INO80 promotes and safeguards bivalency [Mnase-seq]. INO80 promotes and safeguards bivalency [Mnase-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

INO80参与多种染色质依赖的生物学过程，但其在多能性（pluripotency）中的功能尚未得到完整阐释。本研究探究了Ino80基因敲除对初始态多能干细胞（naïve pluripotent stem cell）与始发态多能干细胞（primed pluripotent stem cell）的影响。研究发现，Ino80敲除在初始态多能干细胞中对细胞自我更新与基因表达仅产生极微弱的影响，但在始发态多能干细胞中会引发细胞分化，并解除发育相关基因的转录抑制。从机制层面而言，INO80可共同占据被H3K4me3与H3K27me3双价标记（bivalently marked）的基因启动子区域。进一步研究表明，INO80的占据对于H3K27me3的建立与维持，以及下游基因的转录抑制均不可或缺。最终，INO80可促进H2A.Z在双价结构域上的占据，这一过程进而助力多梳抑制复合体2（polycomb repressive complex 2, PRC2）的招募。综上，本研究结果确认INO80-H2A.Z调控轴是维持双价染色质与poised基因表达（poised gene expression）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。实验设计概述：探究INO80敲除对小鼠初始态与始发态多能干细胞的转录组（RNA测序，RNA-seq）与表观组（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。