‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming [RNA-Seq]

The function and retention/reprogramming of epigenetic marks during the germline-to-embryo transition is a key issue in developmental and cellular biology, with relevance to stem cell programming and trans-generational inheritance. In zebrafish, DNAme patterns are programmed in transcriptionally-quiescent early cleavage embryos; paternally-inherited patterns are maintained, whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a ‘placeholder’ nucleosome, containing the histone H2A variant H2A.Z(FV) and H3K4me1, occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors. Upon genome-wide transcriptional onset, genes with the Placeholder become either active H3K4me3-marked or silent H3K4me3/K27me3-marked (bivalent). Importantly, functional perturbation causing Placeholder loss confers DNAme acquisition, whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus, during transcriptionally quiescent stages (gamete-zygote-cleavage), an H2A.Z(FV)/H3K4me1-containing Placeholder nucleosome deters DNAme, poising parental genes for either gene-specific activation or facultative repression.

表观遗传标记在生殖系向胚胎转化过程中的功能、维持与重编程，是发育生物学与细胞生物学领域的核心议题之一，其研究与干细胞重编程及跨代遗传密切相关。
在斑马鱼中，转录静默的早期卵裂胚胎内的DNA甲基化（DNA methylation, DNAme）模式会被程序化建立；父本遗传的甲基化模式得以保留，而母本模式则会被重编程以匹配父本模式。
本研究发现，一种携带组蛋白H2A变体H2A.Z(FV)与组蛋白H3赖氨酸4单甲基化（H3K4me1）的占位核小体（placeholder nucleosome），几乎占据了精子与卵裂胚胎中所有不含DNA甲基化的区域，并富集于编码管家基因与早期胚胎转录因子的启动子区域。
当全基因组转录启动后，携带该占位核小体的基因会分别被标记为活性状态的H3K4me3（组蛋白H3赖氨酸4三甲基化）修饰，或是沉默状态的H3K4me3/K27me3（组蛋白H3赖氨酸27三甲基化）双修饰（二价结构域，bivalent）。
值得注意的是，若通过功能扰动使占位核小体丢失，会导致该区域获得DNA甲基化修饰；反之，占位核小体的获得与扩张则会引发DNA低甲基化与异常的基因激活。
因此，在转录静默阶段（配子-合子-卵裂期），携带H2A.Z(FV)/H3K4me1的占位核小体能够阻止DNA甲基化的建立，从而使亲本基因处于可进行特异性激活或兼性沉默的预备状态。