Abstract
Long noncoding RNAs (lncRNAs) are a type of transcript that is >200 nucleotides long with no protein-coding capacity. Accumulating studies have suggested that lncRNAs contain open reading frames (ORFs) that encode peptides. Although several noncoding RNA-encoded peptide-related databases have been developed, most of them display only a small number of experimentally validated peptides, and resources focused on lncRNA-encoded peptides are still lacking. We used six types of evidence, coding potential assessment tool (CPAT), coding potential calculator v2.0 (CPC2), N6-methyladenosine modification of RNA sites (m6A), Pfam, ribosome profiling (Ribo-seq), and translation initiation sites (TISs), to evaluate the coding potential of 883,804 lncRNAs across 39 species. We constructed a comprehensive database of lncRNA-encoded peptides, LncPep (http://www.shenglilabs.com/LncPep/). LncPep provides three major functional modules: 1) user-friendly searching/browsing interface, 2) prediction and BLAST modules for exploring novel lncRNAs and peptides, and 3) annotations for lncRNAs, peptides and supporting evidence. Taken together, LncPep is a user-friendly and convenient platform for discovering and investigating peptides encoded by lncRNAs.
Highlights
Long noncoding RNAs are defined as RNAs longer than 200 nucleotides and have been shown to be extensively expressed and exert powerful regulatory functions (Marchese et al, 2017)
The Open Reading Frame (ORF) length was set to ≥10 aa, and the longest ORF was selected when multiple ORFs overlapped in the same Long noncoding RNAs (lncRNAs)
Five different pieces of evidence to support translation are included in LncPep (Figure 1), including coding potential assessment tool (CPAT), coding potential calculator v2.0 (CPC2), Riboseq, translation initiation site (TIS), and m6A sites
Summary
Long noncoding RNAs (lncRNAs) are defined as RNAs longer than 200 nucleotides (nt) and have been shown to be extensively expressed and exert powerful regulatory functions (Marchese et al, 2017). A growing amount of evidence has demonstrated that lncRNAs are able to encode functional peptides that play vital roles in physiological processes (Anderson et al, 2015; Matsumoto et al, 2017; Anastasia et al, 2019; Niu et al, 2020; Cai et al, 2021; Zhang et al, 2021). The lncRNA HOXB-AS3 was discovered to encode a conserved 53 amino acid (aa) peptide that suppresses colon cancer growth by competitively binding to the arginine residues in the RGG motif of hnRNP A1 (Huang et al, 2017). These studies expand our understanding of lncRNAs and the coding potential of the genome. With increasing numbers of experimentally validated lncRNA-encoded peptides, a comprehensive identification and annotation of peptides translated from lncRNAs is urgently needed
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