Journal: Nucleic Acids Research

Article Title: Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets

doi: 10.1093/nar/gkt1034

Figure Lengend Snippet: Artificial TF induction of GFP in yeast. We previously described a system to induce an artificial ZF-EV with β-estradiol . Activation of GFP can be induced with β-estradiol if a target complementary to the zinc finger used is placed in the promoter upstream of the GFP coding sequence. To provide a sense of relative specificity and affinity, the helices described in , and the GAG-binding fingers described in , were challenged with a set of similar targets, listed across the bottom of the chart. Each experiment included a positive control, the Zif268 activity when paired with its consensus target. This allows for the GFP output to be normalized in each experiment to the positive control output. Here, the normalized GFP output for each zinc finger and binding site pair is shown as a heat plot. For reference, a key is provided that shows the normalized GFP output when Zif268 is paired with binding sites of known affinity relative to the consensus . Asterisk: helices underlined and in italics were tested as suggested in the literature to bind the target noted on the left .

Article Snippet: Induction of ZF-EV activators by 100 nM β-estradiol (Tocris Biosciences, Ellisville, MO, USA) was performed in cells during log-phase growth (culture absorbance = 50–100 Klett units).

Techniques: Activation Assay, Sequencing, Binding Assay, Positive Control, Activity Assay

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: TRIM24 as a therapeutic target in endocrine treatment–resistant breast cancer

doi: 10.1073/pnas.2507571122

Figure Lengend Snippet: TRIM24 binds together with ERα at the same genomic locations, and its binding is hormone dependent. ( A ) Snapshots of ERα and TRIM24 ChIP-seq signal at GREB1, TFF1, and IGFBP4 loci. The genomic coordinates are annotated. ( B ) Heatmap disclosing ChIP-seq signal for Input, ERα, and TRIM24 in full medium. Regions were sorted according to decreasing ERα signal. Data are centered at each factor peak, depicting a ±1 kb window around the peak center. ( C ) Correlation plot between ERα and TRIM24 ChIP-seq signal at ERα peaks. Pearson’s correlation coefficient (R) is indicated. Red line depicts the linear regression (glm, y ~ x) ± SE. Color scale indicates the dot density. ( D ) Motif enrichment analysis at TRIM24 binding sites. Font size represents log 10 ( P -value) × 10 3 . ( E ) GIGGLE enrichment analysis for the top transcription factors binding at the enriched TRIM24 sites. ( F ) Snapshots of TRIM24 ChIP-seq signal at GREB1, TFF1, and IGFBP4 loci upon treatment with DMSO or E2 for 3 h. The genomic coordinates are annotated.

Article Snippet: For ligand treatment, 10 nM estradiol (E2) (HY-B0141; MedChemExpress) was used.

Techniques: Binding Assay, ChIP-sequencing

Journal: Biochimica et biophysica acta. Molecular and cell biology of lipids

Article Title: PCSK9 deficiency results in a specific shedding of excess LDLR in female mice only: Role of hepatic cholesterol.

doi: 10.1016/j.bbalip.2022.159217

Figure Lengend Snippet: Fig. 3. Shedding of excess LDLR in PCSK9-deficient mice depends on estrogen and is achieved by metalloproteases. (A) Plasma levels of shed LDLR (sLDLR) were assessed in all mouse models and normalized to WT male levels. n = 4–5 mice. (B) sLDLR was measured for 28 h in WT and KO male mice after vehicle (Veh) or E2 injection (50 μg/kg; n = 4–6 mice). (C) WT and KO female mice received an intraperitoneal injection of vehicle or the metalloprotease inhibitor BB-94 (12.5 mg/kg; n = 4–5 mice). Mean ± SEM were normalized to WT Veh value at t = 0 and set to 1. P values were determined using Mann-Whitney U test (A; non parametric data) and 2-way ANOVA followed by Tukey’s multiple comparisons test (B and C).

Article Snippet: Male mice were treated with E2 (see above) and male or female mice were treated with the metalloprotease inhibitors BB-94 and ZLDI-8 resuspended in DMSO (MedChemExpress, Princeton, NJ) and diluted ≥10-fold in corn oil before intraperitoneal injection.

Techniques: Clinical Proteomics, Injection, MANN-WHITNEY