Background: Black bone sheep was first discovered in Yunnan province of China in 1970, with unique black pigmentation on the body and internal organs. Endothelin 3(EDN3) has been known as a key gene causing hyperpigmentation in black bone chicken, the Silky fowl.Methods: In this study, EDN3 was employed as a candidate gene for regulating black color pigmentation. First,EDN3 was cloned from sheep to obtain the full-length cDNA by using the rapid amplification of cDNA ends(RACE).Genomic EDN3 was screened and a total of thirty predicted single nucleotide polymorphisms(SNPs) were genotyped for allele and genotype frequency analysis in a case-control study involving two black bone sheep populations. Genomic copy number analysis of EDN3 in sheep was conducted to measure the variation in copy number. EDN3 expression levels were observed among the groups in adult liver, lymph node, and kidney tissues, as well as embryo kidney samples. Also, among the tissues of black bone and non-black bone sheep.Results: The size of the full-length cDNA was 1,578 bp, which included 426 bp of 5′-untranslated region(5′-UTR),an open reading frame(ORF) of 639 bp encoding a protein of 212 amino acids, and a 3′-UTR of 513 bp. Genotype and allele frequencies of all the discovered SNPs were found insignificantly different in black bone and non-black bone sheep(P > 0.05). Genomic copy number analysis of EDN3 in sheep revealed no significant difference between the two sheep groups. No significant variations were found in the adult liver and kidney embryo samples. However,the expression in lymph node and kidney tissue was significantly higher in black bone sheep than that in non-black bone sheep(P < 0.05). Significant variations in the EDN3 expression levels were observed among the tissues of nonblack bone sheep.Conclusions: The findings of the present study indicate that unlike in Silky chickens, EDN3 is not responsible for hyperpigmentation but may play a key functional role in immune and excretory systems of black bone sheep.
Hesham Y.A.DarwishYuanyuan ZhangKai CuiZu YangDeping HanXianggui DongHuaming MaoWeidong DengXuemei Deng
Background: The widely observed RNA-DNA differences(RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing(i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA(ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like(APOBEC)family during the transcriptional process is considered common and essential for the development of an individual.To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals;however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues.Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes.Conclusions: Our study is the first to investigate RNA editing events in sheep. We screened out 607 and 994 RNA editing sites in three biological replicates of the ovine kidney and spleen and annotated 164 and 247 genes in the kidney and spleen, respectively. The gene function and conservation analysis of these RNA editing-related genes suggest that RNA editing is associated with important gene function in sheep. The putative functionally important RNA editing sites reported in the present study will help future studies on the relationship be
Yuanyuan ZhangDeping HanXianggui DongJiankui WangJianfei ChenYanzhu YaoHesham Y.A.DarwishWansheng LiuXuemei Deng
