title: Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.
abstract: BACKGROUND
  The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates.
  
  
  RESULTS
  We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO) term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates.
  
  
  CONCLUSIONS
  The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems to be selection pressure on economy in genes with a wide tissue distribution, i.e. these genes are more compact. A comparative analysis showed that the expression patterns of orthologous genes are conserved in the terrestrial vertebrates during evolution.
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
authors.forename: Haisheng
authors.initials: H
authors.lastname: Nie
authors.forename: Richard P M A
authors.initials: RP
authors.lastname: Crooijmans
authors.forename: Aart
authors.initials: A
authors.lastname: Lammers
authors.forename: Evert M
authors.initials: EM
authors.lastname: van Schothorst
authors.forename: Jaap
authors.initials: J
authors.lastname: Keijer
authors.forename: Pieter B T
authors.initials: PB
authors.lastname: Neerincx
authors.forename: Jack A M
authors.initials: JA
authors.lastname: Leunissen
authors.forename: Hendrik-Jan
authors.initials: HJ
authors.lastname: Megens
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics*; D051379:Mice; D009928:Organ Specificity; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic