(A) MSigDB Pathway and Gene Ontology (GO) Cellular Compartment analysis of BCL6 ChIP-seq binding sites. (B) Motif enrichment analysis of BCL6-bound regions. (C) Gene expression as measured by reads …
(A, B) MSigDB Pathway/Gene Ontology analysis (A) and motif densities (B) for BCL6 ChIP-seq peaks identified in wild-type livers, as determined by enrichment over input chromatin or over BCL6 …
(A) Fed and fasted BCL6 (top) and PPARα (bottom) ChIP-seq tag densities at all respective sites (left panel) or at shared sites (right panel). (B) Histogram of distances between BCL6 and PPARα peak …
(A) BCL6 ChIP-seq tag densities in C57BL/6 and Ppara-/- livers at shared BCL6-PPARα peaks (left). PPARα tag density in Bcl6fl/fl and Bcl6LKO livers at shared BCL6-PPARα peaks (right). (B) BCL6 tag …
(A) qPCR gene expression of Ppard and Bcl6 genes in control (PpardWT) and PpardLKO mouse livers. N = 2 per group. (B) PPARδ tag densities in fed or fasted mouse livers at all PPARδ peaks. N = 3 per …
(A) Volcano plots showing log2 fold change (LFC) in expression of fed Bcl6LKO over Bcl6fl/fl livers. Blue dots represent |LFC| greater than one with an adjusted p-value less than 0.05. Red dots …
(A) qPCR analysis of Bcl6 in Bcl6fl/fl and Bcl6LKO livers. N = 7 per group. (B) Western blots of BCL6 protein in Bcl6fl/fl and Bcl6LKO livers. Densitometric quantification is shown normalized to …
(A) Enriched motifs for SMRT, NCoR and HDAC3 binding sites. For each corepressor, enriched motifs are shown in all peaks (all), peaks shared with BCL6 (BCL6 shared), and BCL6-exclusive peaks …
(A) Pathway enrichment analysis for genes differentially expressed (|LFC| greater than one and an adjusted p-value less than 0.05) with fasting or Bcl6 deletion in liver. (B) Volcano plots showing …
(A) Clustered heatmap of a distance matrix across fed and fasted Bcl6fl/fl and Bcl6LKO RNA-seq samples at genes differentially expressed with fasting. N = 4 per group. (B) Gene ontology analysis for …
(A) Distribution of fasting genes annotated with BCL6 and/or PPARα binding peaks. Differential fasting genes here include all significantly different genes with fasting (adjusted p-value<0.05). (B) …
(A) Heatmap of RPKM values at fasting-regulated genes that are dysregulated in Ppara-/- mice. 209 genes have partially or completely restored expression upon fasting in Ppara-/-;Bcl6LKO mice. N = 4 …
qPCR analysis of PPARα- and fasting-regulated transcripts in overnight fasted Bcl6fl/fl, Ppara-/-, and Ppara-/-;Bcl6LKO mouse livers, N = 5–6 per group. A one-way ANOVA and Holm-Sidak’s post-hoc …
(A–B) UCSC genome browser tracks showing (A) RNA-seq and H3K27ac ChIP-seq data in fasted control Bcl6fl/fl, Ppara-/-, and Ppara-/-;Bcl6LKO livers at Aldh3a2 and Acot4/3. (B) H3K27ac tags in Ppara-/-;…
(A) Serum β-hydroxybutyrate levels were measured in mice over the course of a 48 hr fast. N = 8–12 per group. (B) Rates of 14C-palmitate oxidation in Bcl6fl/fl and Bcl6LKO liver homogenates measured …
(A–B) Overnight fasted serum (A) glucose and (B) insulin in Bcl6fl/fl and Bcl6LKO mice after 17 weeks of high-fat diet. N = 6–9 per group. (C) Western blots showing phosphorylated AKT (pAKT) and …
(A) STAT5 ChIP-seq tag density in Ppara-/- and Ppara-/-;Bcl6LKO livers at BCL6-PPARα peaks near rescued upregulated and downregulated fasting genes. ChIP was performed in biological triplicate. (B) …
(A) PPARδ ChIP-seq tag density in Ppara-/- and Ppara-/-;Bcl6LKO livers at shared BCL6-PPARα peaks near up- and downregulated non-rescued fasting genes. (B) Log2 ratio of PPARδ ChIP-seq tag density …
(A) qPCR analysis of Bcl6 in control and Bcl6LTG livers. N = 3-7 per group. (B) Western blot of BCL6 protein in control and Bcl6LTG livers. Densitometric quantification is shown normalized to actin …
(A) Comparison of log fold change (LFC) at significant (p-value <0.05) differentially expressed genes in both Bcl6LKO and Ncor/Smrt double knockout (DKO) livers over control samples. (B) Pathway …
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional Information |
---|---|---|---|---|
Genetic reagent (Mus musculus) | Bcl6fl/fl | PMID 30566857 | ||
Genetic reagent (Mus musculus) | Albumin-cre | Jackson Laboratory | Stock #003574 | |
