Dogcatcher2: Improved statistical detection of transcriptional readthrough and repetitive element analysis across sequencing platforms.

Downstream of Gene (DoG) transcription occurs when RNA polymerase II fails to terminate normally at the transcription end site, resulting in extended transcription downstream of the gene. This is a widespread phenomenon linked to cellular stress, cancer and neurodegeneration. Existing tools for DoG detection from short-read RNA-seq rely on absolute coverage thresholds and sliding window approaches that are sensitive to sequencing depth and expression level. Here we present Dogcatcher2, which applies improved statistical detection methods to gene body-normalized coverage profiles. Using long-read ground truth across multiple datasets, we show that Dogcatcher2 outperforms existing methods in both detection sensitivity and boundary accuracy while maintaining high precision even at low sequencing depths. Dogcatcher2 further improves detection on pseudobulk scRNA-seq and snRNA-seq data. Analysis of DoG regions in human reveals specific enrichment for Alu elements including inverted Alu pairs capable of forming double-stranded RNA, with transposable elements within DoG regions showing elevated expression, connecting readthrough transcription to dsRNA generation and innate immune signaling.