EMBO/SourceData huggingface dataset:
Figure legend: "Cyclin E-expressing BJ cells were grown for 7 days with and without folate.Examples of nuclei with γH2AX and 53BP1 foci following cyclin E expression (CycE) (n = 65), empty vector (n = 65), folate-free medium for 7 days (empty vector −folate) (n = 67) or oncogene expression under folate-free conditions (CycE −folate) (n = 70). Red: γH2AX; green: 53BP1; blue: DAPI staining.Percent of nuclei with the indicated number of γH2AX-53BP1 co-localized foci. **P &lt; 0.01."
NCBI gene IDs:
"CycE: 9134///898
Cyclin E: 9134///898
cyclin E: 9134///898"
Figure legend: "Cyclin E-expressing BJ cells grown for 7 days with and without folate.Immunoblotting with anti-phosphorylated ATM and anti-phosphorylated CHK1 antibodies. Anti-β-catenin and anti-actin antibodies were used as loading controls.Protein level quantification."
NCBI gene IDs:
"Cyclin E: 9134///898"
Figure legend: "Cyclin E-expressing BJ cells grown for 7 days with and without folate.Examples of nuclei with RAD51 foci following cyclin E expression (CycE) (n = 67), empty vector (n = 65), folate-free medium for 7 days (−folate) (n = 71) or oncogene expression under folate-free conditions (CycE −folate) (n = 75). Green: RAD51, blue: DAPI staining.Percent of nuclei with the indicated number of RAD51 foci (n = 66). **P &lt; 0.01."
NCBI gene IDs:
"CycE: 9134///898
Cyclin E: 9134///898
cyclin E: 9134///898"
Figure legend: "A, B Cyclin E- and Ras (H-RasV12)-expressing 3T3 cells grown in 100 nM folate for 4 weeks and then two additional weeks in a normal medium. Control cells were grown in a normal medium for the whole period. (A) Examples of anchorage-independent growth in soft agar of 3T3 cells. (B) Average number of colonies per soft agar plate of 3T3 cells. The number of colonies per plate is expressed as the average ± SEM from three independent experiments."
NCBI gene IDs:
"Cyclin E: 12448///12447
H-Ras: 15461
Ras: 15461"
Figure legend: "C-E Ras (H-RasV12)-expressing MCF10A cells grown in 100 nM folate for 4 weeks and then two additional weeks in a normal medium. Control cells were grown in a normal medium for the whole period. (C) Examples of anchorage-independent growth in soft agar of MCF10A cells. (D) Average number of colonies per soft agar plate of MCF10A cells. The number of colonies per plate is expressed as the average ± SEM from three independent experiments. (E) Percentage of tumor-free flanks at the indicated time points after cell injection. Ten mice were injected in both sides in each group."
NCBI gene IDs:
"H-Ras: 15461
Ras: 15461"
Figure legend: "Correlation between evolutionary divergences (16S rRNA percent identity) and pairwise Pearson correlation of transcriptional profiles. Dashed line represents linear regression."
NCBI gene IDs:
"16S rRNA: "
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. BAT; Immunoblotting of Afadin S1795 phosphorylation (n=4-5)."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. BAT quantification of Afadin S1795 phosphorylation (n=4-5). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. sWAT; Immunoblotting of Afadin S1795 phosphorylation (n=4-5)."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. sWAT; quantification of Afadin S1795 phosphorylation (n=4-5). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. Liver; Immunoblotting of Afadin S1795 phosphorylation (n=4-5)."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. Liver quantification of Afadin S1795 phosphorylation (n=4-5). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. (G) Quantifications of phosphorylated Insulin Receptor β and phosphorylated Akt across the three tissues (n=4-5). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. (H) Quantifications of Total IRβ/tubulin in BAT, sWAT and Liver (n=5-6). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. (I) Insulin-induced lipogenesis in isolated mature adipocytes from CTRL and FAKO (Mllt4-/-) mice (n=5). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "(A) CRISPR/nCas9-mediated ablation of Afadin protein levels in a clonal cell population termed Afdn-KO."
