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https://library.wur.nl/oai
oai:library.wur.nl:wurpubs/395492
2024-03-09
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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