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19 protocols using ab9053

1

Histone Extraction and Western Blot Analysis

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Histone extraction and Western blot analyses were performed from 10 larvae as described previously [46 (link)].
Primary antibodies used were mouse anti-H3K27me3 (1:1000; ab6002, Abcam, Paris, France), rabbit anti-H3K27me2 (1:500; ab24684, Abcam), rabbit anti-H3K27me1 (1:500; ab84932, Abcam), rabbit anti-H2AK119ub (1:2000; DC27C4; Cell Signaling), rabbit anti-H3K9me3 (1:1000; AB8898; Millipore-Sigma Aldrich S.a.r.l., Saint-Quentin-Follavier, France), rabbit anti-H4K20me3 (1:1000; ab9053; Abcam), rabbit anti-H3K27ac (1:1000; ab4729; Abcam) and rabbit anti-H3 (1:5000; ab1791, Abcam). The secondary antibodies were peroxidase conjugated anti-mouse antibody (1:10,000; 115-035-003, Jackson ImmunoResearch, Ely, UK) and peroxidase conjugated anti-rabbit antibody (1:10,000; 711-035-152, Jackson ImmunoResearch).
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2

Antibody-based Protein Quantification in Cellular Studies

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Antibodies for β-actin (sc-47778), COX2 (sc-19999), MMP1 (sc-21731), NRF1 (sc-101102), and SOD2 (sc-30080) were obtained from Santa Cruz Biotechnology. Antibodies for acetyl-histone H4 K5, K8, K12, and K16 (H4K5,8,12,16ac, #PA5-40084) were obtained from Invitrogen. Antibodies for anti-histone H3 acetyl K9, K14, K18, K23, K27 (H3K9, 14, 18, 23, 27ac, ab47915), ERα (ab3575), ERβ (ab3576), H4K20me1 (ab9051), H4K20me3 (ab9053), H4R3me1 (ab17339), H3K9me2 (ab1220), H3K9me3 (ab8898), H3K27me2 (ab24684) and H3K27me3 (ab6002), H2AX (ab20669), and γH2AX (ab2893) were obtained from Abcam. The antibody for 8-oxo-dG (4354-MC-050) was obtained from Novus Biologicals. The 3-nitrotyrosine (3-NT) was measured using 3-Nitrotyrosine ELISA Kit (ab116691 from Abcam) per manufacturers’ instructions. The mitochondrial fraction was isolated using a Pierce Mitochondria Isolation Kit (Pierce Biotechnology) according to manufacturers’ instructions. The protein concentration was measured using the Coomassie Protein Assay Kit (Pierce Biotechnology) per manufacturers’ instructions. Luciferase activity assay was carried out using the Dual-Luciferase™ Assay System (Promega) and the transfection efficiency was normalized using a cotransfected renilla plasmid (23 (link)). 17β-estradiol (E2, #E2758) and TNFα (#T0157) were obtained from Sigma.
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3

Chromatin Isolation and Antibody Binding

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Samples were immediately subjected to formaldehyde crosslinking (final concentration, 1%), and chromatin was isolated according to a method previously described (Durand-Dubief and Ekwall 2009 (link)). Antibodies against H4K20me1 (Abcam ab9051), H4K20me2 (Abcam ab9052), H4K20me3 (Abcam ab9053), HA (Abcam ab9110), T7 (EMD chemicals 69522), H3cter (Abcam ab1791), and H4 Pan (Millipore 05-858, clone 62-141-13) were used.
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4

