College of Life Science, Foshan University, Foshan, Guangdong 528231, China.
Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China.
Biomed Res Int. 2017;2017:6152582. doi: 10.1155/2017/6152582. Epub 2017 Sep 14.
Long noncoding RNAs (lncRNAs) are non-protein-coding RNAs that are involved in a variety of biological processes. The pig is an important farm animal and an ideal biomedical model. In this study, we performed a genome-wide scan for lncRNAs in multiple tissue types from pigs. A total of 118 million paired-end 90 nt clean reads were obtained via strand-specific RNA sequencing, 80.4% of which were aligned to the pig reference genome. We developed a stringent bioinformatics pipeline to identify 2,139 high-quality multiexonic lncRNAs. The characteristic analysis revealed that the novel lncRNAs showed relatively shorter transcript length, fewer exons, and lower expression levels in comparison with protein-coding genes (PCGs). The guanine-cytosine (GC) content of the protein-coding exons and introns was significantly higher than that of the lncRNAs. Moreover, the single nucleotide polymorphism (SNP) density of lncRNAs was significantly higher than that of PCGs. Conservation analysis revealed that most lncRNAs were evolutionarily conserved among pigs, humans, and mice, such as CUFF.253988.1, which shares homology with human long noncoding RNA . The findings of our study significantly increase the number of known lncRNAs in pigs.
长链非编码 RNA（lncRNA）是参与多种生物过程的非蛋白编码 RNA。猪是一种重要的家畜动物，也是一种理想的生物医学模型。在本研究中，我们对猪的多种组织类型进行了全基因组范围内的 lncRNA 扫描。通过定向 RNA 测序共获得了 1.18 亿对 90nt 双端清洁读数，其中 80.4%与猪参考基因组比对。我们开发了严格的生物信息学管道来鉴定 2139 个高质量的多外显子 lncRNA。特征分析表明，与蛋白质编码基因（PCG）相比，新鉴定的 lncRNA 具有较短的转录长度、较少的外显子和较低的表达水平。蛋白质编码外显子和内含子的鸟嘌呤-胞嘧啶（GC）含量明显高于 lncRNA。此外，lncRNA 的单核苷酸多态性（SNP）密度明显高于 PCG。保守性分析表明，大多数 lncRNA 在猪、人和小鼠中是进化保守的，例如 CUFF.253988.1，它与人的长非编码 RNA . 具有同源性。本研究的发现显著增加了猪中已知 lncRNA 的数量。
