Whole-genome landscape of histone H2AX and ?-H2AX

Phosphorylation of the histone variant H2AX forms ?-H2AX that marks DNA double-strand break (DSB). Here we generated the sequencing-based maps of H2AX and ?-H2AX positioning in resting and proliferating cells before and after ionizing irradiation. Genome-wide locations of possible endogenous and exogenous DSBs were identified based on ?-H2AX distribution in dividing cancer cells without irradiation and that in resting cells upon irradiation, respectively. ?-H2AX-enriched regions of endogenous origin in replicating cells included telomeres and active transcription start sites, apparently reflecting replication- and transcription-mediated stress during rapid cell division. Surprisingly, H2AX itself, prior to phosphorylation, was specifically located at these endogenous hotspots. This phenomenon was only observed in dividing cancer cells but not in resting cells. Endogenous H2AX was concentrated on the transcription start site of actively transcribed genes but was irrelevant to pausing of RNA polymerase II (pol II), which precisely coincided with ?-H2AX of endogenous origin. ?-H2AX enrichment upon irradiation also coincided with actively transcribed regions, but unlike endogenous ?-H2AX, it extended into the gene body and was not specifically concentrated on the pausing site of pol II. Subtelomeres were not responsive to external DNA damage. Our findings provide insight into DNA repair programs of cancer and may have implications for cancer therapy. Overall design: Profiles of H2AX and gamma-H2AX in normal resting and cancer T cells with and without ionizing irradiation.