Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle.
Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle.
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转录组分析揭示了猪产前骨骼肌中的嵌合 RNA、单核苷酸多态性和等位基因特异性表达。
DOI：
10.1038/srep29039
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发表时间：
2016-06-29
影响因子：
4.6
通讯作者：
Li K
中科院分区：
文献类型：
--
作者：
Yang Y;Tang Z;Fan X;Xu K;Mu Y;Zhou R;Li K
产前骨骼肌发育从基因上决定了猪的产后肌肉特征，例如生长和肉质。然而，产前骨骼肌发育的分子机制仍不清楚。在这里，我们对猪产前骨骼肌中的嵌合 RNA、单核多态性 (SNP) 和等位基因特异性表达 (ASE) 进行了首次全基因组分析。我们鉴定了产前骨骼肌中表达的 14,810 个蛋白质编码基因和 163 个高置信度嵌合 RNA。超过94.5%的嵌合RNA遵循规范的GT/AG剪接规则并且是反式剪接事件。十个和两个 RNA 分别与人和小鼠嵌合转录物比对。我们检测到 106,457 个高质量 SNP（6,955 个新颖），其中大部分（89.09%）位于生产性状 QTL 内。高比例的非外显子SNP揭示了当前猪参考基因组注释的不完整状态。 ASE 分析显示，11,300 个杂合 SNP 显示等位基因不平衡，而 131 个 ASE 变异位于嵌合 RNA 中。此外，4 个 ASE 变异与猪的各种经济相关性状相关。总而言之，我们的数据为猪育种的嵌合 RNA 和生物标志物的研究提供了来源，同时阐明了哺乳动物产前骨骼肌发育的复杂转录事件。
Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals.