EMBO/SourceData huggingface dataset:
Figure legend: "Flow cytometric cell cycle analysis of MLS cell lines following shRNA‑mediated YAP1 knockdown. Error bars represent the mean ± SD of three independent experiments, two-way ANOVA; ns, not significant."
NCBI gene IDs:
"YAP1: 10413"
Figure legend: "Senescence‑associated β‑galactosidase (SABG) staining intensity in MLS cell lines following shRNA-mediated YAP1 knockdown. Error bars represent the mean ± SD of ten random microscopic fields, two-way ANOVA)."
NCBI gene IDs:
"YAP1: 10413"
Figure legend: "Expression of CDKN1A, CDKN2A, total and phosphorylated RB1, and TP53 in MLS cell lines following shRNA‑mediated YAP1 knockdown. One of at least two independent experiments with similar results is shown."
NCBI gene IDs:
"YAP1: 10413"
Figure legend: "Expression of cleaved PARP and cleaved caspase 3/8 in MLS cell lines following shRNA-mediated YAP1 knockdown. One of at least two independent experiments with similar results is shown."
NCBI gene IDs:
"YAP1: 10413"
Figure legend: "Expression of YAP1 and downstream effectors in SCP-1 cells transduced with FUS‑DDIT3 or EV. One of at least three independent experiments with similar results is shown."
NCBI gene IDs:
"DDIT3: 1649
FUS: 2521"
Figure legend: "Expression of YAP1 and downstream effectors in cytoplasmic (yellow) and nuclear (blue) fractions from SCP-1 cells transduced with FUS‑DDIT3 or EV. One of at least two independent experiments with similar results is shown."
NCBI gene IDs:
"DDIT3: 1649
FUS: 2521"
Figure legend: "YAP1-responsive luciferase activity in SCP-1 cells transduced with FUS‑DDIT3. Relative luciferase activity is displayed as fold change relative to control. Error bars represent the mean ± SD of three independent experiments, unpaired t-test."
NCBI gene IDs:
"DDIT3: 1649
FUS: 2521"
Figure legend: "Co‑IP of transiently expressed FUS‑DDIT3 and YAP1 from HEK293T cells. V5-tagged YAP1 was pulled down using an anti-V5 antibody, and interacting proteins were detected by immunoblotting. One of at least two independent experiments with similar results is shown."
NCBI gene IDs:
"DDIT3: 1649
FUS: 2521
YAP1: 10413"
Figure legend: "YAP1-responsive luciferase activity in MLS cell lines transfected with a constitutively active YAP1S127A mutant and treated with 1 µM verteporfin. Relative luciferase activity is displayed relative to control. Error bars represent the mean ± SD of three independent experiments, unpaired t-test."
NCBI gene IDs:
"YAP1: 10413"
Figure legend: "Tumor formation on chicken CAM of MLS cell lines following shRNA-mediated YAP1 knockdown. The number of tumors is given above each bar, Fisher exact test; ns, not significant."
NCBI gene IDs:
"YAP1: 10413"
Figure legend: "Ex vivo generation of CAR T cells. Activated human PBMC were left untransduced or incubated with CD8-LVCD19CAR at an MOI of 2. Five days later, expression of CD19-CAR and CD8 were determined on CD3+ cells. Numbers indicate the percentage of cells in the respective gate."
NCBI gene IDs:
"CD19CAR: 
CD8: 925"
Figure legend: "Mice were transplanted with B-cell depleted human PBMC and then received CD8-LVCD19CAR (filled circle) or PBS (open circle). As control, CD8-LVCD19CAR or PBS were injected into mice transplanted with non-depleted PBMC. Data represent mean ± SD for all groups (CD8-LVCD19CAR: n=6 in D, n=4 in G; CD8-LVRFP: n=4; PBS: n=4 in G, all others n=3)."
NCBI gene IDs:
"CD19CAR: 
RFP: 
CD8: 925"
Figure legend: "CAR T cell levels in the CD8+ and CD8- T cells harvested from blood, spleen and bone marrow of PBS (PBS) or vector-injected (CAR) mice determined by flow cytometry."
