INO80 promotes and safeguards bivalency [ChIP-seq]

INO80 is involved in many chromatin-dependent functions. However, its role in pluripotency has not been fully defined. We examined the impact of Ino80 deletion in the naïve and primed pluripotent stem cells. We found that Ino80 deletion had minimal effect on self-renewal and gene expression in the naïve state, but led to cellular differentiation and de-repression of developmental genes in the primed state. Mechanistically, INO80 co-occupied gene promoters that were bivalently marked by H3K4me3 and H3K27me3. Further, its occupancy was required for H3K27me3 installation and maintenance, as well as downstream gene repression. Finally, INO80 promoted H2A.Z occupancy at the bivalent domains, which in turn facilitated the polycomb repressive complex 2 (PRC2) recruitment. Together, our results identified the INO80-H2A.Z axis as an essential step for bivalent chromatin and poised gene expression and uncovered an epigenetic mechanism by which chromatin remodeling, histone variant, and histone modification coordinately control cell fate. Overall design: Effects of INO80 deletion on the transcriptome (RNAseq) and epigenome (ChIP-seq, MNase-seq) in mouse naïve and primed pluripotent stem cells

INO80参与诸多染色质依赖性功能，但其在细胞多能性调控中的作用尚未得到完全阐明。本研究检测了Ino80基因缺失对幼稚态（naïve）与始发态（primed）多能干细胞的影响。研究结果显示，Ino80基因缺失对幼稚态细胞的自我更新能力与基因表达谱仅存在极微弱影响，却会诱导始发态细胞发生分化，并解除发育基因的转录抑制。机制层面分析表明，INO80可共同占据同时被H3K4me3与H3K27me3双价标记的基因启动子区域。进一步研究证实，INO80的染色质占据对于H3K27me3的建立与维持，以及下游基因的转录抑制均必不可少。此外，INO80能够促进组蛋白变体H2A.Z在双价染色质结构域的占据，进而助力多梳抑制复合体2（polycomb repressive complex 2, PRC2）的招募。综上，本研究确认INO80-H2A.Z轴是维持双价染色质与预备型（poised）基因表达的关键步骤，并揭示了染色质重塑、组蛋白变体与组蛋白修饰协同调控细胞命运的表观遗传机制。实验整体设计：探究INO80基因缺失对小鼠幼稚态与始发态多能干细胞的转录组（RNA测序（RNA-seq））及表观组（染色质免疫共沉淀测序（ChIP-seq）、微球菌核酸酶测序（MNase-seq））的影响。