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April 2nd, 2025
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State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
plant biology
biorxiv

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

Chen, Z.Open in Google Scholar•Lin, H.Open in Google Scholar•Wei, L.Open in Google Scholar•Wang, S.Open in Google Scholar•Peng, T.Open in Google Scholar•Song, W.Open in Google Scholar•Wang, D.Open in Google Scholar•Wu, Y.Open in Google Scholar•Wu, L.Open in Google Scholar•Wu, J.Open in Google Scholaret al.

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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