Jungmin Seo1, Sang Cheol Kim2, Heun-Sik Lee1, Jung Kyu Kim1, Hye Jin Shon3, Nur Lina Mohd Salleh4, Kartiki Vasant Desai4, Jae Ho Lee5, Eun-Suk Kang3, Jin Sung Kim6,* and Jung Kyoon Choi4,7,*
1Research Institute of Bioinformatics, Omicsis, Inc., BVC, KRIBB, Daejeon 305-333, Korea, 2Korean Bioinformation Center, KRIBB, Daejeon 305-333, Korea, 3Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea, 4Genome Institute of Singapore, Singapore 138672, Republic of Singapore, 5Laboratory of Molecular Oncology, Cheil General Hospital & Women’s Healthcare Center, Kwandong University College of Medicine, Seoul 100-380, Korea, 6Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea and 7Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea
*To whom correspondence should be addressed
Correspondence may also be addressed to Jin Sung Kim.
Phosphorylation of the histone variant H2AX forms γ-H2AX that marks DNA double-strand break (DSB). Here, we generated the sequencing-based maps of H2AX and γ-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 γ-H2AX distribution in dividing cancer cells without irradiation and that in resting cells upon irradiation, respectively. γ-H2AX-enriched regions of endogenous origin in replicating cells included sub-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 γ-H2AX of endogenous origin. γ-H2AX enrichment upon irradiation also coincided with actively transcribed regions, but unlike endogenous γ-H2AX, it extended into the gene body and was not specifically concentrated on the pausing site of pol II. Sub-telomeres were less responsive to external DNA damage than to endogenous stress. Our findings provide insight into DNA repair programs of cancer and may have implications for cancer therapy.