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 eutherians mammals and marsupials, but not in monotremes or birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any reliable 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 by using high-throughput sequencing.

To unquestionably 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 (4.5 days) were sequenced using NGS technology, producing around 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. Even if conducting this study on the whole embryo at a precise stage of development may have prevented from detecting tissue and stage specific genomic imprinting, these results come together, without any a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in birds.