Discovery of potential piRNAs from next generation sequences of the sexually mature porcine testes.
Discovery of potential piRNAs from next generation sequences of the sexually mature porcine testes.
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从性成熟猪睾丸的下一代序列中发现潜在的 piRNA。
DOI：
10.1371/journal.pone.0034770
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Li F
中科院分区：
文献类型：
--
作者：
Liu G;Lei B;Li Y;Tong K;Ding Y;Luo L;Xia X;Jiang S;Deng C;Xiong Y;Li F
Piwi相互作用RNA（piRNA）是从哺乳动物睾丸中发现的一类新的小分子RNA，参与生殖细胞中逆转录转座子和其他遗传元件的转录沉默。为了鉴定在性成熟的猪睾丸中表达的piRNA的全转录组，提取小RNA级分并进行Solexa深度测序。我们克隆了6，913，561个猪小RNA（18-30 nt）的干净读段并进行功能表征。猪小RNA呈双峰长度分布，在21 nt和29 nt处有两个峰。然后从938，328个深度测序的小RNA（26-30 nt）中，通过k-mer方案鉴定了375，195个piRNA，并且通过同源性搜索鉴定了326个piRNA。然后通过短寡核苷酸分析包（SOAP）将通过k-mer方案预测的所有piRNA定位到猪基因组，并且所有独特定位的piRNA（197，673）中的81.61%定位到1124个定义的基因组区域（5.85 Mb）。在这些区域内，536和501个皮尔纳簇通常仅分布在基因组负链或正链上，48个皮尔纳簇分布在两条链上但以发散的方式分布，39个皮尔纳簇以重叠的方式分布在两条链上。此外，通过同源性搜索鉴定的7种piRNA的表达模式显示5种piRNA显示普遍存在的表达模式，尽管2种piRNA在睾丸中特异性表达。总之，我们的研究结果提供了猪piRNA的新信息，并且它们在猪睾丸中的特异性表达模式表明piRNA在调节精子发生中具有作用。
Piwi- interacting RNAs (piRNAs), a new class of small RNAs discovered from mammalian testes, are involved in transcriptional silencing of retrotransposons and other genetic elements in germ line cells. In order to identify a full transcriptome set of piRNAs expressed in the sexually mature porcine testes, small RNA fractions were extracted and were subjected to a Solexa deep sequencing. We cloned 6,913,561 clean reads of Sus Scrofa small RNAs (18–30 nt) and performed functional characterization. Sus Scrofa small RNAs showed a bimodal length distribution with two peaks at 21 nt and 29 nt. Then from 938,328 deep-sequenced small RNAs (26–30 nt), 375,195 piRNAs were identified by a k-mer scheme and 326 piRNAs were identified by homology searches. All piRNAs predicted by the k-mer scheme were then mapped to swine genome by Short Oligonucleotide Analysis Package (SOAP), and 81.61% of all uniquely mapping piRNAs (197,673) were located to 1124 defined genomic regions (5.85 Mb). Within these regions, 536 and 501 piRNA clusters generally distributed across only minus or plus genomic strand, 48 piRNA clusters distributed on two strands but in a divergent manner, and 39 piRNA clusters distributed on two strands in an overlapping manner. Furthermore, expression pattern of 7 piRNAs identified by homology searches showed 5 piRNAs displayed a ubiquitous expression pattern, although 2 piRNAs were specifically expressed in the testes. Overall, our results provide new information of porcine piRNAs and their specific expression pattern in porcine testes suggests that piRNAs have a role in regulating spermatogenesis.
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影响因子：
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影响因子：
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