NCBI gene IDs:
"CAR: "
Figure legend: "Immunohistochemistry of paraffin embedded sections from the lungs, brain meninges, brain striatum, spleen and liver of the vector-injected mouse M16 (CAR) and a control mouse injected with PBS (PBS) stained against CD8 (αCD8), the CAR (αCAR), CD4 (αCD4), or CD19 (αCD19). Black arrowheads point at infiltrated lymphocytes, red arrowheads at histiocytes, and the yellow line indicates B-lymphocyte rich zones."
NCBI gene IDs:
"CAR: "
Figure legend: "(K). The mRNA expression of CD137, CD40, TBX1, TMEM26, CITED1 and slc27a1 in iWAT of male mice supplemented with AKG for 11 weeks (n = 8 per group)."
NCBI gene IDs:
"CD40: 21939
CITED1: 12705
slc27a1: 26457
TBX1: 21380
TMEM26: 327766
CD137: 21942"
Figure legend: "(R). The mRNA expression of PPARγ, FASN and ACC in the gWAT and iWAT from male mice supplemented with AKG for 11 weeks (n = 6 per group)."
NCBI gene IDs:
"ACC: 100705///107476
FASN: 14104
PPARγ: 19016"
Figure legend: "(B). The mRNA expression of OXGR1 in different tissues of 12-weeks male C57BL/6 mice (n = 3 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(D). The mRNA expression of OXGR1 in the adrenal gland of male mice 3 hrs after i.p. injection of saline or 10 mg/kg AKG, or immediately after 40-mins resistance exercise (n=8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(E). Immunoblots and quantification of OXGR1 protein expression in adrenal chromaffin cells treated with negative control (NC) siRNA or siOXGR1 (n = 3 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(F). E level in the medium from adrenal chromaffin cell cultured with vehicle + NC, vehicle + siOXGR1, AKG (100 μM) + NC or AKG + siOXGR1 for 30 mins (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(G). Intracellular calcium ion [Ca2+] changes in adrenal medulla cell cultured with vehicle + NC, vehicle + siOXGR1, AKG (100 μM) + NC or AKG + siOXGR1 (n = 30 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(H-I). Body weight gain (H) and cumulative food intake (I) of male WT control (littermates) or OXGR1 global knock out (OXGR1KO) mice. At 12 weeks of age, both control and KO mice were switched to HFD and further divided into two groups, receiving tap water or water supplemented with 2% AKG for 13 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(J-K). Representative images of body composition (J) and fat and lean mass index (K) of male WT or OXGR1KO mice treated with AKG for 13 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(L-M). Weight index of iWAT (L) and gWAT (M) in male WT or OXGR1KO mice treated with AKG for 13 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "(N-O). Immunoblots (N) and quantification (O) of p-HSL and ATGL protein in gWAT of male WT or OXGR1KO mice treated with AKG for 13 weeks (n = 4 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Oxygen consumption (P-Q) of male WT or OXGR1KO mice treated with AKG for 13 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "RER (R-S) of male WT or OXGR1KO mice treated with AKG for 13 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Body weight gain and cumulative food intake of male OXGR1 adrenal-specific reexpression mice (OXGR1REAG). Male OXGR1KO mice (8 weeks) were adrenal-specifically injected with control HBAAV2/9-GFP (OXGR1KO control) or HBAAV2/9-OXGR1 (OXGR1REAG). Two weeks after injections, mice were switched to HFD and further divided into two groups, receiving tap water or water supplemented with 2% AKG for 12 weeks (n = 8 per group)."
