Journal: bioRxiv

Article Title: Mitochondrial carrier SLC25A34 links clock, diet, and temperature control of interorganellar lipid cycling

doi: 10.64898/2026.05.30.724257

Figure Lengend Snippet: A, schematic of the multi-omic approach to discover Slc25a34 ; comparing the proteome of BAT from (1) cold-exposed mice (top left, 3 weeks cold exposure vs thermoneutrality, FC>2) and (2) Rev-erbα WKO mice (bottom left, Rev-erbα WKO vs Control, FC>2), (3) cistrome of BAT from Control and Rev-erbα WKO mice (top right, REV-ERBα binding sites located within 10 kb of the nearest gene that show higher occupancy in cold conditions than at thermoneutrality), and (4) BAT transcriptome from cold-exposed Rev-erbα/β dBKO mice (bottom right, genes induced by cold in control mice (FC > 2, FDR < 0.05) and genes induced by double Rev-erbα/β knockout in BAT at thermoneutrality (FC > 2, FDR < 0.05). B , Slc25a34 expression across tissues, fold change relative to the expression level in the tissue at 29°C. C , Slc25a34 and Slc25a35 mRNA and, D , protein levels in BAT during cold adaptation, significance indicates effects of cold exposure compared to 29°C. E , Slc25a34 mRNA levels in scWAT during cold adaptation, significance indicates effects of cold exposure compared to 29°C. F , Circadian expression of Slc25a34 and Slc25a35 mRNA levels in control and Rev-erbα WKO mice acclimated to 29°C. G , SLC25A34 and SLC25A35 protein in BAT of control and Rev-erbα WKO mice at 22°C at ZT10. H , Slc25a34 mRNA levels in BAT of control and Rev-erbα WKO mice at 29°C and after 1.5h of 4°C exposure (ZT4 – ZT5.5). I , REV-ERBα occupancy in the proximal Slc25a34 promoter in BAT at 29°C and after 6 h of 4°C exposure of control and Rev-erbα WKO mice (ZT10). J , Slc25a34 mRNA levels in BAT from control and Hdac3 AKO mice at 22°C and after 3h at 4°C. K , Schematic depicting the role of REV-ERBα in coordinating circadian and cold-mediated regulation of Slc25a34 expression. For all panels, data are represented as mean ±SEM, p < 0.05 = *, p < 0.01 = **, p < 0.001 = ***, p < 0.0001 = ****, unpaired two-tailed multiple t-tests (B, H), One-way ANOVA with the Benjamini, Krieger, and Yekutieli two-stage linear step-up procedure for multiple comparisons correction (C-E), Two-way ANOVA with the Benjamini, Krieger, and Yekutieli two-stage linear step-up procedure for multiple comparisons correction (F, G, J).

Article Snippet: To generate the mouse strain with the adipose-specific Hdac3 knockout ( Hdac3 AKO), Hdac3 f/f mice maintained on a C57BL/6 background were bred to B6;FVB-Tg(Adipoq-Cre)1Evdr/J mice form Jackson laboratory (stock No: 010803) ( ).

Techniques: Control, Binding Assay, Knock-Out, Expressing, Two Tailed Test

Journal: bioRxiv

Article Title: Mitochondrial carrier SLC25A34 links clock, diet, and temperature control of interorganellar lipid cycling

doi: 10.64898/2026.05.30.724257

Figure Lengend Snippet: A , Slc25a35 expression across tissues, fold change relative to the expression level in the tissue at TN. B , Slc25a35 mRNA levels in scWAT during cold adaptation. C , Slc25a35 mRNA levels in BAT of control and Rev-erbα KO mice at TN and cold. D , Slc25a35 mRNA levels in BAT from control and Hdac3 AKO mice at TN and after 6 h of cold exposure (ZT10). For all panels, error bars represent ±SEM, p < 0.05 = *, p < 0.01 = **, p < 0.001 = ***, p < 0.0001 = ****, unpaired two-tailed multiple t-tests (A), One-way ANOVA (B) and Two-way ANOVA (C, D) with the Benjamini, Krieger, and Yekutieli two-stage linear step-up procedure for multiple comparisons correction.

Article Snippet: To generate the mouse strain with the adipose-specific Hdac3 knockout ( Hdac3 AKO), Hdac3 f/f mice maintained on a C57BL/6 background were bred to B6;FVB-Tg(Adipoq-Cre)1Evdr/J mice form Jackson laboratory (stock No: 010803) ( ).

