Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.

中文翻译：

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涡肠中的细胞类型多样性和区域化基因表达

正确的功能和对消化系统的修复对大多数动物至关重要。破解这些过程涉及的机制需要基因表达和细胞类型的地图集。在这里，我们应用激光捕获显微切割术（LCM）和RNA序列来表征Schmidtea mediterranea的肠道转录组，一种涡虫扁虫，可以再生包括肠道在内的所有器官。我们鉴定了数百种先前方法未检测到的具有肠道表达的基因。系统分析表明，与其他动物（包括人类）相比，消化生理和细胞类型得到了广泛的保护。此外，空间LCM使我们能够发现沿平顶-中轴，特别是在肠杯状细胞中，在涡状肠中未表达的基因表达区域。最后，我们确定了两个肠道富集的转录因子，它们专门调节再生（刺猬信号传导物gli-1）或维持（RREB2）的杯状细胞。总之，这项工作为进一步研究与胃肠功能，修复和再生有关的机制提供了资源。