NCBI gene IDs:
"GFP: 
OXGR1: 239283"
Figure legend: "Representative image of body composition and fat and lean mass index of male OXGR1REAG mice treated with AKG for 12 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Weight index of gWAT and iWAT in male OXGR1REAG mice treated with AKG for 12 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Immunoblots and quantification of p-HSL and ATGL protein in gWAT of male OXGR1REAG mice treated with AKG for 12 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Oxygen consumption of male OXGR1REAG mice treated with AKG for 12 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "RER of male OXGR1REAG mice treated with AKG for 12 weeks (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Body weight gain in male WT littermates and OXGR1KO mice. At 8 weeks of age, male C57BL/6 WT control or OXGR1KO mice were switched to HFD. After 12 weeks of HFD feeding, mice were further divided into two groups, receiving non-exercise or resistance exercise for 14 days. (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Exercise-induced body weight loss in male WT littermates and OXGR1KO mice. Body weights from exercise mice were subtracted by the average body weight of non-exercise control group for each genotype (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Exercise-induced fat mass loss in male WT littermates and OXGR1KO mice. Fat mass from exercise mice were subtracted by the average fat mass of non-exercise control group for each genotype (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Cumulative food intake of male WT littermates and OXGR1KO mice after 14-day resistance exercise (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Weight index of gWAT (E) and iWAT (F) of male OXGR1KO mice after 14-days resistance exercise (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Body composition of male OXGR1KO mice after 14-days resistance exercise (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Serum AKG levels of male WT and OXGR1KO mice after resistance exercise. Male WT and OXGR1KO mice (10 weeks) fed with normal chow were receiving resistance exercise for 40 min (n = 8 per group). The serum AKG levels were tested before and immediately after exercise."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Serum E level in male OXGR1KO mice after 14-day resistance exercise (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "The mRNA expression in the BAT of male OXGR1KO mice after 14-day resistance exercise (n = 4 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "protein expression of UCP1 in the BAT of male OXGR1KO mice after 14-day resistance exercise (n = 4 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "the mRNA expression of HSL and ATGL n the gWAT of male OXGR1KO mice after 14-day resistance exercise (n = 4 per group)."
NCBI gene IDs:
"HSL: 16890
OXGR1: 239283
ATGL: 66853"
Figure legend: "Oxygen consumption in male OXGR1KO mice after 14-day resistance exercise (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "RER in male OXGR1KO mice after 14-day resistance exercise (n = 8 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "Immunoblots and quantification of p-IKK/IKK, p65, p-IκB/IκB and OXGR1 protein in adrenal chromaffin cells cultured with vehicle + NC, vehicle + siOXGR1, AKG (100 μM) + NC or AKG + siOXGR1 for 3 hrs (n = 3 per group)."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "p65 translocation in adrenal chromaffin cells cultured with vehicle + NC, vehicle + siOXGR1, AKG (100 μM) + NC or AKG + siOXGR1 for 3 hrs (n = 3 per group). Scale bars, 100 μm."
NCBI gene IDs:
"OXGR1: 239283"
Figure legend: "C-D) Immunoblots and quantification of lysates from Cos-1 cells transfected with plasmid pCI-mDGKk-HA or non-transfected (NT) and pre-transfected 24h before with siRNA control (siC) or against FMRP (siFMR1). GAPDH was used as a loading control. For quantification, the DGKk and FMRP signals were normalized against GAPDH signal and presented relative to the signal for siC treated cells (C). Immunoblots and quantification of lysates from Cos-1 cells transfected with pCI (empty plasmid), pCI-HA-∆N-DGKk, or pCI-mDGKk-HA, and pre-treated with siRNA control (siC) or against FMRP (siFMR1) (D). Quantifications as in C."
NCBI gene IDs:
"HA: 
DGKk: 331374
FMR1: 2332"
Figure legend: "A) HeLa cells transfected with indicated plasmids expressing mouse (m) or human (h) DGKk were analyzed by immunofluorescence confocal microscopy for HA tag (red) and Dapi staining (blue). ∆C1-hDGKk construct bears deletion of phorbol ester C1 domain (328-449)."
NCBI gene IDs:
"DGKk: 139189"
Figure legend: "B) Immunoblots and quantification of lysates from Cos-1 cells transfected with plasmid pCI-HA-∆N-DGKk, untransfected (NT), or plasmid pCI control, with the indicated amount of plasmid (µg) and after 24h, incubated with puromycin (20µg/ml, 30 min) to measure rates of protein synthesis. GAPDH was used as a loading control. 0 indicates no puromycin treatment, -/+ indicates treatment without or with DGK inhibitor (DGKi) 3 µM R59022 and 0.2 µM R59949 at 6 µM, 15 min. Densitogram of puromycin incorporation is presented as change relative to mock transfected conditions."
NCBI gene IDs:
"HA: 
DGKk: 331374"
Figure legend: "C) Representative immunofluorescence staining of cortical neuron cultures transduced at 8 DIV (days in vitro) with 10e9 VG/ml of AAVRh10-GFP or AAVRh10-∆N-DGKk and assessed after 5 days using anti-MAP2 and anti-HA for ∆N-DGKk or direct 488 nm excitation for GFP. DAPI was used to visualize nuclei on merged images."
NCBI gene IDs:
"GFP: 
DGKk: 331374"
Figure legend: "D) Representative immunoblots of lysates from WT and Fmr1-KO cortical neurons transduced with AAVRh10-∆N-DGKk (AAV ∆N-DGKk), at the indicated titers (VG/ml culture volume) and quantification of phosphorylation and total levels of eIF4E. GAPDH was used as a loading control. For quantification, the phospho-protein signal was normalized first against total protein signal and is presented relative to the signal for WT culture."
NCBI gene IDs:
"DGKk: 331374
Fmr1: 14265"
Figure legend: "B) Viral titers (viral genome copy VG per cell) determined by qPCR in cortical, hippocampal and rest of brain areas of Fmr1-KO mice treated with saline solution (Vehicle), AAVPHP.eB-∆N-DGKk (PHP.eB), AAVRh10-∆N-DGKk (Rh10) 8 weeks after injections. Data are mean ± SEM. Each dot represents an individual mouse."
NCBI gene IDs:
"DGKk: 331374
Fmr1: 14265"
Figure legend: "C) Immunoblots and quantification of ∆N-DGKk protein in lysates from brain areas of mice treated as in B. GAPDH was used as a loading control. Densitogram of ∆N-DGKk expression is presented as change relative to vehicle conditions."
NCBI gene IDs:
"DGKk: 331374"
Figure legend: "D) Representative coronal brain sections processed for detection of ∆N-DGKk using immunohistochemistry on Fmr1-KO mice treated with indicated treatment, 8 weeks post-injections, counter stained with eosin hematoxylin. Adjacent sections were immunolabelled with NeuN. 3 mice per genotype were processed. The sections shown are between Bregma levels -1.50 mm and -1.80 mm. Scale bar is 2 mm. Magnifications of regions of cortex (c), hippocampus (h), and striatum (s) are shown in side panels, scale bar 200 µm."
NCBI gene IDs:
"Fmr1: 14265"
Figure legend: "E) Total phosphatidic acid (PA) level measure by mass spectrometry in cortex of WT mice treated with saline solution (WT-S) and Fmr1-KO mice treated with saline (Fmr1-S), AAVPHP.eB-∆N-DGKk (Fmr1-PHP.eB), AAVRh10-∆N-DGKk (Fmr1-Rh10) 8 weeks after injections. Data are expressed as mol % of total lipids and represented as median with interquartile range with minimum and maximum values. Statistics: one-way ANOVA and Tukey's multiple comparisons test, n=8 individual animals, except for WT-S and Fmr1-S n=11. **P &lt; 0.01, ***P &lt; 0.001."
NCBI gene IDs:
"DGKk: 331374
Fmr1: 14265"
Figure legend: "A. SHOXprotein representation and luciferase assay. The variants found in SHOX are indicated in red. Luciferase assays to test the impact of SHOX mutations on its transcriptional activity were performed on FGFR3 promoter in U2OS cells (n = 4). Experiments were performed in triplicates. pcDNA4-TO empty vector was used as control. R153L represents a mutation known to affect SHOXprotein activity and was used as positive control (Schneider et al., 2005). Homeodomain, DNA binding domain; Src Homology 3 domain; OAR, OtpAristalessRax domain. RLU, Relative Light Units."
NCBI gene IDs:
"FGFR3: 2261
SHOX: 6473"
Figure legend: "B. CYP26C1protein representation and luciferase assay. Variants found in CYP26C1 are indicated in green. Cignal-RARE system luciferase assays to test the impact of CYP26C1 variants on its RA degradation activity were performed in U2OS cells treated with 250 nM all-trans retinoic acid (ATRA) for 24 hours (n = 4). Experiments were performed in triplicates.pIRES2-EGFP empty vector was used as control. The residue C459 represents the Iron binding residue (Q6VOL0, UniProtKB) and was mutated to Ala and used as a positive control. TM, Transmembrane helix; P450, cytochrome p450 domain. RLU, Relative Light Units."
NCBI gene IDs:
"CYP26C1: 340665"
Figure legend: "A. Left panel, RT-PCR showing the expression of CYP26C1 mRNA in human primary chondrocytes. SOX9 was used as chondrocyte marker."
NCBI gene IDs:
"CYP26C1: 340665
SOX9: 6662"
Figure legend: "B. Relative expression of SHOX mRNA normalized to the reference genes SDHA and HPRT in human primary chondrocytes treated with ATRA 100 nM for 6h (n = 5). One outlier with high relative expression (2.3 fold) was excluded from ATRA 100 nM treatment (two-sided Grubb's test, Z value 2.34, p-value &lt; 0.05)."
NCBI gene IDs:
"HPRT: 
SDHA: 
SHOX: 6473"
Figure legend: "C. SHOX promoter was cloned in pGL3basic for luciferase reporter experiments as previously described (Verdin et al, 2015). In silico analysis of SHOX promoter identified three putative RXRa binding sites which were mutated to test their direct effect on SHOX expression upon treatment with ATRA 250 nM in U2OS cells (n = 4). Experiments were performed in triplicates. RLU, Relative Light Units."
NCBI gene IDs:
"RXRa: 6256
SHOX: 6473"
Figure legend: "A-C. Wild type embryos injected with control MO or with shox MO. (A) Lateral views of the embryos at 55 hours post fertilization (hpf). (B) Dorsal view and magnification on the lateral view of the embryos. Dotted line, pectoral fins. shox morphants show smaller fins compared to controls (n = 30 embryos)."
NCBI gene IDs:
"shox: 664748"
Figure legend: "A-C. Wild type embryos injected with control MO or with shox MO. C. Expression of col2a1 at 55 hpf was examined by in situ hybridization in wild type embryos injected with control MO and with shox MO. Arrow and dotted line indicate the pectoral fin."
NCBI gene IDs:
"col2a1: 562496
shox: 664748"
Figure legend: "A-C. Wild type embryos injected with control MO or with shox MO. D. Pectoral fin area was measured by imageJ (n = 30 embryos)."
NCBI gene IDs:
"shox: 664748"
Figure legend: "A-D. Wild type embryos injected with control MO or with cyp26c1 MO. (A) Lateral views of the embryos at 55 hours post fertilization (hpf). (B) Dorsal view and magnification on the lateral view of the embryos. Dotted line, pectoral fins; *, otic vesicle. cyp26c1 morphants show smaller fins compared to controls (n = 30 embryos)."
NCBI gene IDs:
"cyp26c1: 554036"
Figure legend: "A-D. Wild type embryos injected with control MO or with cyp26c1 MO. (C, D) Expression of col2a1(C) and shox (D) at 55 hpf was examined by in situ hybridization in embryos injected with control MO or with cyp26c1 MO. (C) Dorsal view and magnification on the pectoral fins of col2a1expression. Arrow and dotted line indicate the pectoral fin. (D) Dorsal view and magnification on the pectoral fins of shox expression. Arrow and dotted line indicate the pectoral fin."
NCBI gene IDs:
"col2a1: 562496
cyp26c1: 554036
shox: 664748"
Figure legend: "F. Cignal-RARE system luciferase assay testing cyp26c1 MO on RA acid levels in zebrafishembryos (n = 5 replicates). Embryos were separated in groups of 20-30 and luciferase assayed. RLU, Relative Light Units."
NCBI gene IDs:
"cyp26c1: 554036"
Figure legend: "G. Relative shox mRNA expression normalized to reference genes eef1a and b-actin in zebrafishembryos injected with control MO or cyp26c1 MO (n = 4). RNA was extracted from 10-15 injected embryos at 55 hours post fertilization."
NCBI gene IDs:
"b-actin: 
eef1a: 
cyp26c1: 554036
shox: 664748"
Figure legend: "H. Relative shox mRNA expression normalized to reference genes eef1a and b-actin in zebrafishembryos treated with 100 nM ATRA (n = 4). Embryos were collected at 24 hpf and treated with mock control or ATRA. RNA was extracted from 10-15 embryos after 6 hours treatment."
NCBI gene IDs:
"b-actin: 
eef1a: 
shox: 664748"
Figure legend: "A-C. Wild type embryos injected with control MO, subphenotypic doses of shox MO, cyp26c1 MO or a combination of shox + cyp26c1 MOs. (A) Dorsal views of the embryos at 55 hours post fertilization (hpf). Dotted line, pectoral fins. shox + cyp26c1 double morphants show smaller fins compared to control and single MOs (n = 30 embryos)."
