TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS)

Nucleic Acids Res. 2024 Jan 5;52(D1):D322-D333. doi: 10.1093/nar/gkad1048.


Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.

MeSH terms

  • Animals
  • DNA Transposable Elements* / genetics
  • Databases, Genetic*
  • Humans
  • Internet
  • Mammals / genetics
  • Mice
  • Promoter Regions, Genetic
  • Regulatory Sequences, Nucleic Acid*
  • Sequence Analysis, RNA
  • Transcription Initiation Site*


  • DNA Transposable Elements