Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [RNA-seq]

Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how they are integrated in the genome is poorly understood. Here we identified the Xenopus foregut and hindgut progenitor transcriptomes, which are largely conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/b-catenin acts as a genome-wide toggle between foregut and hindgut programs. In addition to b-catenin-Tcf promoting hindgut gene transcription, we unexpectedly observed Wnt-repressed foregut genes associated with b-catenin-binding to DNA lacking Tcf motifs, suggesting a novel direct repression. We define how BMP and Wnt signaling are integrated in the genome with Smad1 and ß-catenin co-occupying DNA elements associated with hundreds of key regulatory genes. These results extend our understanding of GI organogenesis and how Wnt and BMP may coordinate genomic responses in other contexts. Overall design: mRNA profile of foregut and hindgut explants from BMP and Wnt manipulated embryos.

消化系统发育由内胚层与中胚层之间的组合式信号互作协同调控，但二者的信号互作如何在基因组层面实现整合的机制仍不甚明晰。本研究鉴定了爪蟾（Xenopus）前肠与后肠祖细胞的转录组，该转录组在很大程度上与哺乳动物的对应转录组具有高度保守性。我们通过RNA测序（RNA-seq）与染色质免疫共沉淀测序（ChIP-seq）实验证实，骨形态发生蛋白（BMP）/Smad1可在内胚层与中胚层中调控背腹轴基因表达，而Wnt/β-连环蛋白（Wnt/β-catenin）则作为全基因组层面的调控开关，介导前肠与后肠基因表达程序之间的切换。除β-连环蛋白-T细胞因子（β-catenin-Tcf）复合体可促进后肠基因转录外，我们还意外发现受Wnt信号抑制的前肠基因与β-连环蛋白结合于不含Tcf基序的DNA区域相关，这提示存在一种全新的直接转录抑制机制。我们明确了BMP与Wnt信号通路在基因组层面的整合方式：Smad1与β-连环蛋白共同结合于数百个关键调控基因相关的DNA元件上。本研究结果拓展了我们对胃肠道（GI）器官发生的认知，同时也为阐明Wnt与BMP信号在其他场景中如何协同调控基因组应答提供了新的视角。
实验整体设计：对经BMP与Wnt信号操控的胚胎中分离的前肠、后肠外植体进行mRNA表达谱分析。