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4 protocols using e2f1 sc 193

1

Quantifying E2F-Regulated miRNAs by ChIP-qPCR

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Chromatin immunoprecipitations (ChIPs) and the quantification of immunoprecipitated DNA sequences by Q-PCR were performed as described previously (36 (link)). The localization of E2F motifs in E2F7-regulated miRNAs was carried out with the MotifLocator tool of the TOUCAN program (37 (link)). The search was restricted to the proximal promoter region (−1000 and +500 bp relative to the transcription start site) (38 (link)). Sequences of Q-PCR primers are listed in Supplementary Table S3. Antibodies used for ChIP analysis were: E2F1 (sc-193, Santa Cruz), E2F2 (sc-633, Santa Cruz), E2F3 (sc-878, Santa Cruz), E2F4 (sc-1082, Santa Cruz), E2F7 (sc-66870, Santa Cruz), RB (sc-50 Santa Cruz), p107 (sc-318 Santa Cruz), p130 (sc-317 Santa Cruz), MYC (sc-764 Santa Cruz), RNA polymerase II (sc-899, Santa Cruz) and SV40LT (sc-147, Santa Cruz).
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2

Protein Detection and Quantification

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Sodium dodecyl sulphate-polyacrylamide gel electrophoresis and western blot were performed following standard protocols52 (link). The following antibodies were used: E2F1 (sc-193, Santa Cruz Biotechnology, Santa Cruz, CA, 1:500 dilution), KIF23 (sc-136473, Santa Cruz Biotechnology, 1:200), CDC25C (sc-327, Santa Cruz Biotechnology, 1:1000), B-MYB (LX015.1, kindly provided by Roger Watson53 (link), hybridoma media 1:5) and ß-actin (A5441, Sigma-Aldrich, Munich, Germany, 1:5000).
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3

Chromatin Immunoprecipitation for E2F1 and E2F4

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Chromatin immunoprecipitation was performed as described (33 (link)) using E2F1 (sc-193, Santa Cruz Biotechnology) and E2F4 (sc-866, Santa Cruz Biotechnology) antibodies. Real-time PCR was performed using specific primers flanking the E2F1 binding site of EXO1, MSH2, MSH6, and RAD51, which are listed in Supplementary Table S1. Furthermore, binding of E2F4 to a DREAM-specific binding site in the promoters of E2F1, MSH2 and MSH6, was perfomed using previously described primers (34 (link)) listed in Supplementary Table S1.
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4

Immunoblotting Analysis of Cellular Proteins

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Cells were harvested in lysis buffer containing 62.5 mM Tris-HCl (pH 6.8)/2% SDS, and protease and phosphatase inhibitor cocktails 2 and 3 (Sigma-Aldrich, St. Louis, MO, USA, P8340, P5726, P0044). Protein concentrations were measured using the bicinchoninic acid reagent (Pierce, Waltham, MA, USA, 23228, 1859078). Proteins were resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to polyvinylidene difluoride membrane filter (Bio-Rad, Hercules, CA, USA, 1620177). After transfer, membranes were blocked at 25 °C for 1 h in buffer containing 0.1 M Tris (pH 7.4), 0.9% NaCl, 0.05% Tween 20, and 5% nonfat dry milk.
Membranes were then incubated with the appropriate antibodies overnight at 4 °C, at the dilutions indicated as follows: poly(ADP-ribose) polymerase (PARP, #9542), 1:1000; cleaved lamin A (#2035), 1:2000; cytochrome c oxidase subunit IV (COX IV, #4850), 1:2000 (Cell Signaling, Danvers, MA, USA); β-actin A2228) 1:5000 (Sigma, St. Louis MO, USA, A1978); E2F-1 (sc-193), 1:1000; RET (sc-167), 1:1000; mortalin (sc-133137), 1:5000; p27KIP1 (sc-1641) 1:1000 (Santa Cruz Biotechnology, Santa Cruz, CA, USA). SuperSignal West Pico and Femto chemiluminescence kits (Pierce, Waltham, MA, USA, 34579 and 34094) were used for visualization of the signal. For densitometry, immunoblots were analyzed using Image Lab software (Bio-Rad, Hercules, CA, USA).
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