nucleosome repeat length (Worthington Biochemical)

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Worthington Biochemical nucleosome repeat length

Loss of Hinfp causes S-phase delay. (A) IF staining of Ki-67 (red) as the cell cycle marker was carried out on WT and cKO MEFs. The nuclei were counterstained with DAPI (blue). Scale bar, 50 μm. (B) Quantitation of different Ki-67 patterns revealed that Hinfp -null MEFs show a higher percentage of G 0 cells and persistence of cells with the S-phase pattern. (C) Active DNA synthesis was measured by pulse-labeling of WT and cKO MEFs with BrdU (red). cKO cells at d4 show a substantial decrease in BrdU incorporation. Scale bar, 50 μm. (D) Quantitation of percentage of S phase (BrdU-positive cells) shows a marked decrease in active DNA synthesis (5% in cKO versus 21% in WT) at d4. A total of 400 nuclei were counted from two biological replicates for panels B and D. (E) WT and cKO MEFs were subjected to drug-induced PCC assay. DNA was stained with DAPI (blue). A higher incidence of S-phase-specific (arrowheads) PCC pattern was observed in cKO MEFs. Insets indicate percentage of S-phase-specific PCC patterns. (F) <t>Nucleosome</t> repeat length (NRL) assay of MEF DNA at d4 shows differences in the nucleosome ladder by gel electrophoresis. The images were analyzed using ImageJ software. Line scan analysis revealed broadening of bands and increased nucleosomal spacing in cKO MEFs.

Nucleosome Repeat Length, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 85/100, based on 131 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 85 stars, based on 131 article reviews
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nucleosome repeat length - by Bioz Stars, 2021-01

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Images

1) Product Images from "Fidelity of Histone Gene Regulation Is Obligatory for Genome Replication and Stability"

Article Title: Fidelity of Histone Gene Regulation Is Obligatory for Genome Replication and Stability

Journal: Molecular and Cellular Biology

doi: 10.1128/MCB.01567-13

Figure Legend Snippet: Loss of Hinfp causes S-phase delay. (A) IF staining of Ki-67 (red) as the cell cycle marker was carried out on WT and cKO MEFs. The nuclei were counterstained with DAPI (blue). Scale bar, 50 μm. (B) Quantitation of different Ki-67 patterns revealed that Hinfp -null MEFs show a higher percentage of G 0 cells and persistence of cells with the S-phase pattern. (C) Active DNA synthesis was measured by pulse-labeling of WT and cKO MEFs with BrdU (red). cKO cells at d4 show a substantial decrease in BrdU incorporation. Scale bar, 50 μm. (D) Quantitation of percentage of S phase (BrdU-positive cells) shows a marked decrease in active DNA synthesis (5% in cKO versus 21% in WT) at d4. A total of 400 nuclei were counted from two biological replicates for panels B and D. (E) WT and cKO MEFs were subjected to drug-induced PCC assay. DNA was stained with DAPI (blue). A higher incidence of S-phase-specific (arrowheads) PCC pattern was observed in cKO MEFs. Insets indicate percentage of S-phase-specific PCC patterns. (F) Nucleosome repeat length (NRL) assay of MEF DNA at d4 shows differences in the nucleosome ladder by gel electrophoresis. The images were analyzed using ImageJ software. Line scan analysis revealed broadening of bands and increased nucleosomal spacing in cKO MEFs.

Techniques Used: Staining, Marker, Quantitation Assay, DNA Synthesis, Labeling, BrdU Incorporation Assay, Periodic Counter-current Chromatography, Nucleic Acid Electrophoresis, Software

2) Product Images from "Fidelity of Histone Gene Regulation Is Obligatory for Genome Replication and Stability"

Article Title: Fidelity of Histone Gene Regulation Is Obligatory for Genome Replication and Stability

