The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5′ cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.

人类基因组编码数以万计的环状 RNA (circRNA)，其功能大多未知。如果环状 RNA 要在没有 5' 帽的情况下进行翻译，则需要内部核糖体进入位点 (IRES)。在这里，我们开发了一种高通量筛选来系统地发现可以指导人类细胞中 circRNA 翻译的 RNA 序列。我们确定了超过 17,000 个内源和合成序列作为候选 circRNA IRES。18S rRNA 互补性和 IRES 上的结构化 RNA 元件对于驱动 circRNA 翻译非常重要。核糖体分析和肽组学分析显示了广泛的 IRES-核糖体关联、数百种具有组织特异性分布的 circRNA 编码蛋白以及抗原呈递。我们发现，circFGFR1p（一种由circFGFR1编码的蛋白质，在癌症中下调）可作为 FGFR1 癌蛋白的负调节因子，在应激期间抑制细胞生长。circRNA IRES 元件的系统鉴定可能提供 circRNA 调控、生物功能和疾病之间的重要联系。