The effect of low-dose ionizing radiation on epigenetic changes in chromatin

Jingchuan Li, Steve Ayers, Masaru Miyano, Shutao Cai and Terumi Kohwi-Shigematsu* Lawrence Berkeley National Laboratory, Berkeley, CA.

The major aim of our research is to examine the effects of ionizing irradiation on chromatin structure. In particular, we are studying epigenetic changes induced by ionizing radiation, and mechanisms that assemble DNA damage sites with DNA repair proteins at specific locations in nuclei. At least in T cells, the assembly of DNA damage sites appears to be mediated by the genome organizer SATB1, which is known to organize higher-order chromatin structure and establish regionspecific epigenetic statuses.

Our previous studies revealed that X-ray irradiation induces a major change in chromatin structure. Upon irradiation, even at a dose as low as 0.1Gy, changes occurred in the epigenetic status of silent chromatin. The histone modifications typically found for transcriptionally-silent chromatin (e.g., histone H3 K9 methylation) were converted to those for active chromatin (e.g., histone H3 K9/14 acetylation). This was confirmed at the single-gene level as well as in the entire chromatin population. So far, histone modification such as histone H3 K9/14 acetylation is thought to be specifically associated with actively transcribed genes. Surprisingly, however, we found that transcription remained mostly unchanged for originally silent genes after ionizing radiation, except for a very small number of genes already known to be activated by radiation. Data obtained from an extensive and careful examination of transcription levels, by both Affymetrix analysis and real-time PCR, led to this conclusion. This is an important result, because it is the first to show that a chromatin structure resembling “transcriptionally active structure is not in fact for active gene transcription, but instead is formed in response to DNA damage, probably for DNA repair.

In investigating the repair process, our research team has discovered that SATB1 plays a critical role. We found new evidence demonstrating that SATB1 serves as a nuclear architectural protein in thymocyte nuclei, recruiting DNA damage sites marked by î^³-H2AX to the SATB1 regulatory network. The SATB1 architecture provides a platform for assembling chromatin remodeling/transcription factors for gene regulation. In response to DNA damage, SATB1 may recruit DNA repair proteins. Our data show that in SATB1-null thymocytes, DNA repair is inefficient and much delayed compared to that in wild-type thymocytes. In support of this, we found that SATB1-null thymocytes are hypersensitive to ionizing radiation. Furthermore, we identified DNA repair proteins in the SATB1-containing protein complex, after purification using DNA affinity chromatography. These data indicate that SATB1 has an important role in promoting DNA repair. We are currently testing a hypothesis that resistance to X-ray irradiation by aggressive cancer cells may be due to the presence of SATB1, which would promote DNA repair. We recently demonstrated that SATB1 plays a determinant role in breast cancer progression by reprogramming gene expression. Therefore, the idea we are testing is that the expression of SATB1 in aggressive breast cancer cells is responsible for the acquisition of resistance to drug and radiation treatment. The information generated from these studies is expected to reveal novel insights into the mechanisms underlying how cells prepare themselves for DNA repair. The experiments may also provide important information as to how cancer cells become resistant to ionizing irradiation. This work was supported by the Low Dose Radiation Research Program, Department of Energy Grant # DE-AC02-05 CH11231.

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