Organoids are a valuable three-dimensional (3D) model to study the differentiated functions of the human intestinal epithelium. They are a particularly powerful tool to measure epithelial transport processes in health and disease. Though biological assays such as organoid swelling and intraluminal pH measurements are well established, their underlying functional genomics are not well characterized. Here we combine genome-wide analysis of open chromatin by ATAC-Seq with transcriptome mapping by RNA-Seq to define the genomic signature of human intestinal organoids (HIOs). These data provide an important tool for investigating key physiological and biochemical processes in the intestinal epithelium. We next compared the transcriptome and open chromatin profiles of HIOs with equivalent data sets from the Caco2 colorectal carcinoma line, which is an important two-dimensional (2D) model of the intestinal epithelium. Our results define common features of the intestinal epithelium in HIO and Caco2 and further illustrate the cancer-associated program of the cell line. Generation of Caco2 cysts enabled interrogation of the molecular divergence of the 2D and 3D cultures. Overrepresented motif analysis of open chromatin peaks identified caudal type homeobox 2 (CDX2) as a key activating transcription factor in HIO, but not in monolayer cultures of Caco2. However, the CDX2 motif becomes overrepresented in open chromatin from Caco2 cysts, reinforcing the importance of this factor in intestinal epithelial differentiation and function. Intersection of the HIO and Caco2 transcriptomes further showed functional overlap in pathways of ion transport and tight junction integrity, among others. These data contribute to understanding human intestinal organoid biology.

中文翻译：

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人类结肠类器官的功能基因组学分析确定了关键的转录因子。

类器官是一种有价值的三维（3D）模型，用于研究人肠上皮的分化功能。它们是测量健康和疾病中上皮运输过程的特别强大的工具。尽管生物测定法（如类器官肿胀和管腔内pH测量）已得到很好的确立，但其潜在的功能基因组学尚未得到很好的表征。在这里，我们结合通过ATAC-Seq对全染色质进行全基因组分析，并通过RNA-Seq对转录组作图，以定义人类肠道类器官（HIOs）的基因组特征。这些数据为研究肠道上皮细胞的关键生理和生化过程提供了重要工具。接下来，我们将HIO的转录组和开放染色质图谱与来自Caco2大肠癌系的等效数据集进行了比较，这是肠上皮的重要二维（2D）模型。我们的研究结果定义了HIO和Caco2中肠上皮的共同特征，并进一步说明了该细胞系的癌症相关程序。Caco2囊肿的产生使得能够询问2D和3D培养物的分子差异。开放染色质峰的代表性过高表示分析确定尾型同源盒2（CDX2）是HIO中的关键激活转录因子，但在Caco2的单层培养中却没有。但是，CDX2基序在来自Caco2囊肿的开放染色质中变得过分表达，从而增强了该因子在肠上皮分化和功能中的重要性。HIO和Caco2转录组的交叉点进一步显示了离子迁移和紧密连接完整性等途径中的功能重叠。