P53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of tandem and interspersed repeats
Leonova, Yekaterina I.
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Inactivation or loss of p53 is associated with increased cell sensitivity to the DNA demethylating agent 5-aza-2'-deoxycytidine (5-aza-dC). To identify the factors that trigger apoptotic response under these conditions, we performed microarray-based global gene expression profiling of mouse embryonic fibroblasts (MEFs) isolated from p53-WT and p53-null embryos that were either left untreated or were treated with 5-aza-dC before onset of its toxicity. The microarray analysis revealed a number of important findings. First, it showed that 5-aza-dC treatment induced expression of completely different sets of genes in p53-WT versus p53-null MEFs. All of the protein-coding transcripts induced by 5-aza-dC in p53-WT cells were already highly expressed and irresponsive to the demethylating agent in p53-deficient cells, indicating that p53 is a major driver of DNA methylation-dependent gene silencing. Subsequently, genes that were specifically upregulated in 5-aza-dC-treated p53-null cells included interferon-β and a number of known downstream type I interferon-responsive genes. This interferon response was found to be responsible for 5-aza-dC-induced killing of p53-deficient cells. Since no obvious candidates for the role of IFN-inducing factors were found among the genes represented on the previously used microarray, we carried out high-throughput sequencing of the entire transcriptomes of untreated and 5-aza-dC-treated p53-WT and p53-null MEFs. This revealed striking 5-aza-dC-induced transcriptional upregulation of numerous genetic elements belonging to several classes of normally transcriptionally silent repeats and non-coding RNAs in p53-null, but not p53-WT, cells. The strongest candidates that were induced under these conditions included two major classes of short interspersed mouse retrotransposons (B1 and B2), and near-centromeric gamma-satellite. A more detailed analysis of the sequences of the activated repeats revealed putative p53-binding sites. The abundance of these new transcripts in 5-aza-dC-treated p53-null cells was comparable with total cellular mRNA. We named this phenomenon TRAIN (Transcription of Repeats Activates INterferon). TRAIN occurs naturally in spontaneous mouse tumors, which are commonly deficient in both p53 and DNA methylation, but escape TRAIN-induced death presumably due to inactivation of the mechanism of interferon-mediated apoptosis. These findings define new roles for p53 and interferon in cooperative prevention of expansion of repeats through transcriptional repression and eradication of cells with TRAIN, respectively, and provide a plausible explanation for the deregulation of interferon signaling and increased sensitivity to oncolytic viruses frequently observed in tumors.