Transcriptome Regulation Analysis By Using Alleleic Specific Expression In The Chickens

Allele-specific expression(ASE)is a phenomenon that gene expression levels of two allele from two parents are inconsistent,which characterized by all or most of the gene transcription of mRNA transcribed from one parental allele.By using the allele-specific expression analysis,we could explore the mechanism of gene imprinting,dosage compensation of sex chromosome,and gene regulation.Gene imprinting is a special case of allele-specific expression that some genes always express with a parent-origin specific pattern.The dosage compensation refers to the genetic mechanism that balance the expression level of sex-linked genes between two genders to compensate the effect of different dose in the diplontic genome.Gene regulation of Eukarya on transcriptional level involves the cis-regulatory elements and trans-regulatory factors.Cis-regulatory elements locate at gene transcriptional regulation area,such as promoter,enhancer,silencer and insulator,they could cause the two alleles expressing at different levels;the trans-regulatory factors are proteins that could identify and combine with the core sequence of cis-regulatory elements directly or indirectly,and involved in regulating the transcription efficiency of target genes,which are also known as transcription factors.Imbalance expression of two alleles may be affected by cis-regulatory variant,and those two alleles expressed equally may be controlled by the trans-regulatory factors.In order to study these mechanisms in the chicken genome,we chose two chicken breeds,White Leghorn and Cornish Games as experiment material.We designed two reciprocal crosses,and the white Leghorn and Cornish Games also generated two pure inbreeding separately.Progenies of the four crosses were extracted mRNA from the brain,liver and muscle to perform the RNA-seq,and the DNA of four parents of two reciprocal crosses were re-sequenced,SNPs between parents were screened by re-sequencing data and we used these SNPs to identify which parents did the reads of offspring RNA-seq derived from.After a series of statistical tests and verification experiments,we found that there is no imprinted gene in the brain of 1-day-old chicken.Dosage compensation in birds was weaker than in mammals.They could tolerate expression imbalance between autosomes and sex chromosomes and sex-linked genes between male and female.Gene expression of two alleles on two Z chromosome of the males were roughly equal.There is no sex chromosome inactivation existing in chicken genome.In three tissues,most of the expressed genes was conservative.There were more trans-regulated genes than cis-regulated gene.For the genes regulated by both the cis-and trans-regulatory variants,the regulatory directions of most of them were on the contrary.In the history of chicken evolution,the expression level of genes was always tending to compensate to achieve balance.The sequence of genes regulated by the trans-regulatory factors tend to more conservative and suffered more rigorous selection.