Whole-cell extracts were prepared by freeze and thaw lysis (three cycles) in 600 mM NaCl, 20 mM Tris-HCl pH 7.8, 20% glycerol. After SDS–PAGE, proteins were transferred onto PVDF membrane in semi-dry conditions. The membrane was then blocked in 5% non-fat dry milk buffer and incubated with mouse anti-γH2AX (Clone JBW301, Upstate, 1:5,000). Immunoblots were stained with corresponding
HRP-conjugated secondary antibodies (GE Healthcare, 1:20,000) and detected with the
enhanced chemiluminescence detection system (Amersham Biosciences). Quantification was performed using ImageJ.
For the validation of antibody specificity and cross-reactivity, a dilution series of synthetic peptides (CKATQASQEY; Peptide Specialty Laboratories GmbH), with the underlined serine in either phosphorylated or non-phosphorylated form, was immobilized on a nitrocellulose membrane at the indicated concentrations and probed with anti-γH2AX and anti-H2AX as described above.
CTCF knockdown western blots were developed using a rabbit anti-CTCF (#D31H2, Cell Signaling, 1:700) and a mouse anti-actin (
AC-40, Sigma-Aldrich, 1:1,000) and overnight incubation at 4 °C, followed by a direct immunofluorescence detection using
anti-rabbit-IgG-Cy5 (#711-175-152, Jackson, 1:1,000) and an anti-mouse-IgG-Alexa488 (A11029, Invitrogen, 1:1,000). Images were recorded using a
AI600 Imager (Amersham) and quantified using ImageJ.
Natale F., Rapp A., Yu W., Maiser A., Harz H., Scholl A., Grulich S., Anton T., Hörl D., Chen W., Durante M., Taucher-Scholz G., Leonhardt H, & Cardoso M.C. (2017). Identification of the elementary structural units of the DNA damage response. Nature Communications, 8, 15760.