Locus-specific transcriptional regulation of transposable elements by p53

The tumor suppressor p53 protects genomic integrity in part by regulating transposable elements (TEs). Studies of p53-TE interactions rely on synthetic DNA and reporter assays, estimating expression only at the family or subfamily level and lacking locus-specific resolution. To address this limitation, we developed a computational pipeline for ChIP-seq and RNA-seq analysis that employs advanced algorithms to accurately assign short reads mapping to multiple genomic locations. This approach enables precise quantification of TE transcripts at the locus level. By integrating p53 ChIP peaks with differentially expressed TE transcripts, we performed a global analysis of TE expression upon p53 binding. Applying this framework to lung fibroblast IMR90 and colon cancer HCT116 cells treated with p53 activators, we observed a striking pattern: TEs were predominantly activated in normal IMR90 cells but repressed in HCT116 cancer cells. Further analysis of 24 transcriptomes and 10 cistromes confirmed this trend as a distinguishing hallmark between normal and cancer cells. At the family level, normal cells showed broad TE upregulation, whereas cancer cells exhibited selective repression of Alu and LINE elements. These findings provide the first comprehensive, locus-specific view of TE expression associated with p53 binding, implicating a potential role of chromatin context in TE regulation.