ChIP was conducted as described in [35] with minor variations. Briefly, macrophages were stimulated with 1 ng/mL LPS for 8 h, washed and fixed with a 1% final concentration of formaldehyde (37% HCHO in 10–15% methanol; Fisher). Crosslinking was Veliparib price stopped after 10 min by addition of glycine to a final concentration of 125 mM and incubated for 10 min. Macrophages were then washed three times with ice-cold PBS and spun down, and pellets were flash
frozen in a dry ice/ethanol bath and kept at –80°C until further analysis. To isolate nuclei, macrophages were first resuspended in Cell Lysis Buffer (10 mM HEPES pH 7.9, 0.5% IGEPAL-30, 1.5 mM MgCl2, 10 mM KCl) and kept on ice for 25 min, vortexing every 5 min. Nuclei were then centrifuged at 4°C and resuspended in Nuclear Lysis Buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS), followed by
sonication in a 4°C water bath to create fragments between 200–800 bp in length. Sonicated samples were then precleared with Protein A Dynabeads (Invitrogen) for 30 min at 4°C and supernatants were collected by magnetic separation. The supernatants were then diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8.1, 167 mM NaCl) and incubated with 2 μg of anti-p65/RelA (Santa Cruz) overnight at 4°C. Immunocomplexes were then collected with Protein A Dynabeads and washed with Low Salt selleck screening library buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1), High Salt buffer (same as low salt but selleck with 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP-40, 1% Sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl) and two times with TE buffer. Complexes
were extracted with Elution buffer (1% SDS, 0.1 M NaHCO3) and protein: DNA crosslinks were reversed by treating with RNAse A and Proteinase K at 65°C. DNA was then purified (MoBio UltraClean PCR kit) and analyzed by qPCR. Normalization was accomplished by subtracting Ct values from precleared “input” chromatin. The primer sequences for the Il12b promoter are: 5′-ctttctgatggaaacccaaag-3′ and 5′-ggggagggaggaacttctta-3′. Macrophages were stimulated with indicated concentrations of LPS for various times and lysed in lysis buffer containing 1% Triton X-100, protease inhibitors (mammalian protease inhibitor cocktail, Sigma) and 1 mM sodium orthovanadate (Sigma). For phospho-IκBα blots, macrophages were pretreated with 10 μM MG-132 (Sigma) for 30 min prior to LPS treatment. Lysates were separated by Tris-bis SDS-PAGE gels (Invitrogen) and transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore). Rabbit antibodies specific for IκBα, phospho-IκBα, phospho-p42/44 ERK, phospho-p38, A20, and β actin were from Cell Signaling. Rabbit anti-MyD88 was from Biovision. An HRP-conjugated donkey antirabbit IgG was used as a secondary (GE Healthcare).
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