Nanostructure of DNA repair foci revealed by superresolution microscopy

Induction of DNA double‐strand breaks (DSBs) by ionizing radiation leads to formation of micrometersized DNA‐repair foci, whose organization on the nanometer‐scale remains unknown because of the diffraction limit (~200 nm) of conventional microscopy. Here, we applied diffraction‐unlimited, direct stochastic optical‐reconstruction microscopy (dSTORM) with a lateral resolution of ~20 nm to analyze the focal nanostructure of the DSB marker histone γH2AX and the DNA‐repair protein kinase (DNA‐PK) in irradiated glioblastoma multiforme cells. Although standard confocal microscopy revealed substantial colocalization of immunostained γH2AX and DNA‐PK, in our dSTORM images, the 2 proteins showed very little (if any) colocalization despite their close spatial proximity. We also found that γH2AX foci consisted of distinct circular subunits (“nanofoci”) with a diameter of ~45 nm, whereas DNA‐PK displayed a diffuse, intrafocal distribution. We conclude that γH2AX nanofoci represent the elementary, structural units of DSB repair foci, that is, individual γH2AX‐containing nucleosomes. dSTORM‐based γH2AX nanofoci counting and distance measurements between nanofoci provided quantitative information on the total amount of chromatin involved in DSB repair as well as on the number and longitudinal distribution of γH2AX‐containing nucleosomes in a chromatin fiber. We thus estimate that a single focus involves between ~0.6 and ~1.1Mbp of chromatin, depending on radiation treatment. Because of their ability to unravel the nanostructure of DSB‐repair foci, dSTORM and related single‐molecule localization nanoscopy methods will likely emerge as powerful tools in biology and medicine to elucidate the effects of DNA damaging agents in cells