Histone Modifications Analysis by Western Blot

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Histone protein samples were separated by SDS-PAGE (12 % gel). After electrophoresis (100 V for 20 min, and 200 V for 30 min), proteins were transferred to a PVDF membrane (180 mA for 60 min). Membrane was incubated with 5 % skimmed milk in TBS-T at room temperature for 1 h, followed by primary antibodies either 1:10,000 H4K20me3 (ab9053, Abcam) or 1:20,000 H3K9me3 (ab8898, Abcam) or 1:20,000 H3K4me3 (ab8580, Abcam) antibodies at 4 °C overnight. After washing, membrane was incubated with 1:10,000 corresponding secondary antibodies for 1 h. The immunocomplex signal was developed using the SuperSignal™ West Femto Maximum Sensitivity Substrate (ThermoFisher Scientific) and imaged using the ChemiDoc™ Touch Imaging System (Bio-Rad Laboratories). Histone H4 and Histone H3 were detected as loading controls using 1:10,000 anti-Histone H4 mouse antibodies (mAbcam 31830, Abcam) and 1:20,000 anti-Histone H3 mouse antibodies (14269, Cell Signaling Technology), respectively. Experiments were done in triplicate.
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5

Chromatin Organization Imaging and Analysis

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Confocal imaging, FRAP and FCS experiments, and associated data analysis were conducted with a
Leica TCS SP5 or Zeiss LSM 710 confocal laser scanning microscope as described previously
(Müller et al, 2009 (link); Erdel et
al
, 2010 (link)) and in the Supplementary Materials and Methods.
Immunofluorescence was conducted with primary anti-H3K9me3 (Millipore, Abcam ab8898),
anti-HP1α (Euromedex, 2HP-1H5-AS), anti-HP1β (Euromedex, 1MOD-1A9-AS),
anti-HP1γ (Euromedex, 2MOD-1G6-AS) or anti-H4K20me3 (Abcam, ab9053) antibodies and a
secondary goat anti-rabbit/mouse Alexa 568 antibody or anti-rabbit/mouse Alexa 633 antibody
(Invitrogen, Molecular Probes).
Protein enrichments and H3K9 trimethylation levels were measured from high-resolution microscopy
images using the ImageJ software as described in the Supplementary Materials and Methods. FRAP measurements were fitted either to a
diffusion model, a binding model or a reaction-diffusion model that incorporates both diffusion and
binding processes. The data from the model that yielded the best fit was used for further analysis
and modeling (Müller et al, 2009 (link)).
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6

Multicolor Immunofluorescence of Chromatin Markers

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HP1β was detected with a mouse monoclonal antibody (clone 1 MOD 1A9, Euromedex, 1:250 diluted in 2% bovine serum albumin (BSA) in PBS), using a rhodamine (TRITC)-conjugated anti-mouse secondary antibody (#715–025-151, Jackson ImmunoResearch, USA). The centromeres were labeled with a human CREST antibody which mostly recognizes CENP-A (Immunovision, Cellon Sarl, 1:250 in 2% BSA/PBS), using FITC-conjugated anti-human secondary antibody (#709–095-149, Jackson ImmunoResearch, USA). H3K9me3 and H4K20me3 were detected with rabbit polyclonal antibodies (39161 from Active Motif and ab9053 from Abcam, diluted 1:500 in 2% BAS/PBS) using a Cy5-conjugated anti-rabbit secondary antibody (#711–175-152, Jackson ImmunoResearch, USA). All the Jackson ImmunoResearch secondary antibodies raised in donkey were used at a dilution of 1:200 in 2% BSA/PBS.
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7

Chromatin Immunoprecipitation of Telomeric DNA

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ChIP assay was performed as previously described [15 (link)] with the following antibodies: 3 ug of anti-H3K9me3 (ab8898, abcam), 3 ug of anti-H4K20me3 (ab9053, abcam), 2 ug of anti-TRF2 (NB110–57130, Novus Biologicals), 5 ug of anti-HP-1ɣ (05–690, Sigma) and IgG (sc-2025, Santa Cruz Biotechnology). Samples were transferred to a Hybond-N+ membrane (Amersham) on a dot blot, and hybridized with the same telomeric probe (TTAGGG)n used for TRF. The signal was quantified with the ImageJ software. The amount of telomeric DNA in each ChIP was normalized to total telomeric DNA signal.
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8

