Abstract
Epigenetic and genetic cis-regulatory elements in diploid organisms may cause allele specific expression (ASE) – unequal expression of the two chromosomal gene copies. Genomic imprinting is an intriguing type of ASE in which some genes are expressed monoallelically from either the paternal allele or maternal allele as a result of epigenetic modifications. Imprinted genes have been identified in several animal species and are frequently associated with embryonic development and growth. Whether genomic imprinting exists in chickens remains debatable, as previous studies have reported conflicting evidence. Albeit no genomic imprinting has been reported in the chicken embryo as a whole, we interrogated the existence or absence of genomic imprinting in the 12-day-old chicken embryonic brain and liver by examining ASE in F1 reciprocal crosses of two highly inbred chicken lines (Fayoumi and Leghorn). We identified 5197 and 4638 ASE SNPs, corresponding to 18.3% and 17.3% of the genes with a detectable expression in the embryonic brain and liver, respectively. There was no evidence detected of genomic imprinting in 12-day-old embryonic brain and liver. While ruling out the possibility of imprinted Z-chromosome inactivation, our results indicated that Z-linked gene expression is partially compensated between sexes in chickens.
Highlights
A unique and intriguing type of allele specific expression (ASE) is caused by genomic imprinting, in which autosomal genes are monoallelically expressed from either the paternal or maternal allele
It has been reported that IGF2 is imprinted in some chicken embryos and the expressed allele can be of either paternal or maternal origin[17], but several other studies maintained that IGF2 is biallelically expressed[18,19,20]
Different from previous RNA-Seq studies on genomic imprinting[24,25], our study investigated two tissue types, brain and liver, from Day 12 male chicken embryos, with the aim of scrutinizing the absence or existence of genomic imprinting in chickens
Summary
A unique and intriguing type of ASE is caused by genomic imprinting, in which autosomal genes are monoallelically expressed from either the paternal or maternal allele. It has been reported that IGF2 is imprinted in some chicken embryos and the expressed allele can be of either paternal or maternal origin[17], but several other studies maintained that IGF2 is biallelically expressed[18,19,20]. Fresard et al reported that genomic imprinting is absent in the 4.5-day-old chicken embryos[24]. Wang et al focused on studying brains from day-old chickens posthatch and didn’t identify evidence of genomic imprinting[25]. Pinto et al recently reported finding thousands of SNPs with parent-of-origin effect in chicken hypothalamus, liver and breast muscle at 56 days of age[26]. We examined gene expression on the Z chromosome to study dosage compensation in chickens
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