Journal: bioRxiv

Article Title: Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis

doi: 10.1101/2023.06.28.546894

Figure Lengend Snippet: (A) Heatmap of combinatorial TF binding (percentage enrichment, 0-12 TFs) on VISTA enhancers that have subpallial (SP), pallial and subpallial (SP+P), pallial (P), non-telencephalic (non-tel), and no activity (inactive). (B) Stacked bar plot showing the percentage of newly identified regulatory sequences with high (8-12 TFs), intermediate (5-7 TFs), low (3-4 TFs), and very low (1 TF) binding in BG showing spatial regional activity. (C) Stacked bar plot depicting percentage of novel enhancers across binding clusters showing restricted spatial enhancer activity in the subpallium, pallium and shared among them. (D) Six pREs representing different clusters that were tested for activity in transgenic mouse assays . Clusters are shown in the left column, enhancer names are written in turquoise, and the success ratios are listed next to the name (i.e., 6/6 depicts 6 embryos with forebrain activity out of 6 embryos tested). Schemas predict the regulated genes by the tested enhancers (turquoise). The grey arrow depicts the orientation of the TSS. Green bars show the normalized binding of BG TFs, with color intensity proportional to ChIP-seq intensity. The specific TFs bound are shown above the top bar. Wholemounts (WM) and three sections representing the LacZ expression are shown. H3K27ac (green) and H3K27me3 (red) histone ChIP-seq results from the GE are shown to the right; the turquoise bars correspond to the tested genomic regions. Cx: Cortex; GE: Ganglionic Eminences; L: LGE; M: MGE; C: CGE. (E) Coronal brain section schematization showing: 1. the subregions of the primordial BG (LGE and MGE) as well as the cortex (top left hemisection) ; 2. the subregional laminae of the GEs (VZ, SVZ, and MZ; top right hemisection). Hemisections from 2 VISTA enhancers with specific sub regional activity are shown below with hs1056 showing activity in the VZ and SVZ of the MGE (bottom left hemisection) and hs566 showing activity in the mantle zones of the MGE and LGE (bottom right hemisection). (F) Bar plot depicting cluster classification of enhancers with VZ and non-VZ activity (n=99). See also Figure S4.

Article Snippet: Antibodies used were specific to H3 monomethyl lysine-4 (H3K4me1, Abcam, ab8895), H3 trimethyl lysine-4 (H3K4me3, Abcam, ab8580), H3 trimethyl lysine-27 (H3K27me3, Active Motif, 39157), and H3 acetylated lysine 27 (H3K27ac, Abcam, ab472).

Techniques: Binding Assay, Activity Assay, Transgenic Assay, ChIP-sequencing, Expressing

Journal: iScience

Article Title: Alcohol-sourced acetate impairs T cell function by promoting cortactin acetylation

doi: 10.1016/j.isci.2023.107230

Figure Lengend Snippet: Acetate accumulates in lymphoid organs and impairs T cells migration capacity (A–C) GC/MS quantification of acetate in (A) livers, (B) inguinal lymph nodes (iLN), and (C) spleens of alcohol-fed mice compared with water-fed control mice, expressed in mM concentration (individual data point represents one mouse). (D) Mouse CD4 + T cells treated in vitro with 5 mM 13 C labeled acetate exhibit increased 13 C labeled citrate, quantified by GC-MS. (E) Quantification of western blot analysis of the level of acetylated histone 3 at lysine 27 of mouse CD4 + T cells treated in vitro with 5 mM acetate (also see Figure S1 A). (F and G) Numbers of migrated mouse naive CD4 + T cells and (G) Jurkat T cells in vitro trans -well assay, counted by flow cytometer. (H) The ratio of acetate to control treated mouse CD4 + T cells found in the spleens of recipient mice in an adoptive transfer experiment at 2 h and (I) 48 h post transfer (each point represents one mouse, n = 5) (also see Figure S1 B). (J) Numbers of migrated mouse GPR43KO CD4 + T cells treated with 5 mM acetate in an in vitro trans -well assay, counted by flow cytometry. Representative data shown are either from one of two independent experiments (A–C, E, H–J) or combined three independent experiments (D), or one of three independent experiments (F, G), and expressed as mean ± SD. Statistical difference was determined by Student’s two-tailed t-test. ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001.

Article Snippet: Rabbit Anti-mouse Histone 3 Lysine 27 Acetyl, unconjugated , Abcam, Cambridge, United Kingdom , Cat#ab4729; RRID: AB_2118291.

Techniques: Migration, Gas Chromatography-Mass Spectrometry, Concentration Assay, In Vitro, Labeling, Western Blot, Flow Cytometry, Adoptive Transfer Assay, Two Tailed Test

Journal: iScience

Article Title: Alcohol-sourced acetate impairs T cell function by promoting cortactin acetylation

doi: 10.1016/j.isci.2023.107230

Figure Lengend Snippet:

Article Snippet: Rabbit Anti-mouse Histone 3 Lysine 27 Acetyl, unconjugated , Abcam, Cambridge, United Kingdom , Cat#ab4729; RRID: AB_2118291.

Techniques: Purification, Expressing, Infection, Recombinant, Mutagenesis, Synthesized, Software