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.

Differential DNA damage signalling and apoptotic threshold correlate with mouse epiblast-specific hypersensitivity to radiation

“…after irradiation), is however also accumulated on chromatin under replicative stress. Therefore, γH2AX may be used as a marker of replicative stress in rapidly dividing cells, such as cancer cells (Seo et al, 2012;Ward and Chen, 2001). In untreated E6.5 embryos we detected endogenous γH2AX both in the Epi and in the ExE, suggesting that these tissues are dealing with replicative stress (Fig.…”

Dynamics of chromatin accessibility and epigenetic state in response to UV damage

“…The loss of accessibility is accompanied by a gain of H3, indicating that the progressively occurring chromatin compaction is achieved either by active chromatin remodeling or incorporation of new nucleosomes. Although previous studies have suggested that heterochromatic regions are less prone to DNA damage in response to ionizing irradiation, γ-rays or chemical agents (Falk et al, 2008;Seo et al, 2012;Takata et al, 2013; Wei Yu, Genome-wide analysis of DNA damage and repair, Technische Universität Darmstadt, PhD thesis, 2014), our and other published data indicate that UV-induced DNA damage might occur both in eu-and hetero-chromatic regions (Wei Yu, Genome-wide analysis of DNA damage and repair, Technische Universität Darmstadt, PhD thesis, 2014; Zavala et al, 2014).…”

Histone variants in pluripotency and disease

“…Genome-wide mapping of H2A.X in resting T-cells indicated that the variant was relatively randomly distributed throughout the genome (Seo et al, 2012).…”