Transcriptome-wide investigation of genomic imprinting in chicken.
Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France, ENVT, UMR444 Laboratoire de Génétique Cellulaire, Toulouse F-31076, France, INRA, PEAT Pôle d'Expérimentation Avicole de Tours, Nouzilly F- 37380, France, INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan F-31326, France, INRA, GeT-PlaGe Genotoul, Castanet-Tolosan F-31326, France, INRA, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas F-78350, France, AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas F-78350, France, Department of Computer Sciences, University of California, Los Angeles, CA 90095, USA, INRA, UR83 Recherche Avicoles, Nouzilly F- 37380, France and Agrocampus Ouest, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Animal Genetics Laboratory, Rennes F-35000, France.
Laure
L
Frésard
Sophie
S
Leroux
Bertrand
B
Servin
David
D
Gourichon
Patrice
P
Dehais
Magali San
MS
Cristobal
Nathalie
N
Marsaud
Florence
F
Vignoles
Bertrand
B
Bed'hom
Jean-Luc
JL
Coville
Farhad
F
Hormozdiari
Catherine
C
Beaumont
Tatiana
T
Zerjal
Alain
A
Vignal
Mireille
M
Morisson
Sandrine
S
Lagarrigue
Frédérique
F
Pitel
D000818:Animals; D002642:Chick Embryo; D002645:Chickens / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018392:Genomic Imprinting; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D051379:Mice; D008811:Mice, Inbred DBA; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA; D059467:Transcriptome