RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken

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.

Extraordinary diversity of HLA class I gene expression in single cells contribute to the plasticity and adaptability of human immune system

“…HLA is one of the most polymorphic loci in the human genome. The IMGT/HLA database released less than 1,000 HLA alleles (class I and II alleles combined) in 1998, this figure increased into 3,410 by the end of 2008 (the beginning of next generation sequencing age, NGS age); the latest figure is 23, 907 ( up to 2019 July) and 17,191 are class I alleles accounting for 72% of all HLA alleles (https://www.ebi.ac.uk/ipd/imgt/hla/stats.html). NGS has brought almost a magnitude increase of newly registered HLA genotypes within ten years and also elevated the HLA typing to an unprecedented high resolution, shaking off those annoying mistyping and ambiguities [1][2][3][4].…”

“…This imbalance of allelic expressions could be as dramatic as mono-allelic expression (such as those imprinted genes or X chromosome deactivated genes), or more commonly seen as one parental allele expresses at a level that is significantly higher than another, referring to as allele specific expression (ASE) [14]. ASE, which is large attributable to cis-elements polymorphisms (i.e., sequence variations at promoter or enhancer regions), has been observed for more than half of SNPdistinguishable human genes and may contribute to human variability and heterosis in plants as well [14][15][16][17]. ASE is traditionally studied by sequencing tissues or cell populations (bulk RNA-seq), which measures the averaged signal of cell populations.…”

Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

“…However, gene regulatory divergence in birds could be different from gene regulatory divergence in mammals, insects, or plants, considering some genetic mechanisms involved in ASE in birds are unique. For instance, genomic imprinting has been observed in mammals and some plants [15][16][17], but seems largely absent in birds assessed to date [18][19][20]. Dosage compensation exists in some diploid species to buffer the effect of copy number difference of genes on the sex chromosome [21][22][23], but it has been reported to be incomplete in birds [24][25][26][27][28].…”

Landscape and evolution of cis- and trans-regulation in chicken genome between two contrasted breeds analyzed in three tissues at one day of age

“…Gene expression regulation in birds may be different from mammals, insects or plants. For instance, genomic imprinting has been found in mammals and some plants [15][16][17], but appears to be largely absent in birds thus far assessed [18][19][20]; dosage compensation mechanism exists in some diploid species to buffer the effect of copy number difference of genes on sex chromosome [21][22][23], but it was incomplete in birds [24][25][26][27][28]. Given this, we thought it is important to study the gene expression regulatory mechanisms in birds.…”

“…Chicken is a model animal in researches on birds, and a remarkable example of rapid phenotypic divergence, with artificial selection resulting in major size, behavioral and reproductive differences among breeds [ 29]. Previous studies have identified frequent allele specific expression between different chicken breeds [ 19,20]. The rapid change under domestication offers a unique example to determine the relative importance of cis-versus trans-regulatory variation underlying phenotypic change.…”