IMMAGINA BioTechnology, Trento, Italy.
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States.
Elife. 2021 Feb 17;10:e59303. doi: 10.7554/eLife.59303.
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs.
哺乳动物基因组的很大一部分被转录为长非编码 RNA（lncRNA），在细胞质中发挥作用，但功能大多未知。令人惊讶的是，lncRNA 已被证明与核糖体相互作用、编码肽或作为核糖体海绵。由于缺乏有效的基因组范围内同时鉴定与核糖体相关和产生肽的 lncRNA 的工具，这些功能仍然在很大程度上未被发现和研究。在这里，我们提出了 AHA 介导的核糖体分离（AHARIBO），这是一种用于检测未翻译但与核糖体相关或编码小肽的 lncRNA 的方法。在神经元分化期间的小鼠胚胎干细胞中使用 AHARIBO，我们分离了核糖体保护的 RNA 片段、翻译 RNA 以及相应的从头合成肽。除了鉴定活跃翻译的 mRNA 和相关核糖体外，我们还发现并区分了作为核糖体海绵或编码微小肽的 lncRNA，为更好地理解数百个 lncRNA 的功能奠定了基础。
