Transcriptomic Investigation of Genomic Imprinting in Chicken Embryonic Brain and Liver

Epigenetic and genetic cis-regulatory elements may cause unequal expression of the two autosomal gene copies in diploid organisms. This imbalance is referred to as allele specific expression. An intriguing type of allele specific expression is that some genes are expressed monoallelically from either paternal allele or maternal allele, a phenomenon commonly termed genomic imprinting. Previous studies reported conflicting evidence regarding the existence of genomic imprinting in chickens. Albeit no genomic imprinting has been reported in the chicken embryo as a whole, we investigated whether certain embryonic tissues exhibit genomic imprinting. The present study aims to identify genomic imprinting in chicken embryonic brain and liver by examining the mRNA expression of parental alleles in an F1 generation. Eggs from two inbred chicken lines (Fayoumi and Leghorn) and their reciprocal crosses were collected and incubated for 12 days; then brain and liver were harvested from embryos for cDNA library preparation. Of 65 million reads per sample generated using the Illumina HiSeq 2000 sequencer, 88% were mapped to the chicken reference genome (Ensembl Galgal4). To establish the genotypes of the inbred lines and their F1 hybrids and to minimize reference bias of RNA-Seq sequence alignment, genomic DNA from inbred Fayoumi and Leghorn chickens was pooled separately and each pool was sequenced at 20X coverage. Our results indicate that in the F1 crosses, 9.2% of the heterozygous loci show allele specific expression (binominal test, p value ≤ 0.05), but genomic imprinting is not present at 12-day chicken embryonic brain or liver.