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urn:nbn:nl:ui:32-395492 2024-03-09 urn:nbn:nl:ui:32-395492/mods Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates Nie H. 314598049 0000000396159798 aut Crooijmans R.P.M.A. 204491533 0000-0001-8108-9972 0000000359186746 aut Lammers A. 204459672 0000-0002-1876-9630 0000000391863575 aut van Schothorst E.M. 173904645 0000-0002-3036-5903 0000000390831707 aut Keijer J. 085344079 0000-0002-9720-7491 0000000389549085 aut Neerincx P. 314603263 0000000389614182 aut Leunissen J.A.M. 074258524 0000000387364191 aut Megens H.J.W.C. 241028809 0000-0002-3619-7533 0000000358673278 aut Groenen M.A.M. 072568380 0000-0003-0484-4545 0000000396769510 aut text info:eu-repo/semantics/article 2010 10.1371/journal.pone.0011990 77957785172 000280605400022 en 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. Methodology/Principal Findings - 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 orthologuous 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 WIAS Animal Breeding and Genomics Bioinformatics Human and Animal Physiology Adaptation Physiology clusters eimeria-maxima evolution human housekeeping genes intestine lines responses salmonella infection selection tissues WIAS Fokkerij en Genomica Bioinformatica Fysiologie van Mens en Dier Adaptatiefysiologie PLoS ONE 5 8 7 19326203 urn:nbn:nl:ui:32-395492/obj 2024-03-09 http://purl.org/eprint/accessRights/OpenAccess