Techniques: Expressing, Control, Two Tailed Test

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: Elevated expression of cathepsins in HDAC3 deficient macrophages. A Western blot analysis of HDAC3 in Vector and Hdac3 −/ − RAW264.7 cells. B Volcano plot for genes significantly changed (≥ 2 fold change, P < 0.05) after HDAC3 knockout. C , D Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for genes significantly changed (≥ 2 fold change, P < 0.05) after HDAC3 knockout. E Heat map of relative lysosome related mRNA expression. F PCR analysis of Ctsa , Ctsb , Ctsc , Ctsd , Ctse , Ctsf , Ctsg , Ctsh , Ctsk , Ctsl , Ctso , Ctss , Ctsw , Ctsz in Vector and Hdac3 −/ − RAW264.7 cells. Data are representative of three independent experiments and showed as mean ± SEM. ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Expressing, Western Blot, Plasmid Preparation, Knock-Out

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deficient macrophages have elevated expression of Ctsb . A , B Western blot analysis of CTSB in control and HDAC3 deficient RAW264.7. C , D Confocal micrographs of RAW264.7 cells stained with DAPI (blue, DNA) and antibodies against CTSB (AF488). Scale bar: 100/10 μm. E PCR analysis of Ctsb in Lysm Cre and Lysm Cre Hdac3 f/f BMDMs. F , G Western blot analysis of CTSB in Lysm Cre and Lysm Cre Hdac3 f/f BMDMs. H PCR analysis of Ctsb in Vector, Hdac1 −/− , Hdac2 −/− , Hdac3 −/− , Hdac8 −/− RAW264.7 cells. I , J Western blot analysis of HDAC1, HDAC2, HDAC3, HDAC8 and CTSB in Vector, Hdac1 −/− , Hdac2 −/− , Hdac3 −/− , Hdac8 −/− RAW264.7 cells. Data are representative of three independent experiments and showed as mean ± SEM. * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Expressing, Western Blot, Control, Staining, Plasmid Preparation

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deacetylases the histones on the promoters of cathepsins. A Heat map representation of correlation between each biological replicates of Vector and Hdac3 −/− RAW264.7 cells for H3K27ac. B Distribution of H3K27ac-binding loci relative to transcriptional start site (TSS). C H3K27ac signals in Vector and Hdac3 −/− RAW264.7 at TSS. D Genome-wide distribution of H3K27ac ChIP-seq peaks in RAW264.7 cells. E – J The Integrative Genomics Viewers (IGVs) for H3K27ac occupied on the promoter of Ctsa , Ctsb , Ctsd , Ctsl , Ctss and Ctsz . Each CHIPseq data of histone marks were merged from three individual replicates

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Plasmid Preparation, Binding Assay, Genome Wide, ChIP-sequencing

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: Reduced protein level of RIP1 is observed in HDAC3 deficient macrophage. A – C Western blot analysis of RIP1 in Neuro-2a cells transfected with CTSB. D – G Western blot analysis of RIP1 in control and HDAC3 deificient RAW264.7 and BMDMs. H – M Western blot analysis of RIP1 in Vector and Hdac3 −/− RAW264.7 stimulated with Leupeptin (25 μM), CA-074 (10 μM) or MG132 (10 μM) for 12 h. N – Q Western blot analysis of RIP1 in Lysm Cre and Lysm Cre Hdac3 f/f BMDMs stimulated with Leupeptin (100 μM) or CA-074 (40 μM) for 12 h. R , S Western blot analysis of RIP1 in Vector, Hdac1 −/− , Hdac2 −/− , Hdac3 −/− , Hdac8 −/− RAW264.7 cells. Data are representative of three independent experiments and showed as mean ± SEM. * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Western Blot, Transfection, Control, Plasmid Preparation

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deficiency in macrophages results in impaired RIP1-dependent NF-κB signaling activity. A , B Western blot analysis of phosphorylated and total RIP1 in Vector and Hdac3 −/− RAW264.7 stimulated with TNFα (20 ng/ml) for indicated time. C , D Western blot analysis of phosphorylated and total P65 in control and HDAC3 deficient RAW264.7 stimulated with TNFα (20 ng/ml) for indicated time. E , F Confocal micrographs of RAW264.7 stimulated or unstimulated with TNFα (20 ng/ml) for 15 min stained with DAPI (blue, DNA) and antibodies against P65 (AF488). The nuclear P65 positive cells were calculated. Scale bar: 100/10 μm. Ctl, Control. G PCR analysis of Il1β , Mcp1 , Mip2 and Cox2 in Vector and Hdac3 −/− RAW264.7 stimulated with TNFα (20 ng/ml) for 1 h. Data are representative of three independent experiments and showed as mean ± SEM; * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Activity Assay, Western Blot, Plasmid Preparation, Control, Staining

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deficiency in macrophages aggravates pseudomonas aeruginosa induced acute lung injury due to impaired inflammatory response. A , B ELISA analysis of IL-6 and TNFα in BALF of Lysm Cre and Lysm Cre Hdac3 f/f mice uninstilled or intratracheally instilled with LPS (5 mg/kg) (12 h). C Survival curve of 8-week-olds Lysm Cre and Lysm Cre Hdac3 f/f mice intratracheally received with pseudomonas aeruginosa [Colony forming unit (CFU) = 2 × 10 7 ]. PA, Pseudomonas aeruginosa . D Temperature of Lysm Cre and Lysm Cre Hdac3 f/f mice intratracheally received with pseudomonas aeruginosa (CFU = 2 × 10 7 ) monitored for 36 h. E CFU of pseudomonas aeruginosa in BALF of Lysm Cre and Lysm Cre Hdac3 f/f mice uninstilled or intratracheally instilled with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h was calculated. F , G H&E staining of Lysm Cre and Lysm Cre Hdac3 f/f mice intratracheal unreceived or received with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h and the lung injury score was calculated. Scale bar: 50 μm. H Pulmonary hemorrhage of Lysm Cre and Lysm Cre Hdac3 f/f mice received with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h was judged by the color of BALF. I ELISA analysis of HMGB1 in the BALF of Lysm Cre and Lysm Cre Hdac3 f/f mice uninstilled or intratracheally instilled with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h. J Schematic diagram of how HDAC3 regulates RIP1 mediated inflammatory response of macrophages. Data are showed as mean ± SEM; n = 4–9 mice per group; * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Enzyme-linked Immunosorbent Assay, Staining

Journal: Cell metabolism

Article Title: Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP

doi: 10.1016/j.cmet.2016.10.012

Figure Lengend Snippet: (A) Heat map of ChIP-seq peaks in mouse liver. C57Bl/6 mice (2–3 months old) were tail-vein injected with either AAV8:GFP or AAV8:HA-nSREBP1c and sacrificed 10 days later at ZT10. All ChIPs were performed in parallel. High-confidence peaks were clustered into 3 groups: common peaks where HA-nSREBP1c and HDAC3 peaks overlapped (purple), nSREBP1c-specfic peaks (red), and HDAC3-specific peaks (blue).

Article Snippet: Analysis at Jackson Labs indicated that the Hdac3 f/f / Scap f/f mice were 88% 6J.

Techniques: ChIP-sequencing, Injection

Journal:

Article Title: The histone deacetylase-3 complex contains nuclear receptor corepressors

doi:

Figure Lengend Snippet: Purification of the HDAC3 complex. (A and C) Silver-stained SDS/polyacrylamide gel of the HDAC3 complex. (B and D) Histone deacetylase activity assayed from immunoaffinity-purified complexes. Each assay was performed in duplicate, and the values shown are the averages. w = wash, e = eluate, e + c = eluate and competitor.

Article Snippet: Additional N-CoR deletion plasmids were similarly constructed as described ( 20 ). pcDNA3-F-HDAC3 was constructed by subcloning HDAC3 cDNA downstream of the cytomegalovirus and phage T7 promoters, and in-frame with the FLAG sequence in pcDNA3 (Invitrogen). pCMX-VP16-HDAC3 was constructed by ligating an HDAC3 fragment generated by PCR into the Bam HI/ Eco RI sites of the pCMX-VP16-N expression vector ( 23 ).