NCBI gene IDs:
"Cas9: 
CRISPR: 
Afdn: 17356"
Figure legend: "(B) Oil red O staining and gene expression of selected adipogenic genes in WT-1 and Afdn-KO differentiated adipocytes (n=3). Data are presented as means + SEM; Student's unpaired t-test and ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Afdn: 17356"
Figure legend: "(C) Wild-type, Afdn-KO and Afdn-KO with re-expression FLAG-tagged WT I-Afadin or a non-phosphorylable form (S1795A) stimulated with vehicle or insulin (n=4) for Immunoblotting."
NCBI gene IDs:
"FLAG: 
Afadin: 17356
Afdn: 17356"
Figure legend: "(D) Acetylated α-tubulin levels in isolated mature adipocytes from CTRL and FAKO (Mllt4-/-) mice (n=4). Data are presented as means + SEM; Student's unpaired t-test and ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "(F) Immunolocalization of IR (green) and HDAC6 (red) in Afdn-KO and Afdn-KO with re-expression FLAG-tagged WT Afadin or S1795A Afadin in mature adipocytes stimulated with insulin. Nuclei were stained with DAPI (blue). Co-localization was detected by the appearance of white pixels where the red and green overlap. Scale bars: 25 µm. Representative images are shown. The ratio of IR co-localized with HDAC6 (Mandler's co-localization coefficient) was quantified (98-112 individual cells from two independent experiments). Data are presented as means + SEM; Student's unpaired t-test and ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, NS= no significance."
NCBI gene IDs:
"FLAG: 
Afadin: 17356
Afdn: 17356"
Figure legend: "(G) Immunoprecipitation of IR followed by immunoblotting using an anti-acetyl-Lys antibody in adipocytes lacking Afadin or re-expressing Afadin, with or without insulin stimulation (n=1). Representative Western blots are shown. Data are presented as means + SEM; Student's unpaired t-test and ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, NS= no significance."
NCBI gene IDs:
"Afadin: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given control diet (CD) or high-fat diet (HFD) for 16 weeks (n=5-6). (A) Body weight. Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given control diet (CD) or high-fat diet (HFD) for 16 weeks (n=5-6). (B) Body composition. Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given control diet (CD) or high-fat diet (HFD) for 16 weeks (n=5-6). (C) Sirius Red staining of representative embedded BAT, sWAT and vWAT from mice on HFD and quantification of adipocyte areas (~1000 adipocytes/genotype). Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given control diet (CD) or high-fat diet (HFD) for 16 weeks (n=5-6). (D) IPGTT after 12 weeks of diet and AUC. Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given control diet (CD) or high-fat diet (HFD) for 16 weeks (n=5-6). (E) ITT after 13 weeks of diet and AUC Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given high-fat diet (HFD) for 16 weeks (n=5-6). (F) normalized to basal insulin. Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "Seven-week old CTRL and FAKO (Mllt4-/-) mice were given control diet (CD) or high-fat diet (HFD) for 16 weeks (n=5-6). (G) Plasma insulin levels 5 min after an IPGTT performed after 18 weeks of diet. Data are presented as means + SEM; ANOVA with Tukey or Dunnet's post hoc test: *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, NS= no significance."
NCBI gene IDs:
"Mllt4: 17356"
Figure legend: "C. HEK293  cells were incubated with 5 µg of purified EVCx43- or EVCx43+ for 24 h, in the presence or absence of Bafilomycin A1 (Baf) in the last 6 h. The levels of LC3 were analyzed by WB  and are depicted on graph (LC3-II; n=4 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"Cx43: 2697"
Figure legend: "E. HEK293  cells were incubated with EVCx43- or EVCx43+ for 24 h before WB  analysis of ATP2A2/SERCA2, a predicted target of miRNAs enriched in Cx43-containing EV. Graph depicts quantification of ATP2A2/SERCA2  levels (n=4 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"Cx43: 2697"
Figure legend: "A. Cx43  was immunoprecipitated  (IP) from HEK293Cx43+ cells, after which interaction  with hnRNPA2B1  and hnRNPQ  was analyzed by WB."
