ArticleGenome research2012
Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed, 225 citations in OpenAlex.
- Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants.American journal of physiology. Lung cellular and molecular physiology · 2015Trial
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- An expanded reference catalog of translated open reading frames for biomedical research.Nucleic acids research · 2026Article
- How tailored Ribo-seq methods probe unique translation events.RNA (New York, N.Y.) · 2026Review
- The degradation of extended protein isoforms points to a misfiring translation initiation process.Molecular genetics and genomics : MGG · 2025Article
- Loss of non-canonical translation initiation factors impairs perinatal cardiac function in mice.Experimental animals · 2025Article
- Eukaryotic Microproteins.Annual review of biochemistry · 2025Review
- The translatome of glioblastoma.Molecular oncology · 2025Article
- The rapid degradation of translated upstream regions points to an inefficient translation initiation process.bioRxiv : the preprint server for biology · 2024Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
- Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms.Life science alliance · 2024Article
- CRISPRi screens identify the lncRNA,Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Socialized mitochondria: mitonuclear crosstalk in stress.Experimental & molecular medicine · 2024Review
- Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes.Genome biology · 2024Article
- Microproteins-Discovery, structure, and function.Proteomics · 2023Review
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs.Interdisciplinary sciences, computational life sciences · 2023Article
- Article
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
75 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was trained on the ribosomal footprints observed at previously annotated AUG translation initiation codons (TICs), and used for the ab initio prediction of TISs in 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) in the 5' UTR, 1406 uORFs overlapping with the coding sequence, and 546 N-terminal protein extensions. The TIS detection method was validated on the basis of previously published alternative TISs and uORFs. Among primates, TICs in newly annotated TISs were significantly more conserved than control codons, both for AUGs and near-cognate codons. The transcriptome-wide map of novel candidate TISs derived as part of the study will shed further light on the way in which human proteome diversity is influenced by alternative translation initiation and regulation.
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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.