Han, J., Hendzel, M. J. and Allalunis-Turner, J. Quantitative Analysis Reveals Asynchronous and more than DSB-Associated Histone H2AX Phosphorylation after Exposure to Ionizing Radiation. Radiat. Res. 165, 283–292 (2006).

Rapid phosphorylation of histone H2AX after exposure of cells to ionizing radiation occurs at DSB sites and extends to a region including as much as 30 Mbp of chromatin to form visible microscopic structures called γ-H2AX foci. Although the kinetics of total cellular histone H2AX phosphorylation after irradiation has been characterized, we still know little about the phosphorylation kinetics of individual γ-H2AX foci. In addition, there are hundreds of smaller γ-H2AX foci that are not associated with DNA double-strand breaks. We refer to these sites as DSB-unrelated γ-H2AX foci. By using indirect immunofluorescence microscopy, deconvolution and three-dimensional image analysis, we established an objective method to quantitatively analyze each γ-H2AX focus as well as to discriminate DSB-related γ-H2AX foci from DSB-unrelated γ-H2AX foci. Using this method, we found that histone H2AX phosphorylation at different DSB sites was asynchronous after exposure to ionizing radiation. This may reflect the heterogeneous characteristic of free DNA ends that are generated under these conditions. In addition, we found that increased histone H2AX phosphorylation also occurred outside of DSB sites after exposure to ionizing radiation. The function of this DSB-unassociated phosphorylation is not known.