biostudies-literatureQu XNIA NIH HHSNHGRI NIH HHSNINDS NIH HHS1456-1471https://www.ebi.ac.uk/biostudies/studies/S-EPMC12129084biostudies-literatureUnknown35(6)The relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling of TE expression dynamics under the regulation of TP53 provides valuable resources for more clarity in TP53's roles in cancer. In this study, we characterized the TE transcriptomic landscape using long-read RNA-seq and short-read RNA-seq in three cancer cell lines varying only in <i>TP53</i> genetic status. To identify transcripts that use TEs as potential promoters, we developed a computational pipeline, TEProf3, and identified in total 1942 transcripts with high confidence. Among these TE-derived transcripts, 239 are activated by TP53 and 221 are repressed by TP53. These TP53-responsive TE-derived transcripts are mainly driven by memberGenome researchCharting the regulatory landscape of TP53 on transposable elements in cancer.PMC12129084U01 HG013227U24 NS132103R01 AG078958R01 HG007175McCornack CFronick CLiang YTomlinson CBelter EAXing XWang TQu XMacias-Velasco JFSchmidt HfalseCharting the regulatory landscape of TP53 on transposable elements in cancer.The relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling of TE expression dynamics under the regulation of TP53 provides valuable resources for more clarity in TP53's roles in cancer. In this study, we characterized the TE transcriptomic landscape using long-read RNA-seq and short-read RNA-seq in three cancer cell lines varying only in <i>TP53</i> genetic status. To identify transcripts that use TEs as potential promoters, we developed a computational pipeline, TEProf3, and identified in total 1942 transcripts with high confidence. Among these TE-derived transcripts, 239 are activated by TP53 and 221 are repressed by TP53. These TP53-responsive TE-derived transcripts are mainly driven by member2025-01-01T00:00:00Z2025 Jun2026-06-02T02:41:36.85Z2026-04-13T03:12:14.144ZS-EPMC121290844036018610.1101/gr.279398.124