Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a [RNA-Seq]

Embryonic stem cells (ESCs) maintain pluripotency through unique epigenetic states. When ESCs commit to a specific cell lineage, changes in histone modifications and DNA methylation accompany the transition to more specialized cell types. Investigating how epigenetic regulation maintains pluripotency is a critical component in order to generate the required cell types for future clinical application. Uhrf1 is a widely known hemi-methylated DNA binding protein, playing a role in heterochromatin formation alongside G9a, Trim28 and HDACs. In addition, it has been demonstrated that Uhrf1 functions to maintain DNA methylation through the recruitment of Dnmt1. Although Uhrf1 is not essential in ESC self-renewal, it still remains elusive how Uhrf1 regulates pluripotency. Here, we set out to elucidate the role of Uhrf1 in pluripotent stem cells. We found that Uhrf1 forms a complex with the active trithorax group of transcriptional regulators, in particular the Setd1a/COMPASS complex. Our data show that loss of Uhrf1 causes a dramatic reduction of bivalent histone marks, in particular those associated with neuroectoderm and mesoderm specification. Overall, our data demonstrate that Uhrf1 safeguards the balance between pluripotency and differentiation via the Setd1a/COMPASSS complex, through which Uhrf1 mediates bivalent histone modifications. mRNA profiles of WT and Uhrf1 KO mESCs and EBs

胚胎干细胞（Embryonic stem cells, ESCs）凭借独特的表观遗传状态维持多能性。当ESCs定向分化为特定细胞谱系时，组蛋白修饰与DNA甲基化的改变会伴随其向更特化细胞类型的转归。探究表观遗传调控如何维持多能性，是未来获取临床应用所需细胞类型的核心环节。

Uhrf1是一类广为人知的半甲基化DNA结合蛋白，可与G9a、Trim28及组蛋白去乙酰化酶（HDACs, Histone Deacetylases）协同参与异染色质形成。此外，已有研究证实Uhrf1可通过招募DNA甲基转移酶1（Dnmt1, DNA methyltransferase 1）维持DNA甲基化稳态。尽管Uhrf1并非ESCs自我更新的必需因子，但其调控多能性的具体机制仍有待阐明。

本研究旨在解析Uhrf1在多能干细胞中的功能。我们发现，Uhrf1可与活性三胸家族（trithorax group）转录调控因子形成复合物，其中尤以Setd1a/COMPASS复合物为核心。实验数据显示，敲除Uhrf1会导致二价组蛋白标记显著下调，尤其是与神经外胚层和中胚层谱系特化相关的二价组蛋白标记。

综上，本研究数据表明，Uhrf1可通过Setd1a/COMPASS复合物维系多能性与分化间的动态平衡，并借此介导二价组蛋白修饰。本数据集涵盖野生型（WT）与Uhrf1敲除（KO）小鼠胚胎干细胞（mESCs）及拟胚体（EBs, Embryoid Bodies）的mRNA转录组谱。