Gene bivalency at Polycomb domains regulates cranial neural crest positional identity [RNA-seq]

The cranial neural crest cells are pluripotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. Here, we analyzed the in vivo chromatin landscapes of mouse cranial neural crest subpopulations. Early postmigratory neural crest subpopulations contributing to distinct mouse craniofacial structures displayed similar chromatin accessibility patterns, yet differed transcriptionally. Accessible promoters and enhancers of differentially silenced genes carried H3K27me3/H3K4me2 bivalent chromatin marks embedded in large Ezh2-dependent Polycomb domains, indicating transcriptional poising. These postmigratory bivalent regions were already present in neural crest premigratory progenitors. At Polycomb domains, H3K27me3 antagonized H3K4me2 deposition, which was restricted to accessible sites. Thus, bivalent Polycomb domains provide a chromatin template for the regulation of cranial neural crest cell positional identity in vivo contributing novel insights into the epigenetic regulation of face morphogenesis. RNAseq, ChIPseq (single H3K27me3, H3K4me2 and H3K27ac ChIPseq; sequential H3K27me3/H3K4me2 ChIPseq) and ATACseq profiling of cranial neural crest cell (NCC) progenitors (E8.5) and postmigratory subpopulations (FNP, Mx, Md, PA2; E10.5 and E11.5) of wildtype, Ezh2-conditional knockout, Hoxa2-temporal knockout and Hoxa2-overexpression genotypes.颅神经嵴细胞（cranial neural crest cells）是一类多能细胞，可产生头部成骨间充质，对颅面模式形成至关重要。本研究分析了小鼠颅神经嵴亚群的体内染色质景观。参与构成不同小鼠颅面结构的早期迁移后神经嵴亚群，虽展现出相似的染色质可及性模式，但转录水平存在显著差异。差异沉默基因的可及启动子与增强子，携带有嵌入于大型依赖Ezh2的多梳结构域中的H3K27me3/H3K4me2二价染色质标记，表明其处于转录预备状态。这类迁移后二价区域在神经嵴迁移前祖细胞中便已存在。在多梳结构域中，H3K27me3会拮抗H3K4me2的沉积，而后者仅局限于可及染色质区域。综上，二价多梳结构域为体内调控颅神经嵴细胞的位置身份提供了染色质模板，为颜面形态发生的表观遗传调控提供了全新见解。本研究对野生型、Ezh2条件性敲除、Hoxa2时空特异性敲除以及Hoxa2过表达基因型的颅神经嵴细胞（NCC）祖细胞（胚胎第8.5天，E8.5）及其迁移后亚群（FNP、Mx、Md、PA2；胚胎第10.5天、11.5天，E10.5和E11.5）开展了RNA测序（RNAseq）、染色质免疫沉淀测序（ChIPseq，涵盖单靶点H3K27me3、H3K4me2与H3K27ac ChIPseq，以及连续H3K27me3/H3K4me2 ChIPseq）和ATAC测序（ATACseq）谱型分析。