Enhancer reporters.

After egg fertilization, an initially silent embryonic genome is transcriptionally activated during the maternal-to-zygotic transition. In zebrafish, maternal vertebrate pluripotency factors Nanog, Pou5f3 (OCT4 homolog), and Sox19b (SOX2 homolog) (NPS) play essential roles in orchestrating embryonic genome activation, acting as “pioneers” that open condensed chromatin and mediate acquisition of activating histone modifications. However, some embryonic gene transcription still occurs in the absence of these factors, suggesting the existence of other mechanisms regulating genome activation. To identify chromatin signatures of these unknown pathways, we profiled the histone modification landscape of zebrafish embryos using CUT&RUN. Our regulatory map revealed two subclasses of enhancers distinguished by presence or absence of H3K4me2. Enhancers lacking H3K4me2 tend to require NPS factors for de novo activation, while enhancers bearing H3K4me2 are epigenetically bookmarked by DNA hypomethylation to recapitulate gamete activity in the embryo, independent of NPS pioneering. Thus, parallel enhancer activation pathways combine to induce transcriptional reprogramming to pluripotency in the early embryo.卵子受精后，初始处于转录沉默状态的胚胎基因组会在母源-合子转换（maternal-to-zygotic transition）过程中发生转录激活。在斑马鱼中，母源性脊椎动物多能性因子Nanog、Pou5f3（OCT4同源蛋白）、Sox19b（SOX2同源蛋白）（简称NPS）作为“先驱因子”，通过打开致密染色质并介导激活型组蛋白修饰的建立，在调控胚胎基因组激活进程中发挥核心作用。然而，即便缺失上述因子，部分胚胎基因仍可发生转录，提示存在其他调控基因组激活的未知机制。为鉴定这些未知通路的染色质特征，我们采用CUT&RUN技术对斑马鱼胚胎的组蛋白修饰谱进行了全景式分析。我们构建的调控图谱揭示了两类增强子亚型，其差异在于是否携带H3K4me2（组蛋白H3第4位赖氨酸二甲基化）修饰：缺失H3K4me2的增强子通常需要NPS因子介导从头激活，而携带H3K4me2的增强子则通过DNA低甲基化实现表观遗传书签化，可在不依赖NPS先驱功能的前提下，重现配子在胚胎中的活性模式。综上，多条平行的增强子激活通路协同作用，共同介导早期胚胎向多能性状态的转录重编程。