NCBI gene IDs:
"Cx43: 2697"
Figure legend: "A. Cell free EV biogenesis  was assessed by relative protection of Cx43-luciferase. Reactions were incubated at 4ºC or 30ºC in the presence of membranes  derived from  HEK293Cx43- transiently transfected with Cx43-luciferase  and cytosol  from  HEK293Cx43- cells, except in the negative control. 1% TX100 was used to disrupt membranes, where indicated (n=3 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"luciferase: 
Cx43: 2697
Cx43: 24392"
Figure legend: "B. Crude membranes  and cytosol  from broken  HEK293Cx43+ or HEK293Cx43- cells were mixed in an ATP regenerating system, supplemented with synthetic miR-133b  or miR-509-3p, as indicated. Graph depicts the indicated miRNAs levels, assessed by  RT-qPCR and represented as percent protected after RNAse I  digestion of unincorporated miRNAs (n=7-8 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"Cx43: 2697
miR-133b: 442890
miR-509-3p: 100126301///100126337///574514"
Figure legend: "C. Co-immunoprecipitation  of endogenous  miR-133b and miR-509-3p following UV  crosslinking immunoprecipitation (CLIP) of Cx43  (n=3-5 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"miR-133b: 442890
miR-509-3p: 100126301///100126337///574514"
Figure legend: "D. WB  analysis for Cx43  in samples derived by miRNAs pulldowns  performed with whole lysates of HEK293Cx43+ cells and biotinylated miR-133b and miR-509-3p (n=5 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"Cx43: 2697
miR-133b: 442890
miR-509-3p: 100126301///100126337///574514"
Figure legend: "EMSA  was performed using either Cy3-labeled miR-133b (E , and Cx43  produced by in vitro translation inserted into lipid nanodiscs, For competition EMSA, an excess of unlabeled  miR-133b  was used (competitor). Empty nanodiscs  were used to control unspecific binding."
NCBI gene IDs:
"miR-133b: 442890"
Figure legend: "EMSA  was performed using either Cy3-labeled  miR-133b F) and Cx43  produced by in vitro translation inserted into lipid nanodiscs, in the presence or absence of recombinant GST-hnRNPA2B1  or GST-hnRNPQ, as indicated."
NCBI gene IDs:
"miR-133b: 442890"
Figure legend: "EMSA  was performed using either Cy3-labeled miR-509-3p (G and Cx43  produced by in vitro translation inserted into lipid nanodiscs, For competition EMSA, an excess of unlabeled miR-133b or miR-509-3p  was used (competitor). Empty nanodiscs  were used to control unspecific binding."
NCBI gene IDs:
"miR-133b: 442890
miR-509-3p: 100126301///100126337///574514"
Figure legend: "EMSA was performed using either Cy3-labeled miR-509-3p H) and Cx43  produced by in vitro translation inserted into lipid nanodiscs, in the presence or absence of recombinant GST-hnRNPA2B1  or GST-hnRNPQ, as indicated."
NCBI gene IDs:
"miR-509-3p: 100126301///100126337///574514"
Figure legend: "I. EMSA  was performed using either Cy3-labeled wild type or mutant miR-199a-3p, and Cx43-enriched membranes  prepared from C33a  parental cells (Cx43+). Cx43- membranes  were used to control unspecific binding."
NCBI gene IDs:
"miR-199a-3p: 406977///406976"
Figure legend: "Representative maximum projection images of microscopy-based miRNA-protein interaction using beads coated with GST-tagged NT/CT-Cx43,  hnRNPA2B1 or hnRNPQ, as indicated, following the addition of Cy3-labelled  miR-133b or miR-509-3p. Graph depicts quantification of total fluorescence/bead, as a measure of  protein-miRNAs binding. Scale bars 50 μm (n=2 biological replicates; average of 23 beads analyzed/condition). Data information: p-values were derived by Kruskal-Wallis (Dunn's post-hoc) test. Bars and error bars indicate mean ± SD in all graphs."
NCBI gene IDs:
"miR-133b: 442890
miR-509-3p: 100126301///100126337///574514"
Figure legend: "A. Equal amounts of EVCx43+ and EVCx43- labelled with SYTO® RNASelect™ green fluorescent stain  were incubated with HEK293Cx43+ cells for 30 min, at 37ºC. Scale bars 10 μm (n=5 biological replicates). p-values were derived by Mann-Whitney test."
NCBI gene IDs:
"Cx43: 2697"
Figure legend: "(a) HEK293 cells stably expressing GFP-DFCP1 were transfected with or without shRNA against Atg14L. The cell lysates were subjected to immunoblotting with the indicated antibodies."
NCBI gene IDs:
"Atg14L: 22863"
Figure legend: "(f) HEK293 cells were transfected with GFP-Atg14L with or without mCherry-linked dominant-negative ULK1, and these cells were cultured in complete or starvation medium for 60 min. Bars, 10 µm."
