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    New England Biolabs methodologies sufficiently inhibited adapter dimer formation
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    dimer method  (New England Biolabs)


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    human recombinant histone h2a h2b dimer  (New England Biolabs)


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    New England Biolabs human recombinant histone h2a h2b dimer
    Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and <t>H2A/H2B</t> dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).
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    1) Product Images from "Nucleosome assembly and disassembly pathways in vitro"

    Article Title: Nucleosome assembly and disassembly pathways in vitro

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0267382

    Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and H2A/H2B dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).
    Figure Legend Snippet: Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and H2A/H2B dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).

    Techniques Used: Sequencing

    This schematic representation shows those DNA regions that interact with the different histone dimers in the fully formed NCP. To distinguish the two copies of the H2A/H2B dimer, they are labelled 5’ (light blue, chains G, H) and 3’ (dark blue, chains C, D). Similarly, the two pairs of H3/H4 histones are labelled 5’ (pink, chains E, F) and 3’ (red, chains A, B). The DNA sequence is labelled as SHL (Super Helical Location, defined in Material and Methods). The denominations A, B, … of the histone chains are those commonly used in X-ray structures.
    Figure Legend Snippet: This schematic representation shows those DNA regions that interact with the different histone dimers in the fully formed NCP. To distinguish the two copies of the H2A/H2B dimer, they are labelled 5’ (light blue, chains G, H) and 3’ (dark blue, chains C, D). Similarly, the two pairs of H3/H4 histones are labelled 5’ (pink, chains E, F) and 3’ (red, chains A, B). The DNA sequence is labelled as SHL (Super Helical Location, defined in Material and Methods). The denominations A, B, … of the histone chains are those commonly used in X-ray structures.

    Techniques Used: Sequencing

    dimer formation  (New England Biolabs)


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    h2a h2b dimer  (New England Biolabs)


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    New England Biolabs h2a h2b
    I. Western blot of cell fractionations performed on BAC9 mESC. Chromatin fraction was washed with increasing concentrations of NaCl to release electrostatic interactions with the chromatin. The blot was probed with anti-GCNA (GCNA-1), anti-H3 and anti-tubulin antibodies. Data is representative from three independent experiments. B. Schematic representation of constructs used in (C), (D), (E) and (F). C. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. D. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, <t>anti-H2B</t> and anti-beta-actin antibodies. Data is representative from three independent experiments. E. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. F. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, <t>anti-H2B</t> and anti-beta-actin antibodies. Data is representative from three independent experiments. G. Proximity ligation assay performed with anti-H3 and anti-GCNA (Tra98) antibodies on wild-type and Gcna − /Y adult testis sections. Data is representative from two independent experiments.
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    1) Product Images from "GCNA is a histone binding protein required for spermatogonial stem cell maintenance"

    Article Title: GCNA is a histone binding protein required for spermatogonial stem cell maintenance

    Journal: bioRxiv

    doi: 10.1101/2022.02.21.481287

    I. Western blot of cell fractionations performed on BAC9 mESC. Chromatin fraction was washed with increasing concentrations of NaCl to release electrostatic interactions with the chromatin. The blot was probed with anti-GCNA (GCNA-1), anti-H3 and anti-tubulin antibodies. Data is representative from three independent experiments. B. Schematic representation of constructs used in (C), (D), (E) and (F). C. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. D. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. E. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. F. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. G. Proximity ligation assay performed with anti-H3 and anti-GCNA (Tra98) antibodies on wild-type and Gcna − /Y adult testis sections. Data is representative from two independent experiments.
    Figure Legend Snippet: I. Western blot of cell fractionations performed on BAC9 mESC. Chromatin fraction was washed with increasing concentrations of NaCl to release electrostatic interactions with the chromatin. The blot was probed with anti-GCNA (GCNA-1), anti-H3 and anti-tubulin antibodies. Data is representative from three independent experiments. B. Schematic representation of constructs used in (C), (D), (E) and (F). C. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. D. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. E. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. F. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. G. Proximity ligation assay performed with anti-H3 and anti-GCNA (Tra98) antibodies on wild-type and Gcna − /Y adult testis sections. Data is representative from two independent experiments.

