BACKGROUND Long non-coding RNAs (lncRNAs) are key regulators of diverse cellular processes. Although a number of studies have reported the identification of bovine lncRNAs across many tissues, very little is known about the identity and characteristics of lncRNAs in bovine oocytes. METHODS A bovine oocyte cDNA library was constructed and sequenced using the Illumina HiSeq 2000 sequencing system. The oocyte transcriptome was constructed using the ab initio assembly software Scripture and Cufflinks. The assembled transcripts were categorized to identify the novel intergenic transcripts, and the coding potential of these novel transcripts was assessed using CPAT and PhyloCSF. The resulting candidate long intergenic non-coding RNAs (lincRNAs) transcripts were further evaluated to determine if any of them contain any known protein coding domains in the Pfam database. RT-PCR was used to analyze the expression of oocyte-expressed lincRNAs in various bovine tissues. RESULTS A total of 85 million raw reads were generated from sequencing of the bovine oocyte library. Transcriptome reconstruction resulted in the assembly of a total of 42,396 transcripts from 37,678 genomic loci. Analysis of the assembled transcripts using the step-wide pipeline resulted in the identification of 1535 oocyte lincRNAs corresponding to 1183 putative non-coding genes. A comparison of the oocyte lincRNAs with the lncRNAs reported in other bovine tissues indicated that 970 of the 1535 oocyte lincRNAs appear to be unique to bovine oocytes. RT-PCR analysis of 5 selected lincRNAs showed either specific or predominant expression of 4 lincRNAs in the fetal ovary. Functional prediction of the oocyte-expressed lincRNAs suggested their involvement in oogenesis through regulating their neighboring protein-coding genes. CONCLUSIONS This study provides a starting point for future research aimed at understanding the roles of lncRNAs in controlling oocyte development and early embryogenesis in cattle.

中文翻译：

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系统鉴定牛卵母细胞中表达的长基因间非编码RNA。

背景技术长的非编码RNA（lncRNA）是多种细胞过程的关键调节因子。尽管许多研究报道了跨许多组织的牛lncRNA的鉴定，但对牛卵母细胞中lncRNA的身份和特征了解甚少。方法使用Illumina HiSeq 2000测序系统构建牛卵母细胞cDNA文库并进行测序。使用从头开始组装软件Scripture和Cufflinks构建卵母细胞转录组。将组装的转录物分类以鉴定新的基因间转录物，并使用CPAT和PhyloCSF评估这些新的转录物的编码潜力。进一步评估了生成的候选长基因间非编码RNA（lincRNA）转录本，以确定它们中的任何一个是否在Pfam数据库中包含任何已知的蛋白质编码域。RT-PCR用于分析在各种牛组织中表达卵母细胞的lincRNA的表达。结果通过对牛卵母细胞文库的测序，总共产生了8500万个原始读数。转录组重建导致来自37,678个基因组位点的42,396个转录本的组装。使用全步骤流水线分析组装的转录本，鉴定出1535个卵母细胞lincRNA，它们对应于1183个推定的非编码基因。卵母细胞lincRNA与其他牛组织中报道的lncRNA的比较表明，1535个卵母细胞lincRNA中的970种似乎是牛卵母细胞特有的。对5种选择的lincRNA的RT-PCR分析显示，在胎儿卵巢中有4种lincRNA的特异性或优势表达。卵母细胞表达的lincRNA的功能预测表明，它们通过调节其邻近的蛋白质编码基因参与卵子发生。结论本研究为未来研究的起点，旨在了解lncRNA在控制牛卵母细胞发育和早期胚胎发生中的作用。