NCBI gene IDs:
"ULK1: 8408"
Figure legend: "(a) HEK293 cells were simultaneously transfected with four plasmids harboring One-Strep-Flag (OSF)-tagged Atg14L, Beclin-1, hVps34, and hVps15, and Atg14L was pulled down using Strep-Tactin Sepharose beads. Empty plasmid was used as control instead of Atg14L. The precipitates were subjected to SDS-PAGE and Coomassie brilliant blue staining."
NCBI gene IDs:
"Atg14L: 22863"
Figure legend: "(e) NRK cells were transiently transfected with adenovirus expressing GFP-Atg14L or GFP-Atg14L4C4A and fixed under nutrient-rich conditions. The cells were stained with anticalnexin antibody as an ER membrane marker. Higher magnification of the boxed areas is shown below. Bars, 10 µm."
NCBI gene IDs:
"Atg14L: 305831"
Figure legend: "(a) A549 cells were transiently transfected with adenovirus expressing GFP-Atg14L or GFP-Atg14LCAAX and subjected to starvation. The cells were fixed and stained with anti-Beclin-1 antibody. Higher magnification of the boxed areas is shown below."
NCBI gene IDs:
"Atg14L: 22863"
Figure legend: "(b) HEK293 cells were cotransfected with MEF-hVps34 and GFP or GFP-Atg14LCAAX and stained with anti-Flag antibody. Bars, 10 µm."
NCBI gene IDs:
"Atg14L: 22863"
Figure legend: "Autophagy induction by overexpressed Atg14L. A549 cells were transiently transfected with adenovirus harboring GFP-Atg14L or GFP-Atg14L4C4A. (a and b) The cells before starvation (a) or after starvation (b) were fixed and stained with anti-LC3 antibody. (c) The number of LC3-positive puncta per cell was counted, and mean ± SD values are presented. Bars, 10 µm."
NCBI gene IDs:
"Atg14L: 22863"
Figure legend: "The effect of Atg14L localization on its function. (a) Atg14L knockout mouse ES cells were transfected with GFP, GFP-Atg14L, GFP-Atg14L4C4A, or GFP-ER-Atg14L4C4A of the pCAG vector and subjected to starvation. The cells were fixed and immunostained with anti-Atg16L or anti-LC3 antibodies. (b and c) The number of Atg16L-positive puncta (b) and LC3-positive puncta (c) per cell was counted in at least 10 GFP-positive cells, and mean ± SD values are presented. Bars, 10 µm."
NCBI gene IDs:
"Atg14L: 100504663"
Figure legend: "A, Genome browser images of ChIP-seq for SAGA proteins before and after induction of ER stress at ER stress response genes CHOP, ERP70, and GRP78. ATF4/Xbp1s binding sites are from publicly available datasets (GEO accessions GSE69304 and GSE49952)."
NCBI gene IDs:
"CHOP: 1649
GRP78: 3309
ERP70: 9601"
Figure legend: "A, HCT116 cells were treated with 100 nM Thapsigargin for the indicated times in the presence or absence of shRNA targeting USP22. Cells were harvested and whole-cell lysate was subjected to immunoblotting with the indicated antibodies."
NCBI gene IDs:
"USP22: 23326"
Figure legend: "A, Genome browser images of ChIP-seq for Pol II and Ub-H2B before and after induction of ER stress, with and without USP22 knockdown, at ER stress response genes CHOP, ERP70, and GRP78. ATF4/Xbp1s binding sites are from publicly available datasets (GEO accessions GSE69304 and GSE49952)."
NCBI gene IDs:
"CHOP: 1649
GRP78: 3309
ERP70: 9601
USP22: 23326"
Figure legend: "B, Metagene profiles for Pol II (upper panel) and Ub-H2B (middle panel) ChIP-seq for USP22-dependent, USP22-Bound genes. mRNA analyses of select Bound gene transcripts are presented (lower panel). Three independent experiments are represented as mean ± SEM, with significance measured by Student's t-test, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.005 C, Metagene profiles for Pol II (upper panel) and Ub-H2B (middle panel) ChIP-seq for USP22-dependent, SAGA-Unbound genes. Nonparametric Mann-Whitney analyses of 7 bins (grey shade) surrounding TSS (TSS) and the midpoint of the profiles (Body) in Thaps treated conditions are reported. mRNA analysis of select Unbound gene transcripts are presented (lower panel). Three independent experiments are represented as mean ± SEM, with significance measured by Student's t-test, **p&lt;0.01, ***p&lt;0.005. "
NCBI gene IDs:
"USP22: 23326"
Figure legend: "C, ChIP-qPCR for total RNA Pol II, pSer5 Pol II, and pSer2 Pol II at ERP70, GRP78, and a gene desert (Prom = gene promoter, Coding = downstream coding region - see Appendix Table S1 for primer sequences). Three independent experiments are represented as mean ± SEM. with significance measured by Student's t-test, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.005."
