ArticleGenome research2010
Overlapping codes within protein-coding sequences.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.Synthetic biology (Oxford, England) · 2024Article
- Synonymous sites for accessibility around microRNA binding sites in bacterial spot and speck disease resistance genes of tomato.Functional & integrative genomics · 2023Article
- MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data.NAR genomics and bioinformatics · 2022Article
- Mutational bias and the protein code shape the evolution of splicing enhancers.Nature communications · 2020Article
- High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life.Genome biology · 2020Article
- A model ofPeerJ · 2020Article
- Interplay between coding and exonic splicing regulatory sequences.Genome research · 2019Article
- Exon prediction based on multiscale products of a genomic-inspired multiscale bilateral filtering.PloS one · 2019Article
- Predicting gene structure changes resulting from genetic variants via exon definition features.Bioinformatics (Oxford, England) · 2018Article
- Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.Molecular biology and evolution · 2018Article
- Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies.Genome biology and evolution · 2018Article
- Article
- A novel framework for evaluating the performance of codon usage bias metrics.Journal of the Royal Society, Interface · 2018Article
- Estimating the prevalence of functional exonic splice regulatory information.Human genetics · 2017Review
- Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution.Molecular biology and evolution · 2017Article
- Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent.G3 (Bethesda, Md.) · 2016Article
- NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.PLoS computational biology · 2016Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes encode multiple signals, raising the question of how these different codes are organized along the linear genome sequence. Within protein-coding regions, the redundancy of the genetic code can, in principle, allow for the overlapping encoding of signals in addition to the amino acid sequence, but it is not known to what extent genomes exploit this potential and, if so, for what purpose. Here, we systematically explore whether protein-coding regions accommodate overlapping codes, by comparing the number of occurrences of each possible short sequence within the protein-coding regions of over 700 species from viruses to plants, to the same number in randomizations that preserve amino acid sequence and codon bias. We find that coding regions across all phyla encode additional information, with bacteria carrying more information than eukaryotes. The detailed signals consist of both known and potentially novel codes, including position-dependent secondary RNA structure, bacteria-specific depletion of transcription and translation initiation signals, and eukaryote-specific enrichment of microRNA target sites. Our results suggest that genomes may have evolved to encode extensive overlapping information within protein-coding regions.
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