title: Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome.
abstract: BACKGROUND
  The FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of these regulatory elements to the pig genome could provide useful annotation and evidence to support assignment of orthology.
  
  
  RESULTS
  For human transcription start sites (TSS) associated with annotated human-mouse orthologs, 17% mapped to the pig genome but not to the mouse, 10% mapped only to the mouse, and 55% mapped to both pig and mouse. Around 17% did not map to either species. The mapping percentages were lower where there was not clear orthology relationship, but in every case, mapping to pig was greater than to mouse, and the degree of homology was also greater. Combined mapping of mouse and human CAGE-defined promoters identified at least one putative conserved TSS for >16,000 protein-coding genes. About 54% of the predicted locations of regulatory elements in the pig genome were supported by CAGE and/or RNA-Seq analysis from pig macrophages.
  
  
  CONCLUSIONS
  Comparative mapping of promoters and enhancers from humans and mice can provide useful preliminary annotation of other animal genomes. The data also confirm extensive gain and loss of regulatory elements between species, and the likelihood that pigs provide a better model than mice for human gene regulation and function.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK. christelle.robert@roslin.ed.ac.uk.
authors.forename: Christelle
authors.initials: C
authors.lastname: Robert
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. r.kapetanovic@imb.uq.edu.au.
authors.forename: Ronan
authors.initials: R
authors.lastname: Kapetanovic
authors.affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Center, Robinson Way, Cambridge, CB2 0RE, UK. dario.beraldi@cruk.cam.ac.uk.
authors.forename: Dario
authors.initials: D
authors.lastname: Beraldi
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK. mick.watson@roslin.ed.ac.uk.|Edinburgh Genomics, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK. mick.watson@roslin.ed.ac.uk.
authors.forename: Mick
authors.initials: M
authors.lastname: Watson
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK. alan.archibald@roslin.ed.ac.uk.
authors.forename: Alan L
authors.initials: AL
authors.lastname: Archibald
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK. david.hume@roslin.ed.ac.uk.
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D017124:Conserved Sequence / Q000235:genetics*; D023281:Genomics; D006801:Humans; D008264:Macrophages / Q000378:metabolism*; D051379:Mice; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013552:Swine; D059467:Transcriptome