    Techniques Used: Western Blot, Construct, Immunoprecipitation, Transfection, Proximity Ligation Assay

    A. Representative limited proteolysis assay performed with H3-H4, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 15, 45 and 90 min then analysed by SDS-PAGE followed by silver staining. Data is representative from three independent experiments. B. Representative limited proteolysis assay performed with H2A-H2B, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 2, 4 and 6 hours then analysed by SDS-PAGE followed by silver staining. Data is representative from two independent experiments. C. Schematic representation of the in vitro nucleosome assembly activity assay. A supercoiled plasmid is relaxed by TopoI then DNA was incubated with core histones and the histone chaperone. While nucleosomes are formed, supecoils are also formed into the plasmid and supercoiling is analysed by gel electrophoresis after deproteinisation of the plasmid. D. Representative in vitro nucleosome assembly activity assay with MBP and MBP-mGCNA. In this assay, MBP was used at a concentration of 0.66µM and MBP-mGCNA was used at 0.165, 0.33 or 0.66µM. Data is representative from three independent experiments. E. Quantification of the signal of the supercoiled plasmid in presence of histones and increasing concentrations of MBP-mGCNA (lanes 5 to 7 in (D)), relative to the signal with histones and MBP (lane 4 in (D)). Data represent the mean and S.D.. Data represent three independent experiments. P values were calculated by using an unpaired t-test.
    Figure Legend Snippet: A. Representative limited proteolysis assay performed with H3-H4, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 15, 45 and 90 min then analysed by SDS-PAGE followed by silver staining. Data is representative from three independent experiments. B. Representative limited proteolysis assay performed with H2A-H2B, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 2, 4 and 6 hours then analysed by SDS-PAGE followed by silver staining. Data is representative from two independent experiments. C. Schematic representation of the in vitro nucleosome assembly activity assay. A supercoiled plasmid is relaxed by TopoI then DNA was incubated with core histones and the histone chaperone. While nucleosomes are formed, supecoils are also formed into the plasmid and supercoiling is analysed by gel electrophoresis after deproteinisation of the plasmid. D. Representative in vitro nucleosome assembly activity assay with MBP and MBP-mGCNA. In this assay, MBP was used at a concentration of 0.66µM and MBP-mGCNA was used at 0.165, 0.33 or 0.66µM. Data is representative from three independent experiments. E. Quantification of the signal of the supercoiled plasmid in presence of histones and increasing concentrations of MBP-mGCNA (lanes 5 to 7 in (D)), relative to the signal with histones and MBP (lane 4 in (D)). Data represent the mean and S.D.. Data represent three independent experiments. P values were calculated by using an unpaired t-test.

    Techniques Used: Proteolysis Assay, Incubation, SDS Page, Silver Staining, In Vitro, Activity Assay, Plasmid Preparation, Nucleic Acid Electrophoresis, Concentration Assay

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    New England Biolabs methodologies sufficiently inhibited adapter dimer formation
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    Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and <t>H2A/H2B</t> dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).
    Human Recombinant Histone H2a H2b Dimer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dimer formation
    Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and <t>H2A/H2B</t> dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).
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    New England Biolabs h2a h2b dimer
    Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and <t>H2A/H2B</t> dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).
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    I. Western blot of cell fractionations performed on BAC9 mESC. Chromatin fraction was washed with increasing concentrations of NaCl to release electrostatic interactions with the chromatin. The blot was probed with anti-GCNA (GCNA-1), anti-H3 and anti-tubulin antibodies. Data is representative from three independent experiments. B. Schematic representation of constructs used in (C), (D), (E) and (F). C. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. D. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, <t>anti-H2B</t> and anti-beta-actin antibodies. Data is representative from three independent experiments. E. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. F. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, <t>anti-H2B</t> and anti-beta-actin antibodies. Data is representative from three independent experiments. G. Proximity ligation assay performed with anti-H3 and anti-GCNA (Tra98) antibodies on wild-type and Gcna − /Y adult testis sections. Data is representative from two independent experiments.
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    Image Search Results


    Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and H2A/H2B dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).