Genetic reagent (Mus musculus) | Ppara-/- | Jackson Laboratory | Stock #008154 | |
Genetic reagent (Mus musculus) | Ppardfl/fl | Jackson Laboratory | Stock #005897 | |
Antibody | anti-BCL6 (guinea pig polyclonal) | PMID 30566857 | custom polyclonal 7.5 μg per IP | |
Antibody | anti-PPARδ (guinea pig polyclonal) | PMID 28467934 | custom polyclonal 7.5 μg per IP | |
Antibody | anti-SMRT (guinea pig polyclonal) | PMID 22465074 | custom polyclonal 7.5 μg per IP | |
Antibody | anti-NCoR (guinea pig polyclonal) | PMID 22465074 | custom polyclonal 7.5 μg per IP | |
Antibody | anti-HDAC3 (rabbit polyclonal) | Santa Cruz | Cat. #: sc-11417x | 5 μg per IP |
Antibody | anti-H3K27ac (rabbit polyclonal) | Active Motif | Cat. #: 39133 | 5 μg per IP |
Antibody | anti-pAKT (rabbit monoclonal) | Cell Signaling | Cat. #: 4060 s | (1:1000) |
Antibody | anti-panAKT (rabbit monoclonal) | Cell Signaling | Cat. #: 4691 s | (1:1000) |
Antibody | anti-BCL6 (mouse monoclonal) | Santa Cruz | Cat. #: sc7388 | (1:200) |
Antibody | anti-β-Actin (mouse monoclonal) | Sigma-Aldrich | Cat. #: A1978 | 1:1000) |
Antibody | anti-PPARα (rabbit polyclonal) | Santa Cruz | Cat. #: sc-9000x | 7.5 μg per IP; WB: (1:500) |
Antibody | Peroxidase AffiniPure Goat Anti-Mouse IgG | Jackson ImmunoResearch | Cat. #: 115-035-174 | (1:20,000) |
Antibody | Peroxidase IgG Fraction Monoclonal Mouse Anti-Rabbit IgG | Jackson ImmunoResearch | Cat. #: 211-032-171 | (1:20,000) |
Antibody | Rabit Anti-guinea pig IgG H and L | Abcam | Cat. #: ab6698 | |
Chemical compound, drug | DSG Crosslinker | ProteoChem | Cat. #: c1104 | |
Chemical compound, drug | Formaldehyde, 16%, methanol-free, Ultra Pure | Polysciences, Inc | Cat. #: 18814–20 | |
Chemical compound, drug | RNAlater Stabilization Solution | ThermoFisher Scientific | Cat. #: AM7020 | |
Chemical compound, drug | TRIzol Reagent | ThermoFisher Scientific | Cat. #: 15596018 | |
Chemical compound, drug | Poloxamer 407 | Sigma-Aldrich | Cat. #: 16758 | |
Chemical compound, drug | cOmplete Ultra Tablets, EDTA-free | Sigma-Aldrich | Cat. #: 5892953001 | |
Chemical compound, drug | Deuterium oxide | Sigma-Aldrich | Cat. #: 151882 | |
Chemical compound, drug | Sodium Palmitate | Sigma-Aldrich | Cat. #: P9767 | |
Chemical compound, drug | Palmitic Acid, [1–14C] | MP Biomedicals | Cat. #: 12195 | |
Chemical compound, drug | BODIPY 500/510 C1, C12 | Invitrogen | Cat. #: D3823 | |
Chemical compound, drug | Humulin R | Lilly | NDC 0002-8215-01 | |
Commercial assay or kit | Dynabeads M-280 Sheep Anti-Rabbit IgG | Invitrogen | Cat. #: 11204D | |
Commercial assay or kit | Dynabeads M-280 Tosylactivated | Invitrogen | Cat. #: 14204 | |
Commercial assay or kit | Protein A Agarose/Salmon Sperm DNA | Millipore | Cat. #: 16–157 | |
Commercial assay or kit | iScript cDNA Synthesis Kit | BioRad | Cat. #: 1708891 | |
Commercial assay or kit | iTaq Universal SYBR Green | BioRad | Cat. #: 1725124 | |
Commercial assay or kit | Infinity Triglyceride Assay Kit | ThermoFisher Scientific | Cat. #: TR22421 | |
Commercial assay or kit | β-Hydroxybutyrate (Ketone Body) Colorimetric Assay Kit | Cayman Chemical | Cat. #: 700190 | |
Commercial assay or kit | Ultra Sensitive Mouse Insulin ELISA Kit | Crystal Chem | Cat. #: 90080 | |
Commercial assay or kit | Glucose Colorimetric /Fluorometric Assay Kit | BioVision | Cat. #: K606 | |
Commercial assay or kit | Microvette CB 300 K2E | Sarstedt | Cat. #: 16.444 | |
Commercial assay or kit | MemCode Reversible Protein Stain Kit | ThermoFisher Scientific | Cat. #: 24585 | |
Commercial assay or kit | Whatman qualitative filter paper | Sigma-Aldrich | Cat. #: WHA1003055 | |
Commercial assay or kit | KAPA Hyper Prep Library Prep Kit | Kapa Biosystems | Cat. #: KK8504 | |
Commercial assay or kit | KAPA Stranded RNA-seq Kit with RiboErase | Kapa Biosystems | Cat. #: KK8483 | |
Commercial assay or kit | NextSeq 500/550 High Output Kit v2.5 (75 cycles) | Illumina | Cat. #: 20024906 | |
Other, research diet (45% kcal from fat) | HFD | Research Diets, Inc | Stock #D12451 |
Quantitative PCR primers for chromatin immunoprecipitation.
Quantitative PCR primers for gene expression.