A systematic single-cell analysis of enhancer RNAs across human and mouse

Enhancer RNAs (eRNAs) contribute to gene expression specificity, yet their expression patterns at single-cell resolution remain poorly understood. Across 184 329 high-quality single cells from 187 full-length single-cell RNA-seq datasets, we identified 85 977 human and 82 727 mouse eRNAs, which were sparsely detected at the single-cell level (<5% in humans and <8% in mice) but showed high intercellular heterogeneity and contributed substantially to lineage-specific marker repertoires, accounting for up to 33.5% of human and 46.5% of mouse lineage markers. Through systematic analysis of eRNA expression patterns in embryonic development, brain tissues, and cancer, cell-specific eRNAs in different cell types were identified and corresponding regulatory networks were constructed. Our results indicate that eRNAs play important roles in diverse biological processes through modulation of gene expression. Finally, RACE confirmed the full transcription of a colorectal cancer-associated eRNA, whose elevated plasma levels, diagnostic performance, and postoperative reduction support its potential as a noninvasive biomarker for colon cancer detection and monitoring. Collectively, this study provides a comprehensive single-cell landscape of eRNA expression and offers a valuable resource for understanding eRNA-mediated regulatory mechanisms.