Techniques: Purification, Staining, Histone Deacetylase Assay, Activity Assay

Journal:

Article Title: The histone deacetylase-3 complex contains nuclear receptor corepressors

doi:

Figure Lengend Snippet: In vitro association of HDAC3 with N-CoR. (A) Schematic drawing of N-CoR. The ability of each N-CoR fusion protein to bind HDAC3 is indicated (+ or −). Representative autoradiograms of (B) in vitro translated Gal4-N-CoR protein captured by GST-HDAC3 fusion protein, (C) in vitro translated HDAC3 protein captured by GST-N-CoR fusion proteins, and (D) in vitro translated HDAC4 and HDAC5 proteins captured by GST-N-CoR fusion proteins. Several independent experiments yielded consistent results. The input lanes were loaded with one-tenth the amount of 35S-labeled proteins used in the binding reactions.

Article Snippet: Additional N-CoR deletion plasmids were similarly constructed as described ( 20 ). pcDNA3-F-HDAC3 was constructed by subcloning HDAC3 cDNA downstream of the cytomegalovirus and phage T7 promoters, and in-frame with the FLAG sequence in pcDNA3 (Invitrogen). pCMX-VP16-HDAC3 was constructed by ligating an HDAC3 fragment generated by PCR into the Bam HI/ Eco RI sites of the pCMX-VP16-N expression vector ( 23 ).

Techniques: In Vitro, Labeling, Binding Assay

Journal:

Article Title: The histone deacetylase-3 complex contains nuclear receptor corepressors

doi:

Figure Lengend Snippet: In vivo association of HDAC3 with N-CoR. (A and B) Mammalian two-hybrid assays were used to assess the interaction between N-CoR and HDAC3 or HDAC4 in 293 cells. VP16-HDAC3 and VP16-HDAC4 fusion proteins were expressed from pCMX-VP16-HDAC3 and pCMX-VP16-HDAC4, respectively. pUAS-p36-luc was used as the reporter. The results are the averages ± SD from at least two separate experiments. (C and D) HDAC3 enhances repression by N-CoR HDAC3-interacting domain. HDAC1, HDAC3, HDAC4, HDAC5, and various Gal4-N-CoR fusions were expressed by using plasmids described in Materials and Methods. Transfections were done in HeLa cells with the pGal4-tk-luc reporter. The results are the averages ± SD from three separate experiments.

Article Snippet: Additional N-CoR deletion plasmids were similarly constructed as described ( 20 ). pcDNA3-F-HDAC3 was constructed by subcloning HDAC3 cDNA downstream of the cytomegalovirus and phage T7 promoters, and in-frame with the FLAG sequence in pcDNA3 (Invitrogen). pCMX-VP16-HDAC3 was constructed by ligating an HDAC3 fragment generated by PCR into the Bam HI/ Eco RI sites of the pCMX-VP16-N expression vector ( 23 ).

Techniques: In Vivo, Transfection

Journal:

Article Title: The histone deacetylase-3 complex contains nuclear receptor corepressors

doi:

Figure Lengend Snippet: (A) HDAC3 is involved in N-CoR/Pit-1-mediated repression. A reporter plasmid containing a Pit-1 response element was microinjected into 293 cells in the presence of control IgG, anti-N-CoR, or anti-HDAC3 IgG. The results were quantified as the percentage of injected cells (by rhodamine staining) that also turned blue [by 5-bromo-4-chloro-3-indolyl β-d-galactoside (X-Gal) staining] and shown here as the averages ± SD of two experiments performed in triplicate. (B and C) N-CoR HDAC3-interacting domain enhances deacetylase activity by HDAC3. Recombinant Flag-HDACs and Gal4-N-CoR fusion proteins were expressed in Sf9 cells, immunoprecipitated with an anti-Flag Ab. Precipitates were divided into three equal aliquots and used for deacetylase assays (B), analysis by Western blot by using the anti-Flag Ab (C Left), and analysis by Western blot by using an anti-Gal4 Ab (C Right). Deacetylase results are the averages ± SD from four separate experiments.

Article Snippet: Additional N-CoR deletion plasmids were similarly constructed as described ( 20 ). pcDNA3-F-HDAC3 was constructed by subcloning HDAC3 cDNA downstream of the cytomegalovirus and phage T7 promoters, and in-frame with the FLAG sequence in pcDNA3 (Invitrogen). pCMX-VP16-HDAC3 was constructed by ligating an HDAC3 fragment generated by PCR into the Bam HI/ Eco RI sites of the pCMX-VP16-N expression vector ( 23 ).

Techniques: Plasmid Preparation, Injection, Staining, Histone Deacetylase Assay, Activity Assay, Recombinant, Immunoprecipitation, Western Blot