Frésard Laure, Leroux Sophie, Servin Bertrand, Gourichon David, Dehais Patrice, Cristobal Magali San, Marsaud Nathalie, Vignoles Florence, Bed'hom Bertrand, Coville Jean-Luc, Hormozdiari Farhad, Beaumont Catherine, Zerjal Tatiana, Vignal Alain, Morisson Mireille, Lagarrigue Sandrine, Pitel Frédérique
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.
Nucleic Acids Res. 2014 Apr;42(6):3768-82. doi: 10.1093/nar/gkt1390. Epub 2014 Jan 21.
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.
基因组印记是一种表观遗传机制，通过该机制，一些特定基因的等位基因以亲本来源的方式表达。这种现象已在哺乳动物和有袋动物中观察到，但在鸟类中未观察到。到目前为止，仅对鸡中与哺乳动物印记基因直系同源的少数基因进行了分析，并未发现该物种存在印记的任何证据。然而，一些已发表的观察结果，如家禽中类似印记的数量性状位点或互交效应，使得这个问题仍然悬而未决。因此，我们的主要目标是使用高通量测序技术，在整个胚胎转录组中筛选鸡的整个基因组，以寻找亲本等位基因特异性差异表达。为了确定每个观察到的单倍型的亲本来源，我们使用了两个鸡实验群体，它们尽可能近交且遗传距离较远。通过两个互交产生了两个家系。使用NGS技术对20个胚胎的转录本进行了测序，产生了约200 Gb的序列。通过一种我们通过检测已发表的小鼠数据中的印记而验证的分析方法，这使得我们能够检测到79个潜在的印记单核苷酸多态性。然而，在通过焦磷酸测序测试的23个候选基因中，没有一个能够得到证实。这些结果与先前关于鸡不存在基因组印记的陈述和系统发育考虑因素一致，没有先入之见。