Journal: Molecular and Cellular Biology

doi: 10.1128/MCB.01567-13

Conditional ablation of transcription factor HINFP inactivates histone H4 expression. (A) Schematic diagram showing targeted Hinfp locus to generate conditional Hinfp knockout mice. The arrow indicates the recombined locus that generates a conditional Hinfp -null mutation (−, null). Ovals indicate right- and left-arm probes for Southern blotting. Arrowheads represent genotyping primers for PCR. (B) Autoradiographs of Southern blot analysis of mouse ES cell clones (wild type [+/+] and +/FN) and mouse tail DNA (+/FN, FN/FN, and +/+) that were hybridized to either left- or right-arm probes: 18.0-kb WT allele and either 10.5-kb (LA probe) or 9.6-kb (RA probe) targeted allele. (C) PCR genotyping analysis of DNA from MEFs of wild-type (+/+) and Hinfp -null pups (F/F) with or without infection with Ad5CMVCre-EGFP virus using primers a and b shown in panel A. Lane 1, marker; lane 2, WT MEFs; lane 3, F/F MEFs without Cre infection; and lane 4, Hinfp -null MEFs after Cre treatment. (D and E) RT-qPCR analysis of WT and cKO MEFs without (No Inf.) or with Cre infection (d0 to d2) showing expression of Hinfp mRNA for multiple exons (exons 2-3, 5, 6-7, 7-8) (D) and two histone H4 genes ( Hist2H4 [H4] and Hist1H4m [H4m]) (E). Removal of Hinfp causes a marked decrease in histone H4 gene expression. (F) Western blot analysis of WT and cKO MEFs at d2 and d4 shows reduction of total H4 protein in Hinfp -null cells (see also Fig. S2 in the supplemental material).

Figure Legend Snippet: Conditional ablation of transcription factor HINFP inactivates histone H4 expression. (A) Schematic diagram showing targeted Hinfp locus to generate conditional Hinfp knockout mice. The arrow indicates the recombined locus that generates a conditional Hinfp -null mutation (−, null). Ovals indicate right- and left-arm probes for Southern blotting. Arrowheads represent genotyping primers for PCR. (B) Autoradiographs of Southern blot analysis of mouse ES cell clones (wild type [+/+] and +/FN) and mouse tail DNA (+/FN, FN/FN, and +/+) that were hybridized to either left- or right-arm probes: 18.0-kb WT allele and either 10.5-kb (LA probe) or 9.6-kb (RA probe) targeted allele. (C) PCR genotyping analysis of DNA from MEFs of wild-type (+/+) and Hinfp -null pups (F/F) with or without infection with Ad5CMVCre-EGFP virus using primers a and b shown in panel A. Lane 1, marker; lane 2, WT MEFs; lane 3, F/F MEFs without Cre infection; and lane 4, Hinfp -null MEFs after Cre treatment. (D and E) RT-qPCR analysis of WT and cKO MEFs without (No Inf.) or with Cre infection (d0 to d2) showing expression of Hinfp mRNA for multiple exons (exons 2-3, 5, 6-7, 7-8) (D) and two histone H4 genes ( Hist2H4 [H4] and Hist1H4m [H4m]) (E). Removal of Hinfp causes a marked decrease in histone H4 gene expression. (F) Western blot analysis of WT and cKO MEFs at d2 and d4 shows reduction of total H4 protein in Hinfp -null cells (see also Fig. S2 in the supplemental material).

Techniques Used: Expressing, Knock-Out, Mouse Assay, Mutagenesis, Southern Blot, Polymerase Chain Reaction, Clone Assay, Infection, Marker, Quantitative RT-PCR, Western Blot

$Loss of Hinfp causes deregulation of cell proliferation. WT and cKO MEFs (GFP sorted) were cultured for 4 days. (A) WT and cKO MEFs plated at 0.35 × 10 6 /60-mm dish were harvested at different time points (d0 to d4) to analyze proliferation in culture. cKO cells show severe delay in proliferation. (B) Cell cycle analysis by flow cytometry for DNA content shows increased sub-G 1 population, altered S phase, as well as polyploid cells in cKO MEFs. (C) Senescence-associated β-galactosidase (SA β-Gal) activity was measured at d2 and d4. There is an obvious increase in SA β-Gal-specific staining in cKO MEFs that is enhanced at d4. (D) The distribution of HLBs was determined by staining for NPAT (red). IF microscopy revealed an increase in the fraction of cells with multiple NPAT foci (white arrowheads) or diffused NPAT staining (red arrowheads) in cKO MEFs at d2 and d4. The nuclei were counterstained with DAPI (blue). Scale bar, 50 μm. (E) Quantitation of NPAT staining patterns in WT and cKO MEFs at d2 and d4. Bar graph shows the percentage of cells with specific numbers of NPAT foci. A total of 200 nuclei were counted from two biological replicates per sample for each time point.$
Figure Legend Snippet: Loss of Hinfp causes deregulation of cell proliferation. WT and cKO MEFs (GFP sorted) were cultured for 4 days. (A) WT and cKO MEFs plated at 0.35 × 10 6 /60-mm dish were harvested at different time points (d0 to d4) to analyze proliferation in culture. cKO cells show severe delay in proliferation. (B) Cell cycle analysis by flow cytometry for DNA content shows increased sub-G 1 population, altered S phase, as well as polyploid cells in cKO MEFs. (C) Senescence-associated β-galactosidase (SA β-Gal) activity was measured at d2 and d4. There is an obvious increase in SA β-Gal-specific staining in cKO MEFs that is enhanced at d4. (D) The distribution of HLBs was determined by staining for NPAT (red). IF microscopy revealed an increase in the fraction of cells with multiple NPAT foci (white arrowheads) or diffused NPAT staining (red arrowheads) in cKO MEFs at d2 and d4. The nuclei were counterstained with DAPI (blue). Scale bar, 50 μm. (E) Quantitation of NPAT staining patterns in WT and cKO MEFs at d2 and d4. Bar graph shows the percentage of cells with specific numbers of NPAT foci. A total of 200 nuclei were counted from two biological replicates per sample for each time point.

Techniques Used: Cell Culture, Cell Cycle Assay, Flow Cytometry, Cytometry, Activity Assay, Staining, Microscopy, Quantitation Assay

Hinfp is required for genomic stability and maintenance of DNA replication. WT and cKO MEFs were analyzed for factors associated with double-strand DNA damage by IF microscopy. (A) γ-H2AX S-139 (red); scale bar, 20 μm; (B) 53BP1 (red); scale bar, 20 μm. Nuclei were counterstained with DAPI (blue). cKO MEFs show a higher percentage of cells with both γ-H2AX and 53BP1 foci. (C) DNA fiber assay. WT and cKO MEFs were consecutively labeled with iododeoxyuridine (IdU; green) and chlorodeoxyuridine (CldU; red) at d2 and d4. Representative images of elongating and stalled forks are shown. Hinfp -null MEFs have a higher incidence of stalled replication forks than WT. (D) The bar graph represents percentage of stalled replication forks observed in WT and cKO MEFs at d2 and d4. There is increased frequency of stalled forks in Hinfp -null MEFs.

Figure Legend Snippet: Hinfp is required for genomic stability and maintenance of DNA replication. WT and cKO MEFs were analyzed for factors associated with double-strand DNA damage by IF microscopy. (A) γ-H2AX S-139 (red); scale bar, 20 μm; (B) 53BP1 (red); scale bar, 20 μm. Nuclei were counterstained with DAPI (blue). cKO MEFs show a higher percentage of cells with both γ-H2AX and 53BP1 foci. (C) DNA fiber assay. WT and cKO MEFs were consecutively labeled with iododeoxyuridine (IdU; green) and chlorodeoxyuridine (CldU; red) at d2 and d4. Representative images of elongating and stalled forks are shown. Hinfp -null MEFs have a higher incidence of stalled replication forks than WT. (D) The bar graph represents percentage of stalled replication forks observed in WT and cKO MEFs at d2 and d4. There is increased frequency of stalled forks in Hinfp -null MEFs.

Techniques Used: Microscopy, Labeling

Hinfp ablation results in atypical nuclear and chromosomal morphology. WT and cKO MEFs (post-GFP sorting) were harvested at d1, d2, or d4 in culture. (A) IF microscopy shows obvious differences in nuclear size and shape between WT and cKO MEFs from d2 onwards. Nuclei stained with DAPI (gray) show clear increase in size after removal of Hinfp . Scale bar, 50 μm. (B) IF microscopy of MEFs stained with α-tubulin (red) show increased presence of binucleated cells (arrowheads) in cKO MEFs. The insets indicate percentage of binucleate cells. Scale bar, 50 μm. (C) Mitotic preparations of MEFs at d2 were subjected to DNA-FISH with probes against mouse minor satellite (top) or major satellite (bottom) regions. Hinfp -ablated cells show obvious increase in the chromosome complement. Scale bar, 20 μm. (D) Quantitation of mitotic cells from WT and cKO MEFs at d2 probed with satellite DNA was performed to calculate percent distribution of diploid (∼2n) and polyploid ( > 2n) chromosome complement. A total of 50 metaphases were counted per sample. The bar graph shows higher percentage of polyploidy in cKO MEFs than in WT MEFs. (E) The microtubules of asynchronous WT and cKO MEFs at d2 were stained with α-tubulin (red) and analyzed by IF microscopy. The micrograph shows the presence of mitotic cells with multipolar spindles in cKO MEFs.

