GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
GMA, INRA, Université de Limoges, 87060, Limoges, France.
Sci Rep. 2019 Mar 12;9(1):4297. doi: 10.1038/s41598-019-40781-6.
Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. 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. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3'UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance.
等位基因不平衡是哺乳动物中的一种常见现象，在基因调控中起着重要作用。等位基因特异性表达 (ASE) 方法可用于检测对基因表达具有顺式调控作用的变体。在奶牛中，这种类型的研究仅在荷斯坦牛中进行过一次。在我们的研究中，我们对 19 份利木赞肌肉样本进行了全基因组范围内的 ASE 分析。我们在 13%可检测到表达的基因中鉴定出了 5658 个 ASE SNPs（表现出等位基因特异性表达的单核苷酸多态性）。有趣的是，我们在 AOX1、PALLD 和 CAST 基因中发现了等位基因不平衡。我们还发现了 2107 个位于与肉质或胴体性状相关的基因组区域内的 ASE SNPs。为了鉴定解释 ASE 的因果顺式调控变异，我们搜索了改变转录因子或 microRNA 结合位点的 SNPs。我们在 PRNP 的 3'UTR 区域鉴定出一个 SNP，它可能是一个因果调节变异，改变了几个 miRNA 的结合位点。我们表明 ASE 在我们的肌肉样本中很常见。我们的数据可用于阐明基因表达失衡的分子机制。