    Journal: PLoS ONE

    Article Title: Nucleosome assembly and disassembly pathways in vitro

    doi: 10.1371/journal.pone.0267382

    Figure Lengend Snippet: Changes in the probability of YpY dimer formation are presented in terms of absolute values of log2 of the intensity ratios (|log2(IR)|) along the 601 sequence expressed in SHLs; they are given for decreasing (top panel) or increasing (bottom panel) ionic strengths, as indicated by the green and black arrow respectively. The IR quantities are the ratios calculated between the normalised peak heights associated with each YpY step in the histone plus DNA mixtures and those of DNA alone. Red and blue bars correspond to DNA residues involved in the interface with H3/H4 and H2A/H2B dimers, respectively; black bars correspond to dinucleotides contacted by the two dimers. Minor-groove inward facing regions observed in the nucleosome structures are represented by grey boxes. Error bars are first-order estimations of standard errors calculated on at least 3 independent experiments (see Material and Methods for details).

    Article Snippet: Human recombinant histone H2A/H2B dimer (5.5 μg, 203 pmol) and histone (H3/H4) 2 tetramer (5.5 μg, 102 pmol) (New England BioLabs) were mixed with linearised 601 DNA fragments (10 μg, 23 pmol) in 30 μl of 2M salt buffer (18 mM Tris-HCl, 2 M NaCl, 0.9 mM DTT, 0.9 mM EDTA).

    Techniques: Sequencing

    This schematic representation shows those DNA regions that interact with the different histone dimers in the fully formed NCP. To distinguish the two copies of the H2A/H2B dimer, they are labelled 5’ (light blue, chains G, H) and 3’ (dark blue, chains C, D). Similarly, the two pairs of H3/H4 histones are labelled 5’ (pink, chains E, F) and 3’ (red, chains A, B). The DNA sequence is labelled as SHL (Super Helical Location, defined in Material and Methods). The denominations A, B, … of the histone chains are those commonly used in X-ray structures.

    Journal: PLoS ONE

    Article Title: Nucleosome assembly and disassembly pathways in vitro

    doi: 10.1371/journal.pone.0267382

    Figure Lengend Snippet: This schematic representation shows those DNA regions that interact with the different histone dimers in the fully formed NCP. To distinguish the two copies of the H2A/H2B dimer, they are labelled 5’ (light blue, chains G, H) and 3’ (dark blue, chains C, D). Similarly, the two pairs of H3/H4 histones are labelled 5’ (pink, chains E, F) and 3’ (red, chains A, B). The DNA sequence is labelled as SHL (Super Helical Location, defined in Material and Methods). The denominations A, B, … of the histone chains are those commonly used in X-ray structures.

    Article Snippet: Human recombinant histone H2A/H2B dimer (5.5 μg, 203 pmol) and histone (H3/H4) 2 tetramer (5.5 μg, 102 pmol) (New England BioLabs) were mixed with linearised 601 DNA fragments (10 μg, 23 pmol) in 30 μl of 2M salt buffer (18 mM Tris-HCl, 2 M NaCl, 0.9 mM DTT, 0.9 mM EDTA).

    Techniques: Sequencing

    I. Western blot of cell fractionations performed on BAC9 mESC. Chromatin fraction was washed with increasing concentrations of NaCl to release electrostatic interactions with the chromatin. The blot was probed with anti-GCNA (GCNA-1), anti-H3 and anti-tubulin antibodies. Data is representative from three independent experiments. B. Schematic representation of constructs used in (C), (D), (E) and (F). C. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. D. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. E. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. F. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. G. Proximity ligation assay performed with anti-H3 and anti-GCNA (Tra98) antibodies on wild-type and Gcna − /Y adult testis sections. Data is representative from two independent experiments.

    Journal: bioRxiv

    Article Title: GCNA is a histone binding protein required for spermatogonial stem cell maintenance

    doi: 10.1101/2022.02.21.481287

    Figure Lengend Snippet: I. Western blot of cell fractionations performed on BAC9 mESC. Chromatin fraction was washed with increasing concentrations of NaCl to release electrostatic interactions with the chromatin. The blot was probed with anti-GCNA (GCNA-1), anti-H3 and anti-tubulin antibodies. Data is representative from three independent experiments. B. Schematic representation of constructs used in (C), (D), (E) and (F). C. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. D. Western blot of the FLAG immunoprecipitation. 3T3 cells were transiently transfected with FLAG-mGCNA and a FLAG immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-FLAG, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. E. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H3 and anti-beta-actin antibodies. Data is representative from three independent experiments. F. Western blot of the GFP immunoprecipitation. 293-T cells were transiently transfected with GFP-fused proteins and a GFP immunoprecipitation was performed on the soluble fraction. The blot was probed with anti-GFP, anti-H2B and anti-beta-actin antibodies. Data is representative from three independent experiments. G. Proximity ligation assay performed with anti-H3 and anti-GCNA (Tra98) antibodies on wild-type and Gcna − /Y adult testis sections. Data is representative from two independent experiments.

