Review




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.
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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 Comparison of the salt elution profiles, measured by QINESIn (as in Suppl. Fig. ), of H2A, H2A.X, H2A.Z (detected by the antibody ZAbA; Abcam, ab 97966) and of H3-GFP (used as an internal control) in HeLa nuclei. B Salt elution profile of H2A.Z detected by ZAbA in HeLa nuclei of different cell cycle phases. C Salt elution curves of H2A.Z detected by ZAbB (Thermo Fisher Sci.) and ZAbA, measured separately in HeLa nuclei. In ( A – C ), the elution curves refer to G1 phase nuclei gated according to their DNA fluorescence intensity distribution and the error bars represent SEM of ~600 nuclei measured by LSC. Blue arrows on the elution curves indicate EC50 values (also in the other figures). D , E CLSM images and line-scans showing nuclear localization of H2A.Z as recognized by ZAbA ( D ), or by ZAbB ( E ). F IF staining of H2A.Z (using ZAbA or ZAbB), Lamin B1, HP1, CTCF, Rad21, H1, H3K9me3, and H3K27me3 in halo samples of HeLa nuclei. Representative images are shown. G Hydroxyapatite dissociation chromatography analyses of chromatin assembled in vitro using Xenopus laevis N1/N2- (H3, H4) and recombinant <t>H2A/H2B</t> or H2A.Z.1/H2B (see “Methods”). The H2A/H2B dimers run on the gel as a single band. See full gel image in Suppl. Fig. . Arrows point at the histones eluted at 1 M salt.
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A Comparison of the salt elution profiles, measured by QINESIn (as in Suppl. Fig. ), of H2A, H2A.X, H2A.Z (detected by the antibody ZAbA; Abcam, ab 97966) and of H3-GFP (used as an internal control) in HeLa nuclei. B Salt elution profile of H2A.Z detected by ZAbA in HeLa nuclei of different cell cycle phases. C Salt elution curves of H2A.Z detected by ZAbB (Thermo Fisher Sci.) and ZAbA, measured separately in HeLa nuclei. In ( A – C ), the elution curves refer to G1 phase nuclei gated according to their DNA fluorescence intensity distribution and the error bars represent SEM of ~600 nuclei measured by LSC. Blue arrows on the elution curves indicate EC50 values (also in the other figures). D , E CLSM images and line-scans showing nuclear localization of H2A.Z as recognized by ZAbA ( D ), or by ZAbB ( E ). F IF staining of H2A.Z (using ZAbA or ZAbB), Lamin B1, HP1, CTCF, Rad21, H1, H3K9me3, and H3K27me3 in halo samples of HeLa nuclei. Representative images are shown. G Hydroxyapatite dissociation chromatography analyses of chromatin assembled in vitro using Xenopus laevis N1/N2- (H3, H4) and recombinant <t>H2A/H2B</t> or H2A.Z.1/H2B (see “Methods”). The H2A/H2B dimers run on the gel as a single band. See full gel image in Suppl. Fig. . Arrows point at the histones eluted at 1 M salt.
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A Comparison of the salt elution profiles, measured by QINESIn (as in Suppl. Fig. ), of H2A, H2A.X, H2A.Z (detected by the antibody ZAbA; Abcam, ab 97966) and of H3-GFP (used as an internal control) in HeLa nuclei. B Salt elution profile of H2A.Z detected by ZAbA in HeLa nuclei of different cell cycle phases. C Salt elution curves of H2A.Z detected by ZAbB (Thermo Fisher Sci.) and ZAbA, measured separately in HeLa nuclei. In ( A – C ), the elution curves refer to G1 phase nuclei gated according to their DNA fluorescence intensity distribution and the error bars represent SEM of ~600 nuclei measured by LSC. Blue arrows on the elution curves indicate EC50 values (also in the other figures). D , E CLSM images and line-scans showing nuclear localization of H2A.Z as recognized by ZAbA ( D ), or by ZAbB ( E ). F IF staining of H2A.Z (using ZAbA or ZAbB), Lamin B1, HP1, CTCF, Rad21, H1, H3K9me3, and H3K27me3 in halo samples of HeLa nuclei. Representative images are shown. G Hydroxyapatite dissociation chromatography analyses of chromatin assembled in vitro using Xenopus laevis N1/N2- (H3, H4) and recombinant <t>H2A/H2B</t> or H2A.Z.1/H2B (see “Methods”). The H2A/H2B dimers run on the gel as a single band. See full gel image in Suppl. Fig. . Arrows point at the histones eluted at 1 M salt.
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A Comparison of the salt elution profiles, measured by QINESIn (as in Suppl. Fig. ), of H2A, H2A.X, H2A.Z (detected by the antibody ZAbA; Abcam, ab 97966) and of H3-GFP (used as an internal control) in HeLa nuclei. B Salt elution profile of H2A.Z detected by ZAbA in HeLa nuclei of different cell cycle phases. C Salt elution curves of H2A.Z detected by ZAbB (Thermo Fisher Sci.) and ZAbA, measured separately in HeLa nuclei. In ( A – C ), the elution curves refer to G1 phase nuclei gated according to their DNA fluorescence intensity distribution and the error bars represent SEM of ~600 nuclei measured by LSC. Blue arrows on the elution curves indicate EC50 values (also in the other figures). D , E CLSM images and line-scans showing nuclear localization of H2A.Z as recognized by ZAbA ( D ), or by ZAbB ( E ). F IF staining of H2A.Z (using ZAbA or ZAbB), Lamin B1, HP1, CTCF, Rad21, H1, H3K9me3, and H3K27me3 in halo samples of HeLa nuclei. Representative images are shown. G Hydroxyapatite dissociation chromatography analyses of chromatin assembled in vitro using Xenopus laevis N1/N2- (H3, H4) and recombinant <t>H2A/H2B</t> or H2A.Z.1/H2B (see “Methods”). The H2A/H2B dimers run on the gel as a single band. See full gel image in Suppl. Fig. . Arrows point at the histones eluted at 1 M salt.
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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.
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Image Search Results


