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Structured Review

Abcam rabbit polyclonal anti histone h2b
a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and <t>H2B</t> display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.
Rabbit Polyclonal Anti Histone H2b, supplied by Abcam, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Chromatin organization drives the search mechanism of nuclear factors"

Article Title: Chromatin organization drives the search mechanism of nuclear factors

Journal: Nature Communications

doi: 10.1038/s41467-023-42133-5

a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.
Figure Legend Snippet: a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.

Techniques Used: Microscopy, Diffusion-based Assay



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A, Changes in PDUI score (-0.1 > PDUI > 0.1; P<0.05) denoting 3′-UTR-shortened (red) and lengthened (blue) genes. B, Genes showing lengthening (right) or shortening (left) events (-0.1> PDUI > 0.1; P<0.05) and are differentially expressed (FDR<0.05; fold change >1.5) as color coded. Up=upregulated gene expression, Down=downregulated gene expression. C, Venn diagram showing overlapping genes with significant APA alterations between JTE-607- treated and CPSF3 knockdown cells. D, Heatmap of differentially expressed genes in Panc1 cells treated with JTE-607. Expression is plotted as transformed expression value. Blue triangles denote replication-dependent histone genes. E, Gene set enrichment analysis (GSEA) of RNA-seq data from (D) . F, mRNA expression of <t>H2B</t> and H3 in MiaPaCa2 cells treated with JTE-607. * , P < 0.05, ** , P < 0.01, *** , P < 0.001, Ordinary one-way ANOVA with Dunnett’s multiple comparisons test.
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Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.

Journal: Frontiers in Pharmacology

Article Title: Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells

doi: 10.3389/fphar.2023.1271435

Figure Lengend Snippet: Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.

Article Snippet: The following antibodies were used in this study; goat polyclonal CTSV (BioTechne, AF1080), goat polyclonal cyclin D1/D2 (AF4196, BioTechne), mouse monoclonal cyclin E1 (MAB68101, BioTechne), rabbit monoclonal cyclin B1 (MAB60001, BioTechne), rabbit polyclonal HDAC1 (2062S, Cell Signaling), mouse monoclonal histone H1 (NBP2-45184, BioTechne), rabbit polyclonal histone H2a (NB100-56346, BioTechne), rabbit polyclonal histone H2b (NB100-56633, BioTechne), rabbit monoclonal histone H3 (4499S, Cell Signaling), rabbit monoclonal histone H4 (NBP2-80444, BioTechne), mouse monoclonal Hsc70 (MAB4148, BioTechne), mouse monoclonal Hsp90 (ab13492, Abcam), mouse monoclonal Asf1b (NBP2-61684, BioTechne), rabbit monoclonal NASP (ab181169, Abcam), mouse monoclonal GATA3 (BioTechne, MAB6330), goat polyclonal GAPDH (BioTechne, AF5718), mouse monoclonal CTSL (BioTechne, MAB9521) and rat monoclonal α-Tubulin (ab6160, Abcam).

Techniques: Expressing, Western Blot

a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Chromatin organization drives the search mechanism of nuclear factors

doi: 10.1038/s41467-023-42133-5

Figure Lengend Snippet: a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.

Article Snippet: The antibodies employed in this study were: mouse monoclonal anti-p53 DO-1 (Santa Cruz Biotechnology, cat. sc-126; 1:3000 dilution, incubated 1 h at RT), rabbit monoclonal anti-p21 (Abcam, cat. ab109520; 1:1000 dilution, incubated overnight at 4 °C), rabbit monoclonal anti-GAPDH (Abcam, cat. ab128915; 1:50,000 dilution, incubated 1 h at RT), rabbit monoclonal anti-NF-κB p65 (Cell Signaling cat. D14E12 XP®; dilution 1:1000), rabbit polyclonal anti-Histone H2B (Abcam cat. ab1790, dilution 1:5000), mouse monoclonal anti-HaloTag (Promega G921A, dilution 1:1000), mouse monoclonal anti-vinculin (Thermo-Fisher, cat. MA5-11690; 1:4000 dilution, incubated 1 h at RT).

Techniques: Microscopy, Diffusion-based Assay

Journal: iScience

Article Title: Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation

doi: 10.1016/j.isci.2023.107951

Figure Lengend Snippet:

Article Snippet: Polyclonal rabbit antibodies against human histone 2b , Abcam , ab1790.

