ArticleGenome biology and evolution2011
Putatively noncoding transcripts show extensive association with ribosomes.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
77 citing papers in PubMed, 135 citations in OpenAlex.
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Micropeptides in the oncological dark matter: decoding their roles in tumor progression and therapy resistance.Journal of translational medicine · 2025Review
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Endogenous micropeptides as potential diagnostic biomarkers and therapeutic drugs.Frontiers in pharmacology · 2025Review
- De Novo Genes.Annual review of genetics · 2024Review
- Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome.Genome biology · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- Micropeptides: origins, identification, and potential role in metabolism-related diseases.Journal of Zhejiang University. Science. B · 2023Review
- Ethanol- and PARP-Mediated Regulation of Ribosome-Associated Long Non-Coding RNA (lncRNA) in Pyramidal Neurons.Non-coding RNA · 2023Article
- Evolution and implications of de novo genes in humans.Nature ecology & evolution · 2023Review
- A vast evolutionarily transient translatome contributes to phenotype and fitness.Cell systems · 2023Article
- Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.PLoS genetics · 2023Article
- Rescue ofeLife · 2023Article
- Revealing the small proteome ofmicroLife · 2023Article
- De novo birth of functional microproteins in the human lineage.Cell reports · 2022Article
- Origins, evolution, and physiological implications of de novo genes in yeast.Yeast (Chichester, England) · 2022Review
- The Origins and Functions of De Novo Genes: Against All Odds?Journal of molecular evolution · 2022Review
- Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful.Genome biology and evolution · 2022Article
- From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory.Non-coding RNA · 2021Review
17 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
2 authors at 2 institutions in 1 country.
Funding
Abstract
There have been recent surprising reports that whole genes can evolve de novo from noncoding sequences. This would be extraordinary if the noncoding sequences were random with respect to amino acid identity. However, if the noncoding sequences were previously translated at low rates, with the most strongly deleterious cryptic polypeptides purged by selection, then de novo gene origination would be more plausible. Here we analyze Saccharomyces cerevisiae data on noncoding transcripts found in association with ribosomes. We find many such transcripts. Although their average ribosomal densities are lower than those of protein-coding genes, a significant proportion of noncoding transcripts nevertheless have ribosomal densities comparable to those of coding genes. Most show increased ribosomal association in response to starvation, as has been previously reported for other noncoding sequences such as untranslated regions and introns. In rich media, ribosomal association is correlated with start codons but is not usually consistent and contiguous beyond that, suggesting that translation occurs only at low rates. One transcript contains a 28-codon open reading frame, which we name RDT1, which shows evidence of translation, and may be a new protein-coding gene that originated de novo from noncoding sequence. But the bulk of the ribosomal association cannot be attributed to unannotated protein-coding genes. Our primary finding of extensive ribosome association shows that a necessary precondition for selective purging is met, making de novo gene evolution more plausible. Our analysis is also proof of principle of the utility of ribosomal profiling data for the purpose of gene annotation.
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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.