Department of Molecular Biology and Genetics, Faculty of Sciences and Technology, Aarhus University, DK-8830 Tjele, Denmark.
Biochem Biophys Res Commun. 2013 Aug 23;438(2):346-52. doi: 10.1016/j.bbrc.2013.07.074. Epub 2013 Jul 27.
The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i.e. cerebellum versus heart for differential variation at the gene, isoform, and transcription start site (TSS), and promoter level showed that several of the genes differed at all four levels. Interestingly, these genes were mainly annotated to the "electron transport chain" and neuronal differentiation, emphasizing that "tissue important" genes are regulated at several levels. Furthermore, our analysis shows that the "across tissue approach" has a promising potential when screening for possible explanations for variations, such as those observed at the gene expression levels.
转录组是组织或细胞在采样时的转录物的绝对集合。在这项研究中，采用 RNA-Seq 技术对十种猪组织的转录组谱进行差异分析，以评估组织在基因和异构体表达水平上的差异，同时分析转录起始位点、启动子使用和剪接的变化。总共对 2.23 亿个 RNA 片段进行测序，使用 Cufflinks 鉴定了 59930 个转录基因位置和 290936 个转录本变体，这些基因与大约 13899 个注释的人类基因具有相似性。组织间基因水平的差异表达的成对分析表明，来自猪脑的组织之间的差异最小。有趣的是，异构体水平的差异表达相对水平在组织对比之间通常没有变化。此外，组织间差异启动子使用的分析表明，小脑（CBE）与额叶皮质和小脑与下丘脑（HYP）之间的差异比例高于其余比较。此外，差异转录起始位点的比较表明，这些位点的数量通常在包括下丘脑的比较中增加，而与其他成对评估相比则减少。对组织对比之一（即小脑与心脏）的基因、异构体和转录起始位点（TSS）以及启动子水平的差异变化进行综合分析表明，有几个基因在所有四个水平上都存在差异。有趣的是，这些基因主要被注释为“电子传递链”和神经元分化，这强调了“组织重要”基因在多个水平上受到调控。此外，我们的分析表明，“跨组织方法”在筛选可能的解释方面具有很大的潜力，例如在基因表达水平上观察到的变化。