Figure Legend Snippet: Hinfp ablation results in atypical nuclear and chromosomal morphology. WT and cKO MEFs (post-GFP sorting) were harvested at d1, d2, or d4 in culture. (A) IF microscopy shows obvious differences in nuclear size and shape between WT and cKO MEFs from d2 onwards. Nuclei stained with DAPI (gray) show clear increase in size after removal of Hinfp . Scale bar, 50 μm. (B) IF microscopy of MEFs stained with α-tubulin (red) show increased presence of binucleated cells (arrowheads) in cKO MEFs. The insets indicate percentage of binucleate cells. Scale bar, 50 μm. (C) Mitotic preparations of MEFs at d2 were subjected to DNA-FISH with probes against mouse minor satellite (top) or major satellite (bottom) regions. Hinfp -ablated cells show obvious increase in the chromosome complement. Scale bar, 20 μm. (D) Quantitation of mitotic cells from WT and cKO MEFs at d2 probed with satellite DNA was performed to calculate percent distribution of diploid (∼2n) and polyploid ( > 2n) chromosome complement. A total of 50 metaphases were counted per sample. The bar graph shows higher percentage of polyploidy in cKO MEFs than in WT MEFs. (E) The microtubules of asynchronous WT and cKO MEFs at d2 were stained with α-tubulin (red) and analyzed by IF microscopy. The micrograph shows the presence of mitotic cells with multipolar spindles in cKO MEFs.

Techniques Used: Microscopy, Staining, Fluorescence In Situ Hybridization, Quantitation Assay

Techniques Used: Staining, Marker, Quantitation Assay, DNA Synthesis, Labeling, BrdU Incorporation Assay, Periodic Counter-current Chromatography, Nucleic Acid Electrophoresis, Software

Isolation:

Article Title: Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces mating-type switching
Article Snippet: .. Nuclei were isolated, digested with micrococcal nuclease or DNaseI (Worthington), and DNA was purified as described ( ; ) with modifications detailed in . .. Naked DNA controls were obtained by digesting a PCR product.

Purification:

Concentration Assay:

Article Title: Elucidating combinatorial histone modifications and crosstalks by coupling histone-modifying enzyme with biotin ligase activity
Article Snippet: .. Nuclei were then resuspended in MNase Cutting Buffer containing 3 mM CaCl2 and 2 mM p -chloromercuri-phenylsulfonic acid (pCMPS, Toronto Research Labs; as phosphatase inhibitor), and digested with micrococcal nuclease (MNase, Worthington) at 37°C for 30 min at a concentration of 10U/107 cells. .. Digestion of chromatin by MNase was stopped by addition of EGTA to a final concentration of 5 mM, and equal volume of 2 x Lysis Buffer (30 mM HEPES, pH 7.9, 220 mM KCl, 3 mM MgCl2 , 2 mM EDTA, 0.4% Triton X-100, 20% glycerol) was added to the digested chromatin.

Incubation:

Article Title: Ribosomal Pausing at a Frameshifter RNA Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency
Article Snippet: .. Unprotected mRNA was degraded by incubation with micrococcal nuclease (1 or 2 U/μl; Worthington) and RNase V1 (0.02 U/μl; Pharmacia) at 26°C for 30 min in the presence of 3.5 mM Mg(OAc)2 and 3 mM CaCl2 in a final reaction volume of 40 μl. .. Following addition of 60 μl of buffer T (20 mM HEPES, 150 mM KOAc, 10 mM Mg(OAc)2 , 5 mM EGTA, 2 mM dithiothreitol), the reaction mixture was overlayered onto a 60-μl cushion of 0.25 M sucrose in buffer T and subsequently centrifuged at 30 lb/in2 for 30 min in an A-110 rotor in a Beckman airfuge.

Article Title: A Key Role for Chd1 in Histone H3 Dynamics at the 3? Ends of Long Genes in Yeast
Article Snippet: .. 25–40 units (depending on yeast strain and cell density) of micrococcal nuclease (Worthington Biochemical) were added and spheroplasts were incubated at 37°C for 20 minutes. .. The digestion was halted by shifting the reactions to 4°C and adding 0.5 M EDTA to a final concentration of 10 mM.

