Structured elements drive circular RNA translation and expand the human proteome, part3

The human genome encodes tens of thousands circular RNAs (circRNAs) whose levels correlate with many disease states. While studies have focused on the non-coding functions of circRNAs, emerging evidence suggests that a handful of circRNAs encode proteins. Translation canonically starts by recognition of mRNA 5’cap and scanning to the start codon; how circRNA translation initiates remains unclear. Here, we developed a high-throughput screen to systematically identify and quantify RNA sequences that can direct circRNA translation. We identify and validate over 17,000 circRNA internal ribosome entry sites (IRES) and reveal that 18S rRNA complementarity and a structured RNA element on the IRES are important for facilitating circRNA cap-independent translation. With genomic and peptidomic analyses of the IRES, we identified nearly 1,000 putative endogenous protein-coding circRNAs and hundreds of translational units encoded by these circRNAs. We further characterized circFGFR1p, a protein encoded by circFGFR1, functions as a negative regulator of FGFR1 to suppress cell growth under stress conditions. The circRNA proteome may be important links among circRNA, biological control, and disease.

人类基因组编码了数万种环状RNA（circRNAs），其表达水平与多种疾病状态密切相关。既往研究多聚焦于环状RNA的非编码功能，但越来越多的证据表明，少数环状RNA可编码蛋白质。经典的翻译起始过程依赖于识别mRNA的5’帽结构并扫描至起始密码子；而环状RNA的翻译起始机制仍不明确。本研究开发了一种高通量筛选方法，以系统性地鉴定并定量能够介导环状RNA翻译的RNA序列。我们鉴定并验证了超过17000个环状RNA内部核糖体进入位点（IRES），并揭示18S核糖体RNA（18S rRNA）互补性以及该位点上的结构化RNA元件，对于促进环状RNA的帽非依赖型翻译具有重要作用。通过对该内部核糖体进入位点进行基因组学与肽组学分析，我们鉴定出近1000个推定的内源性编码蛋白环状RNA，以及由这些环状RNA编码的数百个翻译单元。我们进一步对circFGFR1p进行了表征——该蛋白由circFGFR1编码，可作为成纤维细胞生长因子受体1（FGFR1）的负调控因子，在应激条件下抑制细胞生长。环状RNA蛋白质组可能是连接环状RNA、生物学调控与疾病的关键纽带。