H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development [DamID-seq]

Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. Here, we provide evidence that in Xenopus laevis, H3K4 methylation contributes to epigenetic memory of active chromatin states, which is required for faithful zygotic genome activation and successful embryonic development. We find that chromatin configurations of promoters displaying high H3K4me3 intensity and breadth, alongside DNA hypomethylation and increased GC content, are maintained from the gametes to the embryo across multiple cell divisions and a transcriptionally quiescent phase in early development. We show that this maintenance of H3K4 methylation is essential for precise zygotic genome activation. Finally, we demonstrate that Kmt2b and Cxxc1 facilitate transcription-independent maintenance of H3K4me3 and proper zygotic gene expression. In summary, our study establishes a role for H3K4 methylation for memory of active chromatin states in embryos and reveals its importance for successful embryonic development. Overall design: Chromatin Accessibility profiling using Targeted DamID (CATaDa) sequencing performed on pre-ZGA (4.5hpf/256-cell) stage Xenopus laevis embryos. Dam mRNA construct was injected into 1-cell stage embryos and embryos were collected at the stage of interest.

精准构建的转录程序对于胚胎发育的顺利完成至关重要。在合子基因组激活（zygotic genome activation, ZGA）阶段，基因表达在胚胎生命历程中首次启动。胚胎内的先驱转录因子（pioneer transcription factors）对该过程不可或缺，但活跃染色质修饰的具体作用仍不甚明确。目前尚不清楚，配子中建立的活跃染色质修饰是否会作为表观遗传记忆传递至胚胎，以支持合子基因组激活与胚胎发育。本研究以非洲爪蟾（Xenopus laevis）为模型，提供证据表明H3K4甲基化有助于维持活跃染色质状态的表观遗传记忆，而该记忆对于精准的合子基因组激活与胚胎顺利发育必不可少。我们发现，兼具高H3K4me3信号强度与广度、同时伴随DNA低甲基化及GC含量升高的启动子区域，其染色质构象可从配子传递至胚胎，历经多次细胞分裂与早期发育中的转录静默阶段得以维持。研究证实，H3K4甲基化的此类维持过程对于精准的合子基因组激活至关重要。最后，我们证明Kmt2b与Cxxc1可促进不依赖转录的H3K4me3维持过程，并保障合子基因的正常表达。综上，本研究明确了H3K4甲基化在胚胎活跃染色质状态记忆中的作用，并揭示了其对于胚胎顺利发育的重要性。实验设计概述：本研究针对合子基因组激活前（pre-ZGA，即受精后4.5小时/256细胞期）的非洲爪蟾胚胎，采用靶向DamID（Chromatin Accessibility profiling using Targeted DamID, CATaDa）测序技术开展染色质开放性分析。将Dam mRNA构建体注射至1细胞期胚胎，随后在目标发育阶段收集胚胎样本。