Article Title: Development and Application of High-Content Biological Screening for Modulators of NET Production
Article Snippet: .. Neutrophils were pre-incubated at 37°C in 5% CO2 for 30 min prior to stimulation and further incubation at 37°C in 5% CO2 for up to 4 h. Post-incubation samples were treated for 10 min with 1 unit/ml micrococcal nuclease (MNase; Worthington 4789), centrifuged for 10 min at 1,800 rcf and 150 µl of supernatant was transferred to a black 96-well plate (Costar 3915). .. NET-DNA was stained with 1 µM Sytox green® (Invitrogen S7020) and quantified with a fluorometer (Berthold Twinkle2 LB970; ex:485 nm/em:525 nm).

Western Blot:

Article Title: Biochemical Analysis of Dimethyl Suberimidate-crosslinked Yeast Nucleosomes
Article Snippet: .. 6x gel loading dye (New England Biolabs, catalog number: B7042) Agarose (Fisher Scientific, catalog number: BP160) Ethidium bromide (Sigma-Aldrich, catalog number: E7637) CL2B Sepharose beads (Sigma-Aldrich, catalog number: CL2B300) Streptavidin Sepharose beads (GE Healthcare, catalog number: 17-5113-01) Insulin (Sigma-Aldrich, catalog number: I1882) Clarity Western ECL Substrate (Bio-Rad Laboratories, catalog number: 1705060) Primary antibody: anti-V5 tag (Thermo Fisher Scientific, Invitrogen, catalog number: R960-25) Secondary antibody: anti-Mouse IgG (Thermo Fisher Scientific, Invitrogen, catalog number: 31430) Nonfat dry milk (Walmart, Great Value) Yeast nitrogen base without amino acids (United States Biological, catalog number: Y2025) Glucose (Merck, Millipore Sigma, catalog number: DX0145) Micrococcal Nuclease (MNase) (Worthington Biochemical, catalog number: LS004797) Tris hydroxymethyl aminomethane (Tris) (Fisher Scientific, catalog number: BP152) Sodium tetraborate decahydrate (Na borate) (Sigma-Aldrich, catalog number: S9640) Sodium chloride (NaCl) (Fisher Scientific, catalog number: S271) Hydrochloric acid (HCl) (Fisher Scientific, catalog number: A144) Phenylmethylsulfonyl fluoride (PMSF) (RPI, catalog number: P20270) Sodium dodecylsulfate (SDS) (RPI, catalog number: L22010) Glycerol (Fisher Scientific, catalog number: G33) Bromophenol blue (Sigma-Aldrich, catalog number: B7021) 2-Mercaptoethanol (Sigma-Aldrich, catalog number: M3148) Tween 20 (Sigma-Aldrich, catalog number: P2287) Acetic acid, Glacial (Fisher Scientific, catalog number: A38) 40% acrylamide solution (Bio-Rad Laboratories, catalog number: 1610140) 2% Bis solution (Bio-Rad Laboratories, catalog number: 1610142) Ammonium persulfate (Fisher Scientific, catalog number: BP179) Tetramethylethylenediamine (TEMED) (Bio-Rad Laboratories, catalog number: 1610800) Sodium bicarbonate (NaHCO3 ) (Fisher Scientific, catalog number: S233) Sodium carbonate (Na2 CO3 ) (Fisher Scientific, catalog number: S263) Sodium hydroxide (NaOH) (Fisher Scientific, catalog number: S318) Methanol (Fisher Scientific, catalog number: A412) Synthetic media (see Recipes) MNase (see Recipes) Extraction (E) buffer (see Recipes) 2x SDS-sample buffer (SB) (see Recipes) Wash (W) buffer (see Recipes) 17% SDS-PAGE gel (see Recipes) 5% stacking gel (see Recipes) 1x SDS-running buffer (see Recipes) 40x Na carbonate buffer (see Recipes) Blotting buffer (see Recipes) TBST ( T ris- b uffered s aline + T ween 20) (see Recipes) .. Equipment P20, P200 and P1000 Pipettes (Gilson) Labquake Tube Shaker/Rotators (Thermo Fisher Scientific) Swing bucket rotor (Beckman Coulter, model: GH 3.8) Shaker incubator (INFORS HT) Mini-Beadbeater-96 (Bio Spec Product) Tabletop centrifuge (Beckman Coulter, model: Allegra 6R) Centrifuge for microcentrifuge tubes (Eppendorf, model: 5415 D) ChemiDoc Touch Imaging System (Bio-Rad Laboratories, model: ChemiDoc Touch Imaging System) Vortex-Genie 2 (Scientific Industries, model: Vortex-Genie 2) Water bath (Precision Scientific, catalog number: 66551) Vertical Mini-Gel systems (C.B.S.