ArticleGenome research2011
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- Alternatively Spliced Dual-Coding Regions Contribute to the Human Gene Regulatory Program.bioRxiv : the preprint server for biology · 2026Article
- Utilisation of Machine Learning Approaches Improves RNA-Seq Transcriptome Analyses in Alzheimer's Disease Brain.Journal of molecular neuroscience : MN · 2026Article
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches inEcology and evolution · 2024Article
- Article
- Transcriptional Regulation and Implications for ControllingJournal of developmental biology · 2022Review
- Common Features in lncRNA Annotation and Classification: A Survey.Non-coding RNA · 2021Review
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.Nature communications · 2021Article
- Impact of Synonymous Genome Recoding on the HIV Life Cycle.Frontiers in microbiology · 2021Review
- Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy.Nature genetics · 2020Article
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.Research square · 2020Article
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.bioRxiv : the preprint server for biology · 2020Article
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies.Nucleic acids research · 2019Review
- Interplay between coding and exonic splicing regulatory sequences.Genome research · 2019Article
- NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors.BMC bioinformatics · 2019Article
- Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells.Nucleic acids research · 2018Article
- Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies.Genome biology and evolution · 2018Article
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6 authors.
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Abstract
The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes--especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their synonymous sites. We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.
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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.