NCBI gene IDs:
"GRP78: 3309
ERP70: 9601"
Figure legend: "B, HCT116 cells were treated for 2 hrs with 100 nM Thapsigargin in the presence or absence of shRNA targeting USP22. Cells were harvested, fractionated, and fractions were subjected to immunoblotting with the indicated antibodies."
NCBI gene IDs:
"USP22: 23326"
Figure legend: "A, Genome browser image of ChIP-seq for middle and tail Mediator subunits and H3K4me3 HiChIP tracks before and after induction of ER stress at ER stress response gene BHLHE40. H3K4me1 and H3K27ac tracks are from the ENCODE Consortium (GEO accessions GSM945858 and GSM945853). ATF4/Xbp1s binding sites are from publicly available datasets (GEO accessions GSE69304 and GSE49952)."
NCBI gene IDs:
"BHLHE40: 8553"
Figure legend: "(H)  Yeast-2-hybrid assay shows Glr1 interacts  in vivo with both Pex5  full-length and Pex5  N' domain."
NCBI gene IDs:
"Pex5: 851831"
Figure legend: "(B) Metabolomic  analysis focused on strains with over-expression or deletion of the AYT1  gene shows a significant reduction or accumulation, respectively, in  acetyl-glutamate  compared to the matched control strain of each mutant. Only metabolites changing significantly in at least one of the two conditions are presented. D-EIP  is D-erythro-1-(Imidazole-4-yl) glycerol 3-phosphate."
NCBI gene IDs:
"AYT1: 850663"
Figure legend: "(D) A  growth assay in a condition that does not induce high levels of  acetyl-CoA in peroxisomes  (glucose) shows that all strains grow similarly to the control until  stationary phase  when peroxisomes  become vital. In stationary phase, the over-expression (OE) of AYT1  grows to a lower density than the control strain, plausibly due to burdening of peroxisomal  functions. (E) A growth assay in a condition expected to elevate acetyl-glutamate  levels in peroxisomes  (oleate  as a sole carbon  source and glutamate  as a nitrogen  source) demonstrates that the AYT1  overexpressing strain grows faster and to a higher density than the control. Data information: The  growth assays in D and E were done in three biologically independent replicates and error bars were plotted. Note that some error bars are shorter than the symbol, hence are not visible in the graph."
NCBI gene IDs:
"AYT1: 850663"
Figure legend: "(G) A  β-oxidation activity assay of Δlpx1, Δfsh3, and Δlpx1Δfsh3 strains supplemented with labeled  8 carbon- or 18 carbon-free fatty acids in media supplemented with 0.5% glucose  shows a significant reduction in β-oxidation activity compared to the wild type and the two single mutants, suggesting an overlapping role for Fsh3  with Lpx1.This assay was done in three biologically independent replicates. Bars represent the mean and error bars represent the standard deviation."
NCBI gene IDs:
"fsh3: 854454
Fsh3: 854454
lpx1: 854251
Lpx1: 854251"
Figure legend: "(E)  Western blot  analysis of Fbp1-HA  levels in mutants Δpex3 (no peroxisomes), Δpex5 (abolished targeting of GID subunits to peroxisomes), and Δpex7 (no β-oxidation due to loss of Pot1  targeting) demonstrates that two hours after the transition from glucose  to ethanol  (gluconeogenic conditions), control and Δpex7 cells upregulated Fbp1-HA  levels, while for Δpex3 and Δpex5 cells Fbp1-HA  levels remain low. Antibodies were used against the HA  tag (for Fbp1) and Actin  as a loading control."
NCBI gene IDs:
"pex3: 851929
pex5: 851831
pex7: 851720
Pot1: 854646"