Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA-seq]. Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA-seq]

Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos. Overall design: RNA-seq in early Zebrafish embryos.

脊椎动物胚胎在合子基因组激活（zygotic genome activation, ZGA）阶段，通过构建染色质状态以获得发育能力：此类染色质状态可沉默发育基因，同时使其处于预激活状态，为后续谱系特异性激活做好准备。本研究揭示了在ZGA前（preZGA）斑马鱼胚胎中，发育基因的预激活状态是如何从头建立的。预激活状态首先在启动子和增强子区域建立：这些区域初始时便含有携带"占位核小体（Placeholder nucleosomes）"（含H2A.Z、H3K4me1与H3K27ac修饰）的开放/允许性染色质，且存在DNA低甲基化修饰。沉默过程则始于ZGA前及ZGA阶段：多梳抑制复合体1（Polycomb Repressive Complex 1, PRC1）被招募至这些区域，同时催化亚基Rnf2介导H2Aub1修饰的沉积。在ZGA后阶段，H2Aub1可介导含有Aebp2的多梳抑制复合体2（Polycomb Repressive Complex 2, PRC2）招募，并促成H3K27me3修饰的沉积。值得注意的是，通过抑制Rnf2阻断H2Aub1修饰，可消除Aebp2-PRC2复合体的招募与H3K27me3修饰的沉积，并在ZGA阶段引发部分发育基因的转录上调。但该转录上调并不依赖于H3K27me3修饰，由此确定H2Aub1是ZGA阶段关键的沉默修饰。综上，本研究阐明了早期脊椎动物胚胎中，预激活/沉默型发育基因的建立逻辑与分子机制。实验整体设计：早期斑马鱼胚胎的RNA测序（RNA-seq）分析。