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Overlapping codes within protein-coding sequences.
- Source :
-
Genome research [Genome Res] 2010 Nov; Vol. 20 (11), pp. 1582-9. Date of Electronic Publication: 2010 Sep 14. - Publication Year :
- 2010
-
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.
- Subjects :
- Animals
Bacterial Proteins genetics
Bacterial Proteins metabolism
Eukaryotic Cells metabolism
Genetic Code genetics
Humans
Markov Chains
Models, Biological
Monte Carlo Method
Nucleic Acid Conformation
Open Reading Frames physiology
Phylogeny
Proteins genetics
Proteins metabolism
RNA chemistry
RNA genetics
RNA metabolism
Amino Acid Sequence genetics
Base Sequence
Genetic Code physiology
Open Reading Frames genetics
Sequence Alignment
Subjects
Details
- Language :
- English
- ISSN :
- 1549-5469
- Volume :
- 20
- Issue :
- 11
- Database :
- MEDLINE
- Journal :
- Genome research
- Publication Type :
- Academic Journal
- Accession number :
- 20841429
- Full Text :
- https://doi.org/10.1101/gr.105072.110