Laboratory of Basic Biology of Stem Cells (LABCET), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil.
Laboratory of Gene Expression Regulation (LABREG), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil.
Biomolecules. 2021 Nov 11;11(11):1673. doi: 10.3390/biom11111673.
Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal.
核糖体图谱通过捕获核糖体足迹快照来揭示 mRNA 的翻译动态。越来越多的证据表明，一些长非编码 RNA（lncRNA）含有小开放阅读框（smORF），这些 smORF 可以被翻译成具有功能的肽。由于其非常规的特征，在实验和生物信息学领域中，鉴定真正翻译的 smORF 一直是一个挑战。这促使我们从脂肪组织中分离出人脂肪来源干细胞（hASC），并进行核糖体图谱分析，随后对转录组、翻译组和 lncRNA 的核糖体保护片段进行生物信息学分析。在这里，我们证明了 222 个 lncRNA 与 hASC 中的翻译机制有关，包括已经证明的编码微蛋白的 lncRNA。一些转录物的核糖体占有率与 smORF 的翻译一致。总之，我们能够鉴定出一组包含 35 个 smORF 的 15 个 lncRNA，这些 lncRNA 可能编码具有功能的微蛋白，包括之前证明的四个 smORF 衍生的微蛋白，这表明这些 lncRNA 在 hASC 自我更新中可能具有双重作用。