    Article Snippet: In a 100 µl reaction, 1.4 µg of H3-H4 (catalog no. M2509S, New England Biolabs) or H2A-H2B (catalog no. M2508S, New England Biolabs) were incubated with 2.5 µg of MBP or MBP-mGCNA in Binding buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 % glycerol).

    Techniques: Western Blot, Construct, Immunoprecipitation, Transfection, Proximity Ligation Assay

    A. Representative limited proteolysis assay performed with H3-H4, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 15, 45 and 90 min then analysed by SDS-PAGE followed by silver staining. Data is representative from three independent experiments. B. Representative limited proteolysis assay performed with H2A-H2B, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 2, 4 and 6 hours then analysed by SDS-PAGE followed by silver staining. Data is representative from two independent experiments. C. Schematic representation of the in vitro nucleosome assembly activity assay. A supercoiled plasmid is relaxed by TopoI then DNA was incubated with core histones and the histone chaperone. While nucleosomes are formed, supecoils are also formed into the plasmid and supercoiling is analysed by gel electrophoresis after deproteinisation of the plasmid. D. Representative in vitro nucleosome assembly activity assay with MBP and MBP-mGCNA. In this assay, MBP was used at a concentration of 0.66µM and MBP-mGCNA was used at 0.165, 0.33 or 0.66µM. Data is representative from three independent experiments. E. Quantification of the signal of the supercoiled plasmid in presence of histones and increasing concentrations of MBP-mGCNA (lanes 5 to 7 in (D)), relative to the signal with histones and MBP (lane 4 in (D)). Data represent the mean and S.D.. Data represent three independent experiments. P values were calculated by using an unpaired t-test.

    Journal: bioRxiv

    Article Title: GCNA is a histone binding protein required for spermatogonial stem cell maintenance

    doi: 10.1101/2022.02.21.481287

    Figure Lengend Snippet: A. Representative limited proteolysis assay performed with H3-H4, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 15, 45 and 90 min then analysed by SDS-PAGE followed by silver staining. Data is representative from three independent experiments. B. Representative limited proteolysis assay performed with H2A-H2B, MBP and MBP-mGCNA. Proteins were incubated with trypsin for 0, 2, 4 and 6 hours then analysed by SDS-PAGE followed by silver staining. Data is representative from two independent experiments. C. Schematic representation of the in vitro nucleosome assembly activity assay. A supercoiled plasmid is relaxed by TopoI then DNA was incubated with core histones and the histone chaperone. While nucleosomes are formed, supecoils are also formed into the plasmid and supercoiling is analysed by gel electrophoresis after deproteinisation of the plasmid. D. Representative in vitro nucleosome assembly activity assay with MBP and MBP-mGCNA. In this assay, MBP was used at a concentration of 0.66µM and MBP-mGCNA was used at 0.165, 0.33 or 0.66µM. Data is representative from three independent experiments. E. Quantification of the signal of the supercoiled plasmid in presence of histones and increasing concentrations of MBP-mGCNA (lanes 5 to 7 in (D)), relative to the signal with histones and MBP (lane 4 in (D)). Data represent the mean and S.D.. Data represent three independent experiments. P values were calculated by using an unpaired t-test.

    Article Snippet: In a 100 µl reaction, 1.4 µg of H3-H4 (catalog no. M2509S, New England Biolabs) or H2A-H2B (catalog no. M2508S, New England Biolabs) were incubated with 2.5 µg of MBP or MBP-mGCNA in Binding buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 % glycerol).

    Techniques: Proteolysis Assay, Incubation, SDS Page, Silver Staining, In Vitro, Activity Assay, Plasmid Preparation, Nucleic Acid Electrophoresis, Concentration Assay