Epigenetic characterization of pseudogenes across human tissues

Pseudogenes have long been considered non-functional remnants of genome evolution. However, compared to other noncoding elements, their epigenetic regulation remains poorly understood, largely due to their sequence similarity to parent genes and the lack of systematic functional analyses. Here, we leverage matched transcriptomic and epigenomic data from the ENCODE EN-TEx project, spanning ∼30 human tissues, to comprehensively profile pseudogenes and compare them to protein-coding transcripts and lncRNAs. Our analyses reveal epigenetic differences among pseudogene biotypes. Even when transcribed, processed pseudogenes—unlike protein-coding transcripts and unprocessed pseudogenes—lack canonically active histone marks and open chromatin signatures at their promoters. Instead, these regions are frequently associated with retrotransposon sequences, enriched for YY1-binding sites, and often engage distal enhancer-like elements through long-range genomic contacts. These findings suggest that processed pseudogenes may adopt regulatory mechanisms akin to transposable elements such as LINEs, relying on YY1-mediated enhancer-promoter looping or other distal interactions to facilitate transcription. By publicly releasing our catalog of pseudogene promoter regions, we provide a comprehensive resource for investigating the epigenetic and functional roles of pseudogenes in the human genome.