indicated amount of time. PAR polymer generation is induced in WT cells after H2O2 treatment but induction is reduced in NEDP1 KO cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "PARP-1 activity is rescued by re-expression of NEDP1 in NEDP1 KO cells. Western blot analysis of whole cell lysates from WT and NEDP1 KO U2OS cells transfected with the indicated constructs. 72 hours after transfection, cells were treated with the indicated amount of H2O2 and processed for Western blot analysis. PAR polymer generation is reduced in NEDP1 KO cells but can be rescued by the transient re-expression of NEDP1."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "PARP-1 inhibitor Olaparib protects WT cells from H2O2 treatment to the same extent as NEDP1 KO. U2OS cells were plated in 96 well plates and 24 hours later pre-treated with Olaparib (10 μM) for 1 hour before treatment with the indicated concentration of H2O2. 24 hours later, cell viability was measured using the CellTiterGlo assay. NEDP1 deletion protects cells from H2O2 treatment to the same extent as PARP-1 inhibition in WT cells. Olaparib does not provide additional protection to NEDP1 cells from H2O2 treatment."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "AIF translocation to the nucleus is impaired in NEDP1 KO cells. WT and NEDP1 KO cells were plated on coverslips and 24 hours later were treated with H2O2 (600 μM) for the indicated amount of time and then processed for immunofluorescence analysis using α-AIF antibodies and DAPI staining. PARP-1 dependent cell death is induced in WT U2OS cells, as indicated by translocation of AIF from the mitochondria to the nucleus (Scale bar 10 μm)."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Total nuclear AIF intensity from (D) was measured with ImageJ and plotted as a vertical scatter plot with the group mean intensity indicated with a black bar. AIF has translocated to the nucleus after WT cells were exposed to H2O2 but not in NEDP1 KO cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "NEDP1 KO cells express normal levels of PARP-1 and AIF. Western blot analysis of whole cell lysates from WT and NEDP1 KO U2OS cells shows that the proteins necessary for the induction of PARP-1 dependent cell death are present at equal levels in both cell lines."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "NEDP1 KO U2OS cells are not resistant to induction of apoptosis from combined treatment with TNF-α and cycloheximide. U2OS cells were plated in 96 well plates and incubated with cycloheximide (10 μg/mL) before addition of the indicated amount of TNF-α. Cell survival was determined 24 hours later using the CellTiter-Glo assay. Graphs represent the mean ± S.E.M. of the percent survival compared to untreated cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "NEDP1 KO U2OS cells are not resistant to treatment with camptothecin (CPT). WT U2OS and NEDP1 KO cells were plated in 96-well plates and treated with the indicated amount of CPT. 48 hours after exposure cell survival was measured using the CellTiterGlo assay. Graphs represent the mean ± S.E.M. of the percent survival compared to untreated cells."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "NEDD8 trimers co-immunoprecipitate with endogenous PARP-1 in NEDP1 KO cells. Lysates were prepared from U2OS NEDP1 KO cells and immunoprecipitation was performed with PARP-1-Trap or GFP-Trap as a negative control. Bound proteins were resolved by SDS-PAGE and processed for Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"NEDP1: 123228"