Transposable elements (TEs) compose most of the human genome and more than 45% of introns. A major part of intronic TEs are relics containing cryptic splicing, termination signals, and abundant DNA and RNA protein binding sites. As such, intronic TE sequences could interfere with transcription elongation of the genes in which they are integrated, through premature transcription termination, a process known as attenuation. As attenuation appears to be uncommon under control conditions, we hypothesized that safeguarding mechanisms might protect long human genes. To study such mechanisms, we developed an R package, called tepr, to analyze datasets from nascent transcript RNA sequencing (e.g., TT-seq). The software can identify genes with potential attenuation, measure the extent of attenuation, and compare different experimental conditions. Applying this strategy to human fibroblasts cells treated with heat-shock (HS), a condition known to induce attenuation on long genes (Cugusi et., 2022), we identified a specific set of 344 genes experiencing attenuation upon HS. To find potential cellular factors involved in promoting or preventing attenuation, we further screened publicly available eCLIP datasets and discovered RNA-binding proteins enriched in transcripts from HS-attenuated genes, suggesting that these factors could regulate attenuation. Altogether, this work provides a quantitative framework for studying attenuation and sheds light on the regulatory mechanisms protecting transcription elongation through long human introns.

This work is supported by Agence Nationale de la Recherche (ANR-11-LABX-0028; ANR-15-IDEX-0001; ANR-19-CE12-0032), Fondation pour la Recherche Médicale (FDT202304016688) and CNRS GDR 3546.