title: Genome-wide analysis of chimpanzee genes with premature termination codons.
abstract: BACKGROUND
  Premature termination codons (PTCs) cause mRNA degradation or a truncated protein and thereby contribute to the transcriptome and proteome divergence between species. Here we present the first genome-wide study of PTCs in the chimpanzee. By comparing the human and chimpanzee genome sequences we identify and characterize genes with PTCs, in order to understand the contribution of these mutations to the transcriptome diversity between the species.
  
  
  RESULTS
  We have studied a total of 13,487 human-chimpanzee gene pairs and found that ~8% were affected by PTCs in the chimpanzee. A majority (764/1,109) of PTCs were caused by insertions or deletions and the remaining part was caused by substitutions. The distribution of PTC genes varied between chromosomes, with Y having the highest proportion. Furthermore, the density of PTC genes varied on a megabasepair scale within chromosomes and we found the density to be correlated both with indel divergence and proximity to the telomere. Within genes, PTCs were more common close to the 5' and 3' ends of the amino acid sequence. Gene Ontology classification revealed that olfactory receptor genes were over represented among the PTC genes.
  
  
  CONCLUSIONS
  Our results showed that the density of PTC genes fluctuated across the genome depending on the local genomic context. PTCs were preferentially located in the terminal parts of the transcript, which generally have a lower frequency of functional domains, indicating that selection was operating against PTCs at sites central to protein function. The enrichment of GO terms associated with olfaction suggests that PTCs may have influenced the difference in the repertoire of olfactory genes between humans and chimpanzees. In summary, 8% of the chimpanzee genes were affected by PTCs and this type of variation is likely to have an important effect on the transcript and proteomic divergence between humans and chimpanzees.
authors.affiliation: Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-751 85, Sweden. anna.wetterbom@genpat.uu.se
authors.forename: Anna
authors.initials: A
authors.lastname: Wetterbom
authors.forename: Ulf
authors.initials: U
authors.lastname: Gyllensten
authors.forename: Lucia
authors.initials: L
authors.lastname: Cavelier
authors.forename: Tomas F
authors.initials: TF
authors.lastname: Bergström
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D018389:Codon, Nonsense / Q000235:genetics*; D016678:Genome; D002679:Pan troglodytes / Q000235:genetics*; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D018389:Codon, Nonsense; D012333:RNA, Messenger