title: Large-scale evidence for conservation of NMD candidature across mammals.
abstract: BACKGROUND
  Alternatively-spliced (AS) forms can vary protein function, intracellular localization and post-translational modifications. AS coupled with mRNA nonsense-mediated decay (NMD) can also control the transcript abundance. Here, we have investigated the genome-scale conservation of alternatively-spliced NMD candidates (AS-NMD candidates), in mammals.
  
  
  RESULTS
  We mapped>12 million cDNA/EST library transcripts, comprising pooled data from both older and next-generation sequencing techniques, against genomic sequences to annotate AS-NMD candidates generated by in-frame premature termination codons (PTCs), in the human, mouse, rat and cow genomes. In these genomes, we found populations of genes that harbour AS-NMD candidates, varying in number from approximately 149 to 2,051 genes. We discovered that a highly-significant proportion (27%-35%) of AS-NMD candidate genes in mouse, rat and cow, also have human orthologs targeted for NMD. Intron retention was the most abundant type of AS-NMD, ranging from 43% to 67% of genes harbouring an AS-NMD candidate. Groupings of AS-NMD candidate genes either with or without intron retentions also have highly significant AS-NMD conservation, indicating that the trend is not due primarily to conservation of intron retentions. As a subset, the AS-NMD intron retentions are distinguished from non-retained introns by higher GC content, and codon usage similar to the usage in protein-coding sequences. This indicates that most of these alternatively spliced sequences have coded for proteins in the recent evolutionary past. In general, the AS-NMD candidate genes showed a similar pattern of Gene Ontology functional category enrichments in all four species. Genes linked to nucleic-acid interaction and apoptosis, and involved in pathways linked with cancer, were the most common. Finally, we mapped the AS-NMD candidates to mass spectrometry-derived proteomics data, and gathered evidence of truncated polypeptides for at least 10% of all human AS-NMD candidate transcripts.
  
  
  CONCLUSIONS
  In summary, our analysis provides strong statistical evidence for conservation of functional AS-NMD candidature across Mammalia for a large subset of genes. However, because codon usage of AS-NMD intron retentions is similar to the usage in exons, it is difficult to de-couple conservation of AS-NMD-based regulation from conservation for protein-coding ability, for intron retentions.
authors.affiliation: Department of Biology, McGill University, Montreal, Quebec, Canada.
authors.forename: David A
authors.initials: DA
authors.lastname: de Lima Morais
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D002417:Cattle; D018389:Codon, Nonsense / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D006801:Humans; D007438:Introns / Q000235:genetics; D008322:Mammals / Q000235:genetics; D051379:Mice; D020871:RNA Stability / Q000235:genetics; D051381:Rats
chemical_list: D018389:Codon, Nonsense; D018076:DNA, Complementary