Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia.
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53. doi: 10.1073/pnas.1110156109. Epub 2012 Mar 26.
Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies differences in the transcriptional responses of primary human and mouse macrophages to the Toll-like receptor (TLR)-4 agonist lipopolysaccharide (LPS). By using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5' ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologues were identified as "divergently regulated"). We further demonstrate concordant regulation of human-specific LPS target genes in primary pig macrophages. Divergently regulated orthologues were enriched for genes encoding cellular "inputs" such as cell surface receptors (e.g., TLR6, IL-7Rα) and functional "outputs" such as inflammatory cytokines/chemokines (e.g., CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. Functional consequences of divergent gene regulation were confirmed by showing LPS pretreatment boosts subsequent TLR6 responses in mouse but not human macrophages, in keeping with mouse-specific TLR6 induction. Divergently regulated genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced interspecies promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change.
基因表达的进化变化通常被认为是物种间表型差异的主要驱动因素。我们通过分析原代人源和鼠源巨噬细胞对 Toll 样受体（TLR）-4 激动剂脂多糖（LPS）的转录反应中的种间差异，研究了固有免疫的多样化。通过使用允许跨物种询问并结合 mRNA 5' 端深度测序的定制平台，我们鉴定了 LPS 调控的同源基因表达在人类和小鼠之间的广泛差异（24%的同源物被鉴定为“差异调控”）。我们进一步证明了 LPS 靶基因在原代猪巨噬细胞中的一致调控。差异调控的同源物富含编码细胞“输入”（如细胞表面受体（如 TLR6、IL-7Rα））和功能性“输出”（如炎症细胞因子/趋化因子（如 CCL20、CXCL13））的基因。相反，将输入与输出连接的细胞内信号传导成分通常是一致调控的。通过显示 LPS 预处理可增强随后的 TLR6 反应，而不是人源巨噬细胞，与鼠源特异性 TLR6 诱导一致，从而证实了差异基因调控的功能后果。差异调控基因与基因表达的大动态范围相关，并且与特定的启动子结构特征（TATA 盒富集，CpG 岛缺失）相关。令人惊讶的是，调节分歧也与增强的种间启动子保守性相关。因此，由复杂、高度保守的启动子控制的，促进动态调节的基因也是最容易发生进化变化的基因。
