Su Haomiao, Katz Samuel G, Slavoff Sarah A
Department of Chemistry, Yale University, New Haven, CT 06520, USA.
Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA.
bioRxiv. 2024 Oct 25:2024.10.22.619581. doi: 10.1101/2024.10.22.619581.
Overlapping genes were thought to be essentially absent from the human genome until the discovery of abundant, frameshifted internal open reading frames (iORFs) nested within annotated protein coding sequences. However, it is currently unclear how many functional human iORFs exist and how they are expressed. We demonstrate that, in hundreds of cases, alternative transcript variants that bypass the start codon of annotated coding sequences (CDSs) can recode a human gene to express the iORF-encoded microprotein. While many human genes generate such non-coding alternative transcripts, they are poorly annotated. Here we develope a new analysis pipeline enabling the assignment of translated human iORFs to alternative transcripts, and provide long-read sequencing and molecular validation of their expression in dozens of cases. Finally, we demonstrate that a conserved iORF switches the function of this gene from pro- to anti-apoptotic. This work thus demonstrates that alternative transcript variants can broadly reprogram human genes to express frameshifted iORFs, revealing new levels of complexity in the human transcriptome and proteome.
在注释的蛋白质编码序列中嵌套的大量移码内部开放阅读框（iORF）被发现之前，人们认为重叠基因在人类基因组中基本不存在。然而，目前尚不清楚存在多少功能性人类iORF以及它们是如何表达的。我们证明，在数百个案例中，绕过注释编码序列（CDS）起始密码子的可变转录本变体可以对人类基因进行重新编码，以表达iORF编码的微蛋白。虽然许多人类基因会产生此类非编码可变转录本，但它们的注释很差。在这里，我们开发了一种新的分析流程，能够将翻译后的人类iORF分配给可变转录本，并在数十个案例中提供其表达的长读长测序和分子验证。最后，我们证明一个保守的iORF将该基因的功能从促凋亡转变为抗凋亡。因此，这项工作表明可变转录本变体可以广泛地对人类基因进行重新编程，以表达移码的iORF，揭示了人类转录组和蛋白质组新的复杂程度。