NCBI gene IDs:
"cyp26c1: 554036
shox: 664748"
Figure legend: "A-C. Wild type embryos injected with control MO, subphenotypic doses of shox MO, cyp26c1 MO or a combination of shox + cyp26c1 MOs. (B, C) Dorsal view and magnification on the pectoral fins of col2a1expression at 55 hpf. Arrow and dotted line indicate the pectoral fin."
NCBI gene IDs:
"col2a1: 562496
cyp26c1: 554036
shox: 664748"
Figure legend: "E. Relative expression of shox mRNA normalized to reference genes eef1a and b-actin in zebrafishembryos injected with control MO, shox MO, cyp26c1 MO, or shox + cyp26c1 MOs (n = 4). RNA was extracted from 10-15 injected embryos at 55 hours post fertilization."
NCBI gene IDs:
"b-actin: 
eef1a: 
cyp26c1: 554036
shox: 664748"
Figure legend: "(B) A fragment encompassing amino acids 432-520 of Atg13 (wt) or the corresponding FV mutant (FV) was expressed in E. coli and incubated in excess with an immobilized GST‐tagged fragment of Atg1 (amino acids 501-897) purified from E. coli (GST‐Atg1). Input (5.5%) and bound proteins were analysed by coomassie blue staining, which stains proteins proportional to their size. The size of marker proteins (in kDa) is indicated on the left."
NCBI gene IDs:
"Atg13: 856315"
Figure legend: "(C) ATG1‐TAP atg13Δ cells containing endogenously GFP‐tagged Atg17, Atg29 or Vac8 and wild‐type (wt) or the Atg13 FV‐mutant (F468A; V469A) were grown to mid log phase. Atg1 was immunoprecipitated and its association with Atg13 and the GFP‐tagged proteins was analysed by immunoblotting. Extract inputs are shown in Supplementary Figure S1B."
NCBI gene IDs:
"Atg13: 856315
atg13: 856315"
Figure legend: "(D) atg1Δ and atg1Δatg13Δ cells expressing HA‐tagged Atg1 and wild‐type (wt) cells containing an empty plasmid were grown to mid log phase (rich), and then treated with rapamycin (rapa) or starved for 4 h in SD‐N medium (starv). Atg1 was immunoprecipitated and its association with Atg13 analysed by immunoblotting. Note that phosphorylated Atg13 isolated from cells grown in rich medium migrates slightly slower on SDS-PAGE, and the extent corresponds to the shift typically observed under our gel conditions."
NCBI gene IDs:
"atg1: 852695
atg13: 856315"
Figure legend: "(F) Histone3‐HA tagged Atg1 was expressed together with wild‐type (wt) or the Atg13‐FV mutant fused to Suv methylase (Suv) in atg1Δatg13Δ cells, or for control together with Pbs2‐Suv in atg1Δ cells. Logarithmically growing cultures were treated with rapamycin (rapa) for 0 or 120 min, and methylation was monitored by preparing cell extracts and western blotting with an anti‐trimethylation‐specific antibody. Note that Suv‐, GFP‐ or TAP‐tagged Atg13 are fully functional, however, do not show the characteristic phosphorylation‐induced reduced mobility observed with the untagged protein under our gel conditions."
NCBI gene IDs:
"atg1: 852695
Atg13: 856315
atg13: 856315
Pbs2: 853313"
Figure legend: "(G) atg1Δatg13Δ cells containing TAP‐tagged wild‐type Atg1 (wt) or the Atg1 kinase‐dead (kd) K54A mutant and wild‐type Atg13, the Atg13‐FV mutant or an empty plasmid were grown to mid log phase. Atg1 was immunoprecipitated and its autophosphorylation activity was measured by autoradiography in vitro."
NCBI gene IDs:
"Atg1: 852695
atg1: 852695
Atg13: 856315
atg13: 856315"
Figure legend: "(H) pho8Δ60pho13Δatg13Δ cells expressing wild‐type Atg13 (wt), the Atg13‐FV mutant (FV) or an empty plasmid were grown to mid log phase and starved for 4 h in SD‐N medium. Pho8Δ60‐specific alkaline phosphatase (ALP) activity (nmol/min/mg) was measured in three independent experiments as described in 'Materials and methods', and plotted as relative ALP activity with standard deviation (s.d.) compared to the wild‐type controls."
NCBI gene IDs:
"Atg13: 856315
atg13: 856315
pho13: 851362
pho8: 852092"