Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

中文翻译：

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脊椎动物原代细胞的比较转录组学。

已观察到同源组织中的基因表达谱在物种之间是不同的，这可能是由于物种之间在每种细胞类型中基因表达程序的差异，但也可能反映了不同物种中每种组织的细胞类型组成的差异。在这里，我们使用来自 FANTOM5 的 Cap 分析基因表达 (CAGE) 和短 RNA (sRNA) 测序数据比较了人类、小鼠、大鼠、狗和鸡的匹配原代细胞中的表达谱。虽然我们发现不同物种中直系同源基因的表达谱在细胞类型之间高度相关，但在每种细胞类型中，许多基因在物种之间存在差异表达。具有参与转录、RNA 加工和转录调控的产物的基因表达更可能是保守的，而编码参与细胞间通讯的蛋白质的基因的表达更有可能在进化过程中发生分歧。表达的保守性与基因的进化年龄呈正相关，表明对细胞功能至关重要的基因表达水平的差异在进化过程中受到限制。基序活性分析表明，不同物种的启动子和增强子都被相同的转录因子激活。对成熟 miRNA 和 CAGE 鉴定的初级 miRNA 表达水平的分析表明，进化中的老 miRNA 比年轻的 miRNA 更可能具有保守的表达模式。我们得出结论，监管网络的关键方面是保守的，