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（Hedgehog）信号通路是一类异时性通路，可调控从定向心脏祖细胞向分化心肌细胞转变的时序，该功能与其此前已报道的、参与细胞模式形成或细胞增殖的作用截然不同。体内实验证实，刺猬信号通路可阻止过早分化及心脏形态发生异常；体外实验中，刺猬信号通路的转录因子GLI1足以延缓干细胞衍生心脏祖细胞的分化进程。体外实验显示，GLI1可直接激活一个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启动。由GLI1驱动的基因调控网络足以诱导未接触刺猬信号的体外心脏祖细胞，获得与体内第二心区心脏祖细胞相似的表观基因组状态。依赖Hedgehog的GLI转录因子开关充当分化计时器，将祖细胞网络的活性限定于第二心区，并允许心脏内心肌细胞的分化。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进程。我们提出，刺猬信号通路作为一类异时性调控因子，可瞬时维持多种祖细胞群以支持复杂器官的发育，这或许可解释多种依赖刺猬信号通路的生物学现象。本数据集包含心脏与神经祖细胞中刺猬/GLI依赖型调控网络的转录组学及表观基因组学分析数据。