Genome-wide interaction target profiling reveals a novel Peblr20-eRNA activation pathway to control stem cell pluripotency
Genome-wide interaction target profiling reveals a novel Peblr20-eRNA activation pathway to control stem cell pluripotency
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全基因组相互作用靶标分析揭示了一种控制干细胞多能性的新型 Peblr20-eRNA 激活途径。
DOI：
10.7150/thno.39093
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发表时间：
2020
期刊：
影响因子：
12.4
通讯作者：
Jiuwei Cui
中科院分区：
文献类型：
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作者：
Cong Wang;Lin Jia;Yichen Wang;Zhonghua Du;Lei Zhou;Xue Wen;Hui Li;Shilin Zhang;Huiling Chen;Naifei Chen;Jingcheng Chen;Yanbo Zhu;Yuanyuan Nie;Ilkay Celic;Sujun Gao;Songling Zhang;Andrew R.Hoffman;Wei Li;Ji-Fan Hu;Jiuwei Cui
背景：长链非编码RNA（lncRNA）是调控干细胞多能性的重要组成部分。然而，这些lncRNA在控制多能性中所利用的具体机制尚未完全表征。研究方法：我们利用RNA逆转录相关陷阱测序（RAT-seq）方法来分析通过RNA-seq筛选的lncRNA的小鼠全基因组相互作用靶标。结果：我们鉴定了Peblr 20（Pou 5 F1增强子结合lncRNA 20）作为与干细胞重编程相关的新型lncRNA。与诱导多能干细胞（iPSC）相比，Peblr 20在成纤维细胞中差异转录。值得注意的是，我们发现Peblr 20利用反式机制与多个干性基因的调控元件相互作用。使用获得和丧失功能的实验，我们表明，敲低Peblr 20导致iPSCs退出多能性，而过表达Peblr 20激活内源性Pou 5 F1表达。我们进一步证明Peblr 20促进了多能重编程。从机制上讲，我们证明了Peblr 20通过反式结合Pou 5 F1增强子，募集TET 2去甲基化酶并激活增强子转录的RNA来激活内源性Pou 5 F1。结论：我们的数据揭示了一种新的表观遗传机制，lncRNA通过反式调节Pou 5 F1增强子RNA通路来控制干细胞的命运。我们展示了利用lncRNA生物学来增强再生医学干细胞生成的潜力。
Background: Long non-coding RNAs (lncRNAs) constitute an important component of the regulatory apparatus that controls stem cell pluripotency. However, the specific mechanisms utilized by these lncRNAs in the control of pluripotency are not fully characterized. Methods: We utilized a RNA reverse transcription-associated trap sequencing (RAT-seq) approach to profile the mouse genome-wide interaction targets for lncRNAs that are screened by RNA-seq. Results: We identified Peblr20 (Pou5F1 enhancer binding lncRNA 20) as a novel lncRNA that is associated with stem cell reprogramming. Peblr20 was differentially transcribed in fibroblasts compared to induced pluripotent stem cells (iPSCs). Notably, we found that Peblr20 utilized a trans mechanism to interact with the regulatory elements of multiple stemness genes. Using gain- and loss-of-function experiments, we showed that knockdown of Peblr20 caused iPSCs to exit from pluripotency, while overexpression of Peblr20 activated endogenous Pou5F1 expression. We further showed that Peblr20 promoted pluripotent reprogramming. Mechanistically, we demonstrated that Peblr20 activated endogenous Pou5F1 by binding to the Pou5F1 enhancer in trans, recruiting TET2 demethylase and activating the enhancer-transcribed RNAs. Conclusions: Our data reveal a novel epigenetic mechanism by which a lncRNA controls the fate of stem cells by trans-regulating the Pou5F1 enhancer RNA pathway. We demonstrate the potential for leveraging lncRNA biology to enhance the generation of stem cells for regenerative medicine.