ORIGINAL ARTICLE Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue S Rashi-Elkeles 1,5 , R Elkon 1,5 , N Weizman 2 , C Linhart 3 , N Amariglio 4 , G Sternberg 1 , G Rechavi 4 , A Barzilai 2 , R Shamir 3 and Y Shiloh 1 1 The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, Tel Aviv, Israel; 2 Department of Neurobiochemistry, George S Wise Faculty of Life Sciences, Tel Aviv, Israel; 3 School of Computer Science, Tel Aviv, Israel and 4 Department of Pediatric Hemato-Oncology and Functional Genomics, The Chaim Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel The ATM protein kinase, functionally missing in patients with the human genetic disorder ataxia-telangiectasia, is a master regulator of the cellular network induced by DNA double-strand breaks. The ATM gene is also frequently mutated in sporadic cancers of lymphoid origin. Here, we applied a functional genomics approach that combined gene expression profiling and computational promoter analysis to obtain global dissection of the transcriptional response to ionizing radiation in murine lymphoid tissue. Cluster analysis revealed a prominent pattern character- izing dozens of genes whose response to irradiation was Atm-dependent. Computational analysis identified signifi- cant enrichment of the binding site signatures of NF-jB and p53 among promoters of these genes, pointing to the major role of these two transcription factors in mediating the Atm-dependent transcriptional response in the irra- diated lymphoid tissue. Examination of the response showed that pro- and antiapoptotic signals were simulta- neously induced, with the proapoptotic pathway mediated by p53 targets, and the prosurvival pathway by NF-jB targets. These findings further elucidate the molecular network induced by IR, point to novel putative NF-jB targets, and suggest a mechanistic model for cellular balancing between pro- and antiapoptotic signals induced by IR in lymphoid tissues, which has implications for cancer management. The emerging model suggests that restoring the p53-mediated apoptotic arm while blocking the NF-jB-mediated prosurvival arm could effectively increase the radiosensitivity of lymphoid tumors. Oncogene advance online publication, 28 November 2005; doi:10.1038/sj.onc.1209189 Keywords: ATM; NF-kB; p53; IR response; micro- arrays Introduction DNA damage is a major threat to cellular homeostasis and life. The DNA damage response network involves parallel modulation of a wide array of signaling path- ways, including lesion processing and repair, activation of cell cycle checkpoints, the apoptotic pathway, and many less characterized stress signals (Shiloh, 2003; Bakkenist and Kastan, 2004). Characterization of gene expression profiles following DNA damage indicated a wider scope of transcriptional response to such damage than previously estimated (Jelinsky and Samson, 1999; Jelinsky et al., 2000; Gasch et al., 2001). Regulation of transcription is a key process in physiological networks, being an endpoint of many signal transduction pathways emanating from extra- cellular and intracellular triggers. DNA microarrays used to analyse transcriptional networks is a mainstay technology in functional genomics (Lockhart and Winzeler, 2000). Construction of gene expression profiles in different physiological conditions identifies the transcriptional programs that are activated under these conditions. Microarray measurements do not, however, directly reveal the regulators of such re- sponses, that is, the transcription factors that control the observed alterations in gene expression. Combining computational promoter analysis with microarray data can elucidate the regulatory layer of transcriptional networks (Tavazoie et al., 1999; Jelinsky et al., 2000; Elkon et al., 2003). Here, we applied a functional genomics approach that combines genome-scale gene expression profiling with computational promoter analysis to obtain global dissection of the transcriptional response to ionizing radiation (IR) in murine lymphoid tissue, to identify components in this network that are dependent on functional ATM protein, and to reveal major transcrip- tion factors that control the induced transcriptional response. The critical cytotoxic DNA lesion inflicted by IR is the DNA double-strand break (DSB). The ATM protein kinase is a master regulator of the cellular response to this DNA lesion (Shiloh, 2003; Kurz and Lees-Miller, 2004). Following DSB induction, ATM is activated and phosphorylates a series of substrates, each Received 9 August 2005; revised 12 September 2005; accepted 12 September 2005 Correspondence: Dr Y Shiloh, The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, Tel Aviv 66978, Israel. E-mail: yossih@post.tau.ac.il 5 These authors contributed equally to this work. Oncogene (2005), 1–9 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc