title: Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells.
abstract: 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.
authors.affiliation: Research Institute of Bioinformatics, Omicsis, Inc., BVC, KRIBB, Daejeon 305-333, Korea.
authors.forename: Jungmin
authors.initials: J
authors.lastname: Seo
authors.forename: Sang Cheol
authors.initials: SC
authors.lastname: Kim
authors.forename: Heun-Sik
authors.initials: HS
authors.lastname: Lee
authors.forename: Jung Kyu
authors.initials: JK
authors.lastname: Kim
authors.forename: Hye Jin
authors.initials: HJ
authors.lastname: Shon
authors.forename: Nur Lina Mohd
authors.initials: NL
authors.lastname: Salleh
authors.forename: Kartiki Vasant
authors.initials: KV
authors.lastname: Desai
authors.forename: Jae Ho
authors.initials: JH
authors.lastname: Lee
authors.forename: Eun-Suk
authors.initials: ES
authors.lastname: Kang
authors.forename: Jin Sung
authors.initials: JS
authors.lastname: Kim
authors.forename: Jung Kyoon
authors.initials: JK
authors.lastname: Choi
mesh_terms: D002877:Chromosomes, Human / Q000737:chemistry; D053903:DNA Breaks, Double-Stranded; D015894:Genome, Human; D018922:HL-60 Cells; D006657:Histones / Q000032:analysis*; D006801:Humans; D019169:Jurkat Cells; D012319:RNA Polymerase II / Q000032:analysis; D014158:Transcription, Genetic
chemical_list: C468783:H2AX protein, human; D006657:Histones; D012319:RNA Polymerase II