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 Comparison of the salt elution profiles, measured by QINESIn (as in Suppl. Fig. ), of H2A, H2A.X, H2A.Z (detected by the antibody ZAbA; Abcam, ab 97966) and of H3-GFP (used as an internal control) in HeLa nuclei. B Salt elution profile of H2A.Z detected by ZAbA in HeLa nuclei of different cell cycle phases. C Salt elution curves of H2A.Z detected by ZAbB (Thermo Fisher Sci.) and ZAbA, measured separately in HeLa nuclei. In ( A – C ), the elution curves refer to G1 phase nuclei gated according to their DNA fluorescence intensity distribution and the error bars represent SEM of ~600 nuclei measured by LSC. Blue arrows on the elution curves indicate EC50 values (also in the other figures). D , E CLSM images and line-scans showing nuclear localization of H2A.Z as recognized by ZAbA ( D ), or by ZAbB ( E ). F IF staining of H2A.Z (using ZAbA or ZAbB), Lamin B1, HP1, CTCF, Rad21, H1, H3K9me3, and H3K27me3 in halo samples of HeLa nuclei. Representative images are shown. G Hydroxyapatite dissociation chromatography analyses of chromatin assembled in vitro using Xenopus laevis N1/N2- (H3, H4) and recombinant H2A/H2B or H2A.Z.1/H2B (see “Methods”). The H2A/H2B dimers run on the gel as a single band. See full gel image in Suppl. Fig. . Arrows point at the histones eluted at 1 M salt.

Journal: Nature Communications

Article Title: Epigenetic modulation via the C-terminal tail of H2A.Z

doi: 10.1038/s41467-024-53514-9

Figure Lengend Snippet: A Comparison of the salt elution profiles, measured by QINESIn (as in Suppl. Fig. ), of H2A, H2A.X, H2A.Z (detected by the antibody ZAbA; Abcam, ab 97966) and of H3-GFP (used as an internal control) in HeLa nuclei. B Salt elution profile of H2A.Z detected by ZAbA in HeLa nuclei of different cell cycle phases. C Salt elution curves of H2A.Z detected by ZAbB (Thermo Fisher Sci.) and ZAbA, measured separately in HeLa nuclei. In ( A – C ), the elution curves refer to G1 phase nuclei gated according to their DNA fluorescence intensity distribution and the error bars represent SEM of ~600 nuclei measured by LSC. Blue arrows on the elution curves indicate EC50 values (also in the other figures). D , E CLSM images and line-scans showing nuclear localization of H2A.Z as recognized by ZAbA ( D ), or by ZAbB ( E ). F IF staining of H2A.Z (using ZAbA or ZAbB), Lamin B1, HP1, CTCF, Rad21, H1, H3K9me3, and H3K27me3 in halo samples of HeLa nuclei. Representative images are shown. G Hydroxyapatite dissociation chromatography analyses of chromatin assembled in vitro using Xenopus laevis N1/N2- (H3, H4) and recombinant H2A/H2B or H2A.Z.1/H2B (see “Methods”). The H2A/H2B dimers run on the gel as a single band. See full gel image in Suppl. Fig. . Arrows point at the histones eluted at 1 M salt.

Article Snippet: : GR3211735-2, Abcam, Cambridge, UK; 1 mg/ml), rabbit polyclonal anti-H2B (ab52484, lot num.

Techniques: Comparison, Control, Fluorescence, Staining, Chromatography, In Vitro, Recombinant

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