Techniques: Virus, Sterility, Recombinant, Mass Spectrometry, Activation Assay, Software

A, Changes in PDUI score (-0.1 > PDUI > 0.1; P<0.05) denoting 3′-UTR-shortened (red) and lengthened (blue) genes. B, Genes showing lengthening (right) or shortening (left) events (-0.1> PDUI > 0.1; P<0.05) and are differentially expressed (FDR<0.05; fold change >1.5) as color coded. Up=upregulated gene expression, Down=downregulated gene expression. C, Venn diagram showing overlapping genes with significant APA alterations between JTE-607- treated and CPSF3 knockdown cells. D, Heatmap of differentially expressed genes in Panc1 cells treated with JTE-607. Expression is plotted as transformed expression value. Blue triangles denote replication-dependent histone genes. E, Gene set enrichment analysis (GSEA) of RNA-seq data from (D) . F, mRNA expression of H2B and H3 in MiaPaCa2 cells treated with JTE-607. * , P < 0.05, ** , P < 0.01, *** , P < 0.001, Ordinary one-way ANOVA with Dunnett’s multiple comparisons test.

Journal: bioRxiv

Article Title: CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone processing

doi: 10.1101/2022.05.09.491230

Figure Lengend Snippet: A, Changes in PDUI score (-0.1 > PDUI > 0.1; P<0.05) denoting 3′-UTR-shortened (red) and lengthened (blue) genes. B, Genes showing lengthening (right) or shortening (left) events (-0.1> PDUI > 0.1; P<0.05) and are differentially expressed (FDR<0.05; fold change >1.5) as color coded. Up=upregulated gene expression, Down=downregulated gene expression. C, Venn diagram showing overlapping genes with significant APA alterations between JTE-607- treated and CPSF3 knockdown cells. D, Heatmap of differentially expressed genes in Panc1 cells treated with JTE-607. Expression is plotted as transformed expression value. Blue triangles denote replication-dependent histone genes. E, Gene set enrichment analysis (GSEA) of RNA-seq data from (D) . F, mRNA expression of H2B and H3 in MiaPaCa2 cells treated with JTE-607. * , P < 0.05, ** , P < 0.01, *** , P < 0.001, Ordinary one-way ANOVA with Dunnett’s multiple comparisons test.

Article Snippet: Primary antibodies were diluted in 3% BSA in TBST and incubated overnight at 4°C (mouse monoclonal CPSF3 antibody, Abcepta, AT1610a; rabbit polyclonal Histone H3 antibody, Cell Signaling Technology, 9715S; rabbit polyclonal Histone H2B antibody, Cell Signaling Technology, 8135S; mouse monoclonal GAPDH antibody, Proteintech, 60004-1-Ig; rabbit polyclonal FHL1 antibody, Proteintech, 10991-1-AP).

Techniques: Expressing, Transformation Assay, RNA Sequencing Assay

A, IGV-generated density plots of replication-dependent histones highlighting the differences of 3′- UTR coverage between DMSO (red) and JTE-607 (blue) treated cells. B, Western blot of H2B and H3 protein levels in Panc1 cells treated with 0-10μM JTE-607 for 24 and 48hrs. C, IGV-generated density plots of replication-independent histones highlighting the differences of 3′-UTR coverage between DMSO (red) and JTE-607 (blue) treated cells. D, DSeq2 normalized counts of H2AFZ and H3F3A histone variants in Panc1 cells treated with JTE-607. ** , P < 0.001. E-G, Volcano plots of Spearman’s correlation of CPSF3 and: E, all histone genes; F, replication-dependent histone genes; G, replication-independent histone genes. Each dot represents a histone gene. Blue and red dots denote positive and negative correlation, respectively. (Spearman = -0.15>R>0.15, P<0.05).

Journal: bioRxiv

Article Title: CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone processing

doi: 10.1101/2022.05.09.491230

Figure Lengend Snippet: A, IGV-generated density plots of replication-dependent histones highlighting the differences of 3′- UTR coverage between DMSO (red) and JTE-607 (blue) treated cells. B, Western blot of H2B and H3 protein levels in Panc1 cells treated with 0-10μM JTE-607 for 24 and 48hrs. C, IGV-generated density plots of replication-independent histones highlighting the differences of 3′-UTR coverage between DMSO (red) and JTE-607 (blue) treated cells. D, DSeq2 normalized counts of H2AFZ and H3F3A histone variants in Panc1 cells treated with JTE-607. ** , P < 0.001. E-G, Volcano plots of Spearman’s correlation of CPSF3 and: E, all histone genes; F, replication-dependent histone genes; G, replication-independent histone genes. Each dot represents a histone gene. Blue and red dots denote positive and negative correlation, respectively. (Spearman = -0.15>R>0.15, P<0.05).

Article Snippet: Primary antibodies were diluted in 3% BSA in TBST and incubated overnight at 4°C (mouse monoclonal CPSF3 antibody, Abcepta, AT1610a; rabbit polyclonal Histone H3 antibody, Cell Signaling Technology, 9715S; rabbit polyclonal Histone H2B antibody, Cell Signaling Technology, 8135S; mouse monoclonal GAPDH antibody, Proteintech, 60004-1-Ig; rabbit polyclonal FHL1 antibody, Proteintech, 10991-1-AP).

Techniques: Generated, Western Blot