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To the best of our knowledge, it is the first ASE survey in a beef breed and with the largest number of different animals. We used whole-genome sequences (WGS) and RNA-Seq data from these 19 muscle samples in our analysis.
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We distinguished between imprinting (parental mono-allelic expression) and allele specific expression (not mono-allelic expression) to focus on the later. In our study, we performed a genome-wide investigation of ASE using 19 Limousine calf muscle samples. In the second study, they detected 19,082 ASE SNPs (1,060 on average per tissue) across 18 different tissues from one lactating Holstein dairy cow 19. In the first study, they discovered 473 ASE SNPs across 5 bovine blastocysts (among 2,524 different heterozygous SNPs) 18. In cattle, only two studies have been performed so far, both in Holstein. In addition, some ASE genes were detected to impact economically important traits 10, 17. Genome-wide studies of ASE have been performed in different species (human 11, mouse 12 or fruit fly 13) including livestock species (pig 14, chicken 15 or sheep 16). This approach is complementary to identifying variants affecting gene expression with eQTL studies because we can use a smaller number of samples 10. So far, there has been only one performed in dairy cattle, in Holstein-Friesians (HF), Jerseys (J) and HFxJ crossbreeds 8.Īllele specific expression (allelic expression or allelic imbalance) analysis is a robust approach to quantify expression variation between the two haplotypes of a diploid individual distinguished by heterozygous sites 9. However in cattle there is a lack of studies. Many human eQTL mapping studies have been carried out 4– 6 including the recent Genotype-Tissue Expression (GTEx) project 7. Unfortunately this type of analysis needs a large number of samples to minimize false-positives 3. They can be identified by expression genome-wide association studies (eGWAS), an analysis method computing the likelihood of a polymorphism affecting gene expression. The combination of both approaches is highly effective at locating cis- and trans- regulation of gene expression.Īn expression quantitative trait locus (eQTL) is a DNA region with some nucleotide sequence differences (Single Nucleotide Polymorphisms, insertion, deletion) that affects the expression level of a gene in cis or trans. There are different approaches to such studies: expression quantitative trait loci (eQTLs) and Allele Specific Expression (ASE) analyses.
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It is therefore important to study this variability in order to understand gene regulation. In mammalian genomes the variability of gene expression is a current phenomenon 1, 2. Gene regulation is a fundamental process in the development and maintenance of organisms. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance. We showed that ASE is frequent within our muscle samples. We identified one SNP in the 3’UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in the Longissimus thoraci muscle. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. In cattle, this type of study has only been done once in Holstein. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation.