ArticleGenome research2012
Long noncoding RNAs are rarely translated in two human cell lines.
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 226 papers, 1 of them a synthesis that pooled it.
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Who cites it
226 citing papers in PubMed, 1 synthesis or guideline pooled it, 388 citations in OpenAlex.
- Genetic determinants of skin ageing: a systematic review and meta-analysis of genome-wide association studies and candidate genes.Journal of physiological anthropology · 2025Pooled it
- Functions of exosome-derived noncoding RNA-encoded polypeptides/proteins in human diseases.Genes & diseases · 2027Review
- A Deep Learning Framework for Accurate lncRNA-Protein Interaction Prediction via Multi-Kernel Graph Embeddings and Self-Attention.Interdisciplinary sciences, computational life sciences · 2026Article
- AI-Guided Long Non-Coding RNA Target Discovery for Precision Medicine: Integrating GWAS, Multi-Omics, Experimental Validation, and RNA Therapeutics.Biomedicines · 2026Review
- Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome.PLoS computational biology · 2026Article
- The degradation of extended protein isoforms points to a misfiring translation initiation process.Molecular genetics and genomics : MGG · 2025Article
- Pharmaceutical perspectives on oligonucleotide therapeutics and delivery systems.Pharmacological reviews · 2025Review
- Noncoding elements in wheat defence response to fusarium head blight.Scientific reports · 2025Article
- Comprehensive discovery and functional characterization of the noncanonical proteome.Cell research · 2025Article
- Lnc MSTRG 4701.7 targets miR-1786/RORa to competitively regulate proliferation and apoptosis in chicken follicular granulosa cells.Frontiers in veterinary science · 2025Article
- Long non-coding RNA-encoded micropeptides: functions, mechanisms and implications.Cell death discovery · 2024Review
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
- Review
- Challenges in LncRNA Biology: Views and Opinions.Non-coding RNA · 2024Article
- Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors.Journal of biomedical science · 2024Review
- Emerging roles of long non-coding RNAs in human epilepsy.Epilepsia · 2024Review
- LncRNA MAGI2-AS3-Encoded Polypeptide Restrains the Proliferation and Migration of Breast Cancer Cells.Molecular biotechnology · 2024Article
- Long non-coding RNA LINC00930 targeting miR-6792-3p/ZBTB16 regulates the proliferation and EMT of pancreatic cancer.BMC cancer · 2024Article
- More than the SRY: The Non-Coding Landscape of the Y Chromosome and Its Importance in Human Disease.Non-coding RNA · 2024Review
- Tracing vitamins on the long non-coding lane of the transcriptome: vitamin regulation of LncRNAs.Genes & nutrition · 2024Review
166 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
17 authors at 5 institutions in 1 country.
Funding
Abstract
Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA- fractions in the cell lines K562 and GM12878. We used the machine-learning algorithm RuleFit3 to regress the peptide data against RNA expression data. The most important covariate for predicting translation was, surprisingly, the Cytosol polyA- fraction in both cell lines. LncRNAs are ~13-fold less likely to produce detectable peptides than similar mRNAs, indicating that ~92% of GENCODE v7 lncRNAs are not translated in these two ENCODE cell lines. Intersecting 9640 lncRNA loci with 79,333 peptides yielded 85 unique peptides matching 69 lncRNAs. Most cases were due to a coding transcript misannotated as lncRNA. Two exceptions were an unprocessed pseudogene and a bona fide lncRNA gene, both with open reading frames (ORFs) compromised by upstream stop codons. All potentially translatable lncRNA ORFs had only a single peptide match, indicating low protein abundance and/or false-positive peptide matches. We conclude that with very few exceptions, ribosomes are able to distinguish coding from noncoding transcripts and, hence, that ectopic translation and cryptic mRNAs are rare in the human lncRNAome.
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Registered trials
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.