title: Overlapping codes within protein-coding sequences.
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.
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
authors.forename: Shalev
authors.initials: S
authors.lastname: Itzkovitz
authors.forename: Eran
authors.initials: E
authors.lastname: Hodis
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics*; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D005057:Eukaryotic Cells / Q000378:metabolism; D005815:Genetic Code / Q000235:genetics / Q000502:physiology*; D006801:Humans; D008390:Markov Chains; D008954:Models, Biological; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics* / Q000502:physiology; D010802:Phylogeny; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; D012313:RNA