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bioRxiv · 10.1101/2025.04.01.646714

The multiomics landscape of small peptides encoded by long non-coding RNA-derived sORFs in rice

Chen, Z.·Lin, H.·Wei, L.·Wang, S.·Peng, T.·Song, W.·Wang, D.·Wu, Y.·Wu, L.·Wu, J.·Wang, Y.
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Abstract

Long non-coding RNAs (lncRNAs), representing the non-coding RNA regions, constitute a significant portion of the genomes in complex organisms. Recent studies suggest that some lncRNAs have the capability to encode peptides. However, the presence of the lncRNA-derived sORFs-encoded polypeotides (LSEPs) in plants is not well understood. In this study, we developed a multi-omics approach that encompasses transcriptomics, translatomics (Ribo-seq), and proteomics to identify of LSEPs in rice. Among the 2764 identified lncRNAs, 42.69% were found to be bound by the ribosome, indicating a potential for encoding. Optimized small peptide extraction protocol was further developed, and the small peptides from rice leaves were extracted and subjected to LC-MS/MS analysis, leading to the identification of a total of 403 LSEPs across four constructed search databases. This work confirms the peptide-coding ability of lncRNAs in plants. Collectively, our study establishes an efficient multi-omics method for identifiying small peptides encoded by lncRNAs, which may be valuable for large-scare screening of LSEPs in plants.

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Chen, Z., Lin, H., Wei, L., Wang, S., Peng, T., Song, W., Wang, D., Wu, Y., Wu, L., Wu, J., Wang, Y.. 2025-04-02. The multiomics landscape of small peptides encoded by long non-coding RNA-derived sORFs in rice. https://doi.org/10.1101/2025.04.01.646714

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