MicroRNAome of porcine prenatal and postnatal development.

Sus scrofa (pig, or swine) is one of the most important economic animals and a close biological model for complex human diseases such as obesity and diabetes. It is therefore utterly important to decode the porcine microRNAome (miRNAome) as in the literature only a small portion of it is known. In this work, a comprehensive search for porcine microRNAs (miRNAs) by Illumina sequencing was performed in ten small RNA libraries prepared from mixtures of assorted tissues, which included those collected from fetuses to adult pigs. The millions of the sequencing reads were analyzed with reference to 77 known porcine miRNA precursors (pre-miRNAs) and 3,443 distinct pre-miRNAs of other mammals listed in miRBase 13.0, and the most updated porcine genome (Sscrofa9, April 2009) and available EST sequences. Additionally, miRNA candidates specific to pig are predicated by genome & EST match and hairpin folding. Our search found 72 out of 78 (~92%) known porcine miRNAs and miRNA*s, and 36 previously unannotated miRNA*s are also indentified. Furthermore, we discovered 397 novel miRNAs by mapping to the sequencing transcripts to other mammalian pre-miRNAs and 493 candidate miRNAs which do not map to other mammalian miRNAomes and could be pig-specific. We constructed sequence- and genome-position clusters for the total of 998 miRNA candidates originating from 862 pre-miRNAs, which represent 777 unique miRNA sequences. Together with the six known porcine miRNAs that not been observed in our study, we report herein the sequence families of 783 unique miRNAs and genomic distribution patterns of 622 pre-miRNAs. We preformed q-PCR experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing data and the q-PCR data. We envision that our report will serve as a valuable resource for future studies aimed at understanding miRNAome of pig Overall design: Ten small RNA libraries from samples of porcine fetuses (30 days after insemination) to mixed tissues (180 days after birth) at ten developmental stages were sequenced.

家猪（Sus scrofa，又称 swine）是最重要的经济动物之一，同时也是研究肥胖、糖尿病等复杂人类疾病的重要模式生物。因此，解析猪的microRNA组（miRNAome）具有极高的研究价值，目前已有文献仅报道了其中极小一部分的内容。本研究通过Illumina测序技术，对10个小RNA文库中的猪microRNA（miRNA）进行了全面挖掘；这些文库由不同发育阶段的多种组织混合构建，样本覆盖了从胎儿到成年猪的各个时期。本研究以miRBase 13.0数据库中收录的77条已知猪miRNA前体（pre-miRNA）、3443条其他哺乳动物的非冗余miRNA前体，以及最新发布的猪参考基因组（Sscrofa9，2009年4月版）和现有表达序列标签（EST）序列为参照，对海量测序读段进行了分析。此外，本研究通过基因组与EST序列比对、茎环结构折叠预测，筛选得到了猪特异性的miRNA候选序列。本次搜索成功检出了78条已知猪miRNA及miRNA*中的72条（约92%），同时还发现了36条此前未被注释的miRNA*序列。此外，通过将测序转录本比对至其他哺乳动物的miRNA前体序列，本研究还发现了397条全新的miRNA；另有493条候选miRNA无法比对至其他哺乳动物的miRNA组，推测为猪特异性miRNA。本研究对源自862个miRNA前体的总计998条miRNA候选序列进行了序列聚类与基因组位置聚类，这些候选序列共对应777条非冗余miRNA序列。结合本研究中未检出的6条已知猪miRNA，本研究共报道了783条非冗余miRNA的序列家族，以及622条miRNA前体的基因组分布模式。本研究针对47份组织特异性样本中的30条筛选得到的miRNA开展了定量PCR（q-PCR）实验，结果显示测序数据与q-PCR实验结果具有良好的一致性。我们预计本研究成果将为后续解析猪miRNA组的相关研究提供宝贵的参考资源。实验整体设计：本研究对10个不同发育阶段的小RNA文库进行了测序，这些文库的样本覆盖了从受精后30天的猪胎儿到出生后180天的混合组织。