Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

TLDR

Circular RNAs are widespread endogenous RNAs that may regulate gene expression, yet their regulation and function in humans remain largely unknown. The authors performed ribosomal‑depleted RNA‑seq on six normal tissues and seven cancers, identifying ~27,000 circRNAs, then focused on the abundant circHIPK3 from HIPK3 exon 2, which was shown by luciferase assays to sponge nine miRNAs via 18 binding sites. CircRNAs are differentially expressed between normal and cancer tissues; silencing circHIPK3, but not its host mRNA, markedly inhibits cell growth and directly binds miR‑124 to suppress its activity, supporting a regulatory role for circRNAs in human cells.

Abstract

Abstract Circular RNAs (circRNAs) represent a class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates. Many of these circRNAs are differently expressed between the normal and cancerous tissues. We further characterize one abundant circRNA derived from Exon2 of the HIPK3 gene, termed circHIPK3. The silencing of circHIPK3 but not HIPK3 mRNA significantly inhibits human cell growth. Via a luciferase screening assay, circHIPK3 is observed to sponge to 9 miRNAs with 18 potential binding sites. Specifically, we show that circHIPK3 directly binds to miR-124 and inhibits miR-124 activity. Our results provide evidence that circular RNA produced from precursor mRNA may have a regulatory role in human cells.