Histone Modification Analysis by SDS-PAGE

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15% sodium dodecyl sulfate-polyacrylamide gels (SDS-PAGE) were used to isolate proteins (final concentration 40 µg/lane). Next, isolated proteins were transferred to a polyvinylidene difluoride (PVDF) membrane and investigated with primary Abs overnight at 4°C at the defined concentrations; Proteins were assessed by the primary antibodies of H3K9ac, 1:1000 (#ab10812; Abcam, Cambridge, UK); H3K18ac, 1:1000 (#ab1191; Abcam); H4K20me3, 1:1000 (#ab9053; Abcam); H4K16ac, 1:1000 (#ab205718; Abcam), and also as control was employed H3 (#ab1791; Abcam). The membranes were washed 3 times with TBS/0.1% Tween 20 (15 min each) and then for 2 hours incubated with horseradish peroxidase-conjugated goat anti-rabbit secondary antibodies (Sigma). Enhanced chemiluminescence (ECL) Western blot analysis was used to visualize the bands of protein, and blots were exposed to X-ray film. Image J software was used to quantify histone marks.
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9

Immunofluorescence Staining of Embryos

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Embryos were fixed in 4% paraformaldehyde in PBS at room temperature (RT) for 20 min after the removal of the zona pellucidae with acid Tyrode’s solution (pH
2.5). After washing three times in PBS containing 0.3% polyvinylpyrrolidone (PVP K-30; Nacalai Tesque), fixed embryos were treated with 0.5% Triton X-100
(Sigma-Aldrich) in PBS at RT for 40 min, and were blocked in PBST containing 1.5% BSA, 0.2% sodium azide, and 0.02% Tween20 (antibody dilution buffer) at RT for
1 h. Embryos were incubated with primary antibody in antibody dilution buffer at 4°C overnight, for H4K20me1 (1:3000 dilution; ab9051, Abcam, Cambridge, UK),
H4K20me3 (1:5000 dilution; ab9053, Abcam), γH2AX (1:200 dilution; AB_315794, Biolegend, San Diego, CA, USA), and FLAG (1:5000 dilution; F1804, Sigma-Aldrich)
staining. Embryos were washed three times in antibody dilution buffer, and then were incubated with appropriate secondary antibody in antibody dilution buffer
(1:500 dilution; Alexa Fluor 488-conjugated goat anti-mouse IgG or Alexa Fluor 594-conjugated goat anti-rabbit IgG, Invitrogen) at RT for 1 h. After stained
with Hoechst 33342 (Sigma-Aldrich), embryos were mounted on slides in 50% glycerol in PBS and signals were observed using a fluorescence microscopy (BX50 or
FSX100, Olympus, Tokyo, Japan). The number of analyzed embryos is given in each figure legend.
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10

Western Blot Analysis of Chromatin Proteins

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MEFs were lysed in RIPA buffer with protease and phosphatase inhibitors and lysates were processed using standard methods. We used the following primary antibodies: VHL (sc-5575, 1:250; Santa Cruz), PBRM1 (A301-590A, 1:1000; Bethyl Laboratories), alpha-Tubulin (T5168, 1:2000; Sigma), RAD51 (sc-8349, 1:100; Santa Cruz), RPA32 (A300-244A, 1:500; Bethyl Laboratories), pATM (ab36810, 1:1000; Abcam), ATM (ab85213, 1:1000; Abcam), pDNA-PKc (ab18192, 1:1000; Abcam), DNA-PKc (ab70250, 1:1000; Abcam), pCHK1 (#2348 S, 1:500; Cell Signalling), CHK1 (#2360, 1:1000; Cell Signalling), H3K9me3 (ab8898, 1:1000; Abcam), H3K27me3 (ab6002, 1:1000; Abcam), H3K9me2 (ab8898, 1:1000; Abcam), H4K20me3 (ab9053, 1:1000; Abcam), HP1a (ab77256, 1:1000, Abcam), KAP1 (ab10484, 1:1000; Abcam) and H3 (4499, 1:2000; Cell Signalling). Secondary antibodies were conjugated to IRDye 680 or 800 (Li-Cor). Fluorescent signals were imaged using the Odyssey Infrared Imaging System (Li-Cor). Western blot band quantifications were performed with Fiji58 (link). Uncropped scans of presented blots are shown in Supplementary Fig. 7.
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