Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity

Abstract

Circular RNAs (circRNAs), an emerging subclass of noncoding RNAs, have been increasingly recognized as critical regulators in diverse biological functions and cellular processes. Despite their functional significance, the epigenetic mechanisms governing circRNA biogenesis remain poorly understood. Our study reveals that H3K27ac-marked super-enhancers (SEs) significantly enhance both circRNA splicing circularization diversity and transcriptional activation of their host genes. Intriguingly, other histone modifications—including H3K4me3, H3K36me3, H3K27me3, and H3K9me3—exhibit distinct regulatory effects on circRNA transcriptional activity. Through comprehensive analysis of 195 transcriptomic profiles, we identified a pan-cancer epigenomic tumor-suppressor signature termed CircRNA Isoform Reduction for Shortened Enhancers in cancer (CIRSE). Notably, CIRSE demonstrates strong prognostic potential in lung adenocarcinoma, as validated by comprehensive survival analyses. Combining Nanopore sequencing with CLIP-Seq approaches, we further elucidated the dual regulatory mechanism involving circRNA stability maintenance and back-splicing junction selection mediated by specific RNA-binding proteins. Functional validation confirmed that CIRSE-defined tumor-suppressive circRNAs are essential for maintaining malignant phenotypes in cancer models. Our findings not only provide mechanistic insights into the epigenetic regulation of circRNAs, but also pave the way for mutation-agnostic discovery of tumor-suppressive circRNAs in precision oncology applications.