Transcriptome analysis has uncovered a series of long noncoding RNAs (lncRNAs) transcribed during cell differentiation, but how lncRNA is integrated with known transcriptional regulatory network is poorly understood. Here, we utilize human definitive endoderm differentiation as a model system and decipher the functional interaction between lncRNA and key transcriptional factor. We have identified GATA6-AS1, an lncRNA divergently transcribed from the GATA6 locus, is highly expressed during endoderm differentiation. Knockdown of GATA6-AS1 in human pluripotent stem cells has no influence on morphology and pluripotency; however, GATA6-AS1 depletion causes the deficiency of definitive endoderm differentiation. GATA6-AS1 positively regulates the expression of endoderm key factor GATA6. Further investigation shows GATA6-AS1 interacts with SMAD2/3 and activates the transcription of GATA6. In addition, overexpression of GATA6 is able to rescue the defect of endoderm differentiation due to the absence of GATA6-AS1, suggesting that GATA6 is the functional target of GATA6-AS1 during endoderm differentiation. Ultimately, our study reveals that GATA6-AS1 is necessary for human endoderm specification and reveals the underlying mechanism between GATA6-AS1 and GATA6.

转录组分析发现了在细胞分化过程中转录的一系列长非编码RNA（lncRNA），但人们对lncRNA如何与已知的转录调控网络整合的了解却很少。在这里，我们利用人类定形内胚层分化作为模型系统，并破译lncRNA与关键转录因子之间的功能相互作用。我们已经鉴定出GATA6-AS1，从GATA6基因座发散转录的lncRNA，在内胚层分化过程中高度表达。抑制人多能干细胞中的GATA6-AS1对形态和多能性没有影响。但是，GATA6-AS1的消耗会导致内胚层分化的缺乏。GATA6-AS1积极调节内胚层关键因子GATA6的表达。进一步的研究表明GATA6-AS1与SMAD2 / 3相互作用并激活GATA6的转录。另外，由于缺乏GATA6-AS1，GATA6的过表达能够挽救内胚层分化的缺陷，这表明GATA6是内胚层分化过程中GATA6-AS1的功能靶标。最终，我们的研究揭示了GATA6-AS1对于人类内胚层规范是必需的，并揭示了GATA6-AS1与GATA6之间的潜在机制。