The advent of high-throughput sequencing uncovered that our genome is pervasively transcribed into RNAs that are seemingly not translated into proteins. It was also found that non-coding RNA transcripts outnumber canonical protein-coding genes. This mindboggling discovery prompted a surge in non-coding RNA research that started unraveling the functional relevance of these new genetic units, shaking the classic definition of “gene”. While the non-coding RNA revolution was still taking place, polysome/ribosome profiling and mass spectrometry analyses revealed that peptides can be translated from non-canonical open reading frames. Therefore, it is becoming evident that the coding vs non-coding dichotomy is way blurrier than anticipated. In this review, we focus on several examples in which the binary classification of coding vs non-coding genes is outdated, since the same bifunctional gene expresses both coding and non-coding products. We discuss the implications of this intricate usage of transcripts in terms of molecular mechanisms of gene expression and biological outputs, which are often concordant, but can also surprisingly be discordant. Finally, we discuss the methodological caveats that are associated with the study of bifunctional genes, and we highlight the opportunities and challenges of therapeutic exploitation of this intricacy towards the development of anticancer therapies.

高通量测序的出现发现，我们的基因组普遍被转录成 RNA，而这些 RNA 似乎并未翻译成蛋白质。研究还发现，非编码 RNA 转录本的数量超过了经典蛋白质编码基因的数量。这一令人难以置信的发现引发了非编码RNA研究的激增，这些研究开始揭示这些新基因单元的功能相关性，动摇了“基因”的经典定义。虽然非编码 RNA 革命仍在发生，但多核糖体/核糖体分析和质谱分析表明，肽可以从非规范开放阅读框翻译。因此，很明显，编码与非编码的二分法比预期的更加模糊。在这篇综述中，我们重点关注几个例子，其中编码与非编码基因的二元分类已经过时，因为相同的双功能基因既表达编码产物又表达非编码产物。我们讨论了转录本的这种复杂使用对基因表达和生物输出的分子机制的影响，它们通常是一致的，但也可能令人惊讶地不一致。最后，我们讨论了与双功能基因研究相关的方法学注意事项，并强调了利用这种复杂性来开发抗癌疗法的机遇和挑战。