Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (RNA-Seq I)

We report that Hedgehog signaling is a heterochronic pathway that determines the timing of the transition from specified cardiac progenitor to differentiated cardiomyocyte, a function distinct from its previously described roles affecting cellular patterning or proliferation. Hedgehog signaling was required to prevent premature differentiation and disruption of cardiac morphogenesis in vivo and the Hedgehog signaling transcription factor GLI1 was sufficient to delay differentiation in stem cell-derived cardiac progenitors in vitro. GLI1 directly activated a de novo progenitor-specific network in vitro that inhibited the induction of the cardiac differentiation program. The GLI1-driven gene regulatory network is sufficient to induce Hedgehog-naive in vitro cardiac progenitors to adopt an epigenomic state reminiscent of second heart field cardiac progenitors in vivo. A Hh-dependent GLI transcription factor switch functions as a differentiation timer, restricting activity of the progenitor network to the second heart field and permitting cardiomyocyte differentiation in the heart. GLI1 expression is broadly associated with the progenitor state, and its activity also delayed the differentiation of specified neural progenitors in vitro. We posit that Hedgehog signaling functions as a heterochronic regulator that transiently maintains diverse progenitor populations for complex organ development and that may explain diverse Hedgehog signaling-dependent phenomena. Transcriptomic and epigenomic analyses of Hedgehog/GLI dependent-networks in cardiac and neural progenitors

本研究报道，刺猬信号通路（Hedgehog signaling）是一类异时性通路，可调控定向心脏祖细胞向分化心肌细胞转化的时序，其功能区别于此前报道的该通路在细胞模式形成或细胞增殖调控中的作用。体内实验表明，刺猬信号通路可阻止心肌细胞过早分化及心脏形态发生紊乱；体外实验证实，刺猬信号通路转录因子GLI1足以延缓干细胞来源心脏祖细胞的分化过程。GLI1可在体外直接激活一套全新的祖细胞特异性调控网络，该网络能够抑制心脏分化程序的激活。由GLI1驱动的基因调控网络可将原本不依赖刺猬信号的体外心脏祖细胞诱导为表观基因组状态与体内第二心场心脏祖细胞相似的细胞群。一种依赖刺猬信号的GLI转录因子转换机制发挥了分化计时器的功能，将祖细胞网络的活性限定于第二心场区域，并允许心脏内心肌细胞的正常分化。GLI1的表达与祖细胞状态广泛相关，其活性还可延缓体外定向神经祖细胞的分化过程。我们推测，刺猬信号通路作为一类异时性调控因子，可暂时性维持多种祖细胞群以参与复杂器官的发育，这一机制或可解释多种依赖刺猬信号通路的生物学现象。本研究针对心脏及神经祖细胞中依赖刺猬信号/GLI的调控网络开展了转录组学与表观基因组学分析。