LncPep: A Resource of Translational Evidences for lncRNAs

Teng Liu; Jingni Wu; Yangjun Wu; Wei Hu; Zhixiao Fang; Zishan Wang; Chunjie Jiang; Shengli Li

doi:10.3389/fcell.2022.795084

LncPep: A Resource of Translational Evidences for lncRNAs

Front Cell Dev Biol. 2022 Jan 24:10:795084. doi: 10.3389/fcell.2022.795084. eCollection 2022.

Authors

Teng Liu¹, Jingni Wu¹, Yangjun Wu², Wei Hu¹, Zhixiao Fang¹, Zishan Wang³, Chunjie Jiang⁴, Shengli Li¹

Affiliations

¹ Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
² Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
³ Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
⁴ Institute for Diabetes Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.

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.

Keywords: cancer; lncRNA; m6A; peptide; ribo-seq; translation.