Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, People's Republic of China.
PLoS One. 2011 Jan 25;6(1):e16235. doi: 10.1371/journal.pone.0016235.
The domestic pig (Sus scrofa) is an important economic animal for meat production and as a suitable model organism for comparative genomics and biomedical studies. In an effort to gain further identification of miRNAs in the pig, we have applied the Illumina Solexa sequencing technology to carry out an in-depth analysis of the miRNA transcriptome in a pool of equal amounts of RNA from 16 different porcine tissues. From this data set, we identified 437 conserved and 86 candidate novel miRNA/miRNA* in the pig, corresponding to 329 miRNA genes. Compared with all the reported porcine miRNAs, the result showed that 112 conserved and 61 candidate novel porcine miRNA were first reported in this study. Further analysis revealed extensive sequence variations (isomiRs) of porcine miRNAs, including terminal isomiRs at both the 5' and 3' ends and nucleotide variants. Read counts of individual porcine miRNA spanned from a few reads to approximately 405541 reads, confirming the different level of expression of porcine miRNAs. Subsequently, the tissue expression patterns of 8 miRNAs were characterized by Northern blotting. The results showed that miR-145, miR-423-5p, miR-320, miR-26a, and miR-191 are ubiquitously expressed in diverse tissues, while miR-92, miR-200a, and miR-375 were selectively enriched and expressed in special tissues. Meanwhile, the expression of 8 novel porcine-specific miRNAs was validated by stem-loop RT-PCR, and one of these was detected by Northern blotting. Using the porcine miRNA array designed according to our Solexa results, 123 miRNAs were detected expression in porcine liver tissues. A total of 58 miRNAs showed differential expression between the Tongcheng (a Chinese indigenous fatty breed) and Large White pig breeds (a lean type pig). Taken together, our results add new information to existing data on porcine miRNAs and should be useful for investigating the biological functions of miRNAs in pig and other species.
家猪（Sus scrofa）是肉类生产的重要经济动物，也是比较基因组学和生物医学研究的合适模式生物。为了进一步鉴定猪中的 miRNA，我们应用 Illumina Solexa 测序技术对来自 16 种不同猪组织的等量 RNA 混合物进行了 miRNA 转录组的深入分析。从这个数据集，我们在猪中鉴定了 437 个保守和 86 个候选新 miRNA/miRNA*，对应 329 个 miRNA 基因。与所有已报道的猪 miRNA 相比，本研究首次报道了 112 个保守和 61 个候选新的猪 miRNA。进一步分析表明猪 miRNA 存在广泛的序列变异（isomiRs），包括 5'和 3'末端的末端 isomiRs 和核苷酸变异。单个猪 miRNA 的读数范围从几个读数到大约 405541 个读数，证实了猪 miRNA 的不同表达水平。随后，通过 Northern 印迹法对 8 个 miRNA 的组织表达模式进行了表征。结果表明，miR-145、miR-423-5p、miR-320、miR-26a 和 miR-191 在各种组织中广泛表达，而 miR-92、miR-200a 和 miR-375 在特殊组织中选择性富集和表达。同时，通过 stem-loop RT-PCR 验证了 8 个新的猪特异性 miRNA 的表达，并通过 Northern 印迹法检测到其中一个。使用根据我们的 Solexa 结果设计的猪 miRNA 阵列，在猪肝脏组织中检测到 123 个 miRNA 的表达。总共 58 个 miRNA 在通城（一种中国本土脂肪品种）和大白猪（一种瘦肉型猪）之间的表达存在差异。总之，我们的结果为猪和其他物种中 miRNA 的生物学功能研究提供了新的信息。
