ArticleGenome biology2015
Extensive identification and analysis of conserved small ORFs in animals.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.
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Who cites it
120 citing papers in PubMed, 228 citations in OpenAlex.
- Microproteins as a Hidden Player in Breast Cancer: From Molecular Insights to Therapeutic Potential.Cell biochemistry and function · 2026Review
- Deeply conserved and expressed small ORFs in the model beetle Tribolium castaneum.BMC biology · 2026Article
- Application of Proteogenomic Approaches for Refinement of the Entamoeba histolytica Reference Genome Using High Resolution Mass-Spectrometry Data.Acta parasitologica · 2026Article
- Microproteins in Human Physiology and Pathology.Biochemistry · 2026Review
- Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms.Genome biology and evolution · 2026Article
- Proteogenomic Identification of Annotated and Novel smORFs Via Microprotein Enrichment.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Systematic identification of lincRNA-derived immunogenic peptides in melanoma.Oncoimmunology · 2025Article
- Novel non-coding FOXP3 transcript isoform associated to potential transcriptional interference in human regulatory T cells.RNA biology · 2025Article
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- The LINC01315-encoded small protein YAPer-ORF competes with PRP4k to hijack YAP signaling to aberrantly promote cell growth.Cell death and differentiation · 2025Article
- LincNEAT1 Encoded-NEAT1-31 Promotes Phagocytosis by Directly Activating the Aurora-A-PI3K-AKT Pathway.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- Emerging roles for microproteins as critical regulators of endoplasmic reticulum function and cellular homeostasis.Seminars in cell & developmental biology · 2025Review
- Identification of Small Open Reading Frame-encoded Proteins in the Human Genome.Genomics, proteomics & bioinformatics · 2025Article
- A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness.iScience · 2025Article
- Comprehensive discovery and functional characterization of the noncanonical proteome.Cell research · 2025Article
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- De Novo Genes.Annual review of genetics · 2024Review
- The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.Genome biology · 2024Article
60 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is increasing evidence that transcripts or transcript regions annotated as non-coding can harbor functional short open reading frames (sORFs). Loss-of-function experiments have identified essential developmental or physiological roles for a few of the encoded peptides (micropeptides), but genome-wide experimental or computational identification of functional sORFs remains challenging.
resultsHere, we expand our previously developed method and present results of an integrated computational pipeline for the identification of conserved sORFs in human, mouse, zebrafish, fruit fly, and the nematode C. elegans. Isolating specific conservation signatures indicative of purifying selection on amino acid (rather than nucleotide) sequence, we identify about 2,000 novel small ORFs located in the untranslated regions of canonical mRNAs or on transcripts annotated as non-coding. Predicted sORFs show stronger conservation signatures than those identified in previous studies and are sometimes conserved over large evolutionary distances. The encoded peptides have little homology to known proteins and are enriched in disordered regions and short linear interaction motifs. Published ribosome profiling data indicate translation of more than 100 novel sORFs, and mass spectrometry data provide evidence for more than 70 novel candidates.
conclusionsTaken together, we identify hundreds of previously unknown conserved sORFs in major model organisms. Our computational analyses and integration with experimental data show that these sORFs are expressed, often translated, and sometimes widely conserved, in some cases even between vertebrates and invertebrates. We thus provide an integrated resource of putatively functional micropeptides for functional validation in vivo.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.