Dynamics of RNA polymerase II pausing and bivalent histone H3 methylation during neuronal differentiation in brain development [RNA-seq]

Cell fate specification is accompanied by global changes in gene expression from patterns of maintaining stem/progenitor cells to patterns for supporting differentiation. To ensure a proper transition, it is conceivable that genes important for differentiation are kept silent in stem/progenitor cells yet can be readily activated. RNA polymerase II (Pol II) pausing and bivalent chromatin marks are two paradigms that are suited for establishing such a poised state of gene expression, however, their contributions to gene regulation in development are not well understood. Here, using neural progenitor cells (NPCs) and their daughter neurons co-purified from the embryonic mouse cerebral cortex, we characterized Pol II pausing and H3K4me3/H3K27me3 marks in this in vivo setting of neurogenesis. We show that genes paused in NPCs or neurons are well correlated with their respective cell type-specific functions, but pausing and pause release did not predict gene activation. Bivalent chromatin marks, on the other hand, poised the marked genes in NPCs for activation in neurons. Interestingly, our data also revealed a positive correlation between H3K27me3 and paused Pol II. This study thus reveals cell-type specific Pol II pausing and gene activation-associated bivalency during mammalian neuronal differentiation. Transcriptome analyses in neural progenitor cells (NPCs) and their daughter neurons, and their relationship with RNA polymerase II pausing and histone bivalent mark细胞命运特化（cell fate specification）过程伴随基因表达的全局改变，其表达模式从维持干细胞/祖细胞（stem/progenitor cells）状态转向支持细胞分化的状态。为保障这一转变顺利完成，不难推测，对分化至关重要的基因会在干细胞/祖细胞中保持沉默，却可在需要时快速激活。RNA聚合酶II（RNA polymerase II，Pol II）暂停与二价染色质标记（bivalent chromatin marks）是两种适于建立此类基因表达预备状态的范式，然而二者在发育过程中对基因调控的贡献尚未得到充分阐明。本研究从小鼠胚胎大脑皮层（embryonic mouse cerebral cortex）中共纯化分离神经祖细胞（neural progenitor cells，NPCs）及其子代神经元，在此神经发生（neurogenesis）的体内环境中对Pol II暂停以及H3K4me3/H3K27me3标记进行了表征分析。研究发现，在神经祖细胞或神经元中发生暂停的基因与其对应的细胞类型特异性功能密切相关，但基因暂停与暂停释放并不能预测基因的激活状态。而二价染色质标记则可使神经祖细胞中被标记的基因处于预备状态，以便在神经元中被激活。有趣的是，本研究数据还揭示了H3K27me3与暂停状态Pol II之间存在正相关关系。因此，本研究揭示了哺乳动物神经元分化过程中细胞类型特异性的Pol II暂停现象以及与基因激活相关的二价染色质标记特征。对神经祖细胞（NPCs）及其子代神经元的转录组（transcriptome）分析，及其与RNA聚合酶II暂停与组蛋白二价标记（histone bivalent mark）的关联。