RNA-seq of hESC samples upon loss of UPF1.. Homo sapiens

Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-b and BMP signaling, which we found NMD acts through to influence definitive endoderm vs. mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages. Overall design: Examination of differential gene expression in hESCs upon loss of UPF1.

无义介导的RNA降解（Nonsense-mediated RNA decay, NMD）是一类高度保守的通路，可选择性降解特定子集的RNA转录本。本研究证实，NMD可调控人类早期发育的细胞命运。我们发现，NMD因子在人类多能干细胞中的表达水平普遍高于分化细胞，这提示NMD需被下调以允许细胞分化。在人类胚胎干细胞（human embryonic stem cells, hESCs）中开展的功能丧失与功能获得实验表明，NMD下调确实是高效生成定型内胚层的必要条件。RNA测序（RNA-seq）分析鉴定出，在hESCs中抑制NMD时被诱导的NMD靶转录本，其中包含众多编码信号通路组分的转录本。这促使我们探究转化生长因子-β（transforming growth factor-β, TGF-β）与骨形态发生蛋白（bone morphogenetic protein, BMP）信号通路的功能，结果发现NMD正是通过这两条通路来影响定型内胚层与中胚层的细胞命运。本研究结果表明，选择性RNA降解对于特化特定人类胚胎细胞谱系的发育命运至关重要。整体实验设计：检测UPF1缺失后hESCs中的差异基因表达情况。