Epigenetic Regulation of Development and Liver Regeneration by UHRF1

描述(由申请人提供)：通过uhrf1肝再生对发育和肝再生的表观遗传学调节，使因病毒感染、毒素、创伤、缺血和切除而造成的损伤得以恢复。在没有损伤的情况下，分化的肝细胞是静止的，但当肝脏质量受损时，比如切除一部分肝脏，肝细胞就会苏醒并重新进入细胞周期。伴随而来的是数百个驱动增殖的基因的转录激活，一旦恢复原来的肝脏大小，这些基因就会被抑制。在胚胎的肝脏发育过程中也会发生类似的过程，分化的肝细胞迅速增殖，产生大小相称的肝脏。虽然肝脏的发育和再生对不同的刺激有不同的反应，但它们有重要的相似之处。也就是说，这两个过程的特征都是数百个基因的诱导和其他基因的同时抑制，这需要像泛素一样含有PHD和环指结构域-1(Uhrf1)。Uhrf1通过招募组蛋白修饰酶和DNA甲基转移酶(DNMT1)来“读取”修改后的组蛋白密码，并“写入”该密码。这些复杂的功能被认为介导了控制基因表达的动态和多层抑制性表观遗传标记，新的证据表明，表观遗传修饰在调节细胞分裂过程中的染色质动态方面发挥了重要作用。我们推测，在肝脏再生和发育过程中，uhrf1通过通过甲基组介导的直接和间接作用调节细胞周期进程。我们将利用基因表达的生化、遗传和生物信息学分析，结合基因组中甲基化DNA和uhrf1的占据，来确定表观遗传控制小鼠肝脏再生和斑马鱼肝脏生长的机制。在目标1中，我们将利用我们设计的肝细胞特异性敲除uhrf1的小鼠进行一些肝脏再生的首批表观遗传学研究。目的2将确定uhrf1如何在斑马鱼的肝脏生长过程中调节相同的表观遗传修饰。然后，我们将率先使用比较表观基因组学来确定uhrf1介导的表观遗传修饰的保守和差异模式。目标3的工作是基于我们的发现，即uhrf1上保守的丝氨酸的磷酸化是其功能所必需的。我们将阐明磷酸化如何调节uhrf1基因组的占位及其与结合伙伴的相互作用。通过精确定义uhrf1耗竭的肝细胞在再生或发育过程中的细胞周期缺陷、甲基组和转录组的变化，我们将建立表观遗传调节因子、基因表达变化和细胞增殖之间的因果关系。这与两个重要的领域直接相关：我们将通过阐明一种我们可以操纵再生的机制来推进肝脏疾病的潜在治疗，并将提供关于表观基因组在胚胎特定器官发育过程中是如何形成模式的洞察力。

DESCRIPTION (provided by applicant): Epigenetic regulation of development and liver regeneration by UHRF1 Liver regeneration enables recovery from injury due to viral infection, toxins, trauma, ischemia and resection. In the absence of injury, differentiated hepatocytes are quiescent, but when liver mass is compromised such as occurs when a portion of the liver is removed, hepatocytes "awaken" and re-enter the cell cycle. This is accompanied by the transcriptional activation of hundreds of genes that drive proliferation and these same genes are repressed once the original liver size is recovered. A similar process occurs during liver development in embryos, where differentiated hepatocytes rapidly proliferate to generate a liver of proportional size. Although liver development and regeneration occur in response to very different stimuli, they share important similarities. Namely, both processes are characterized by induction of hundreds of genes and simultaneous repression of others, and which require Ubiquitin like containing PHD and RING Finger domains- 1 (Uhrf1). Uhrf1 both "reads" the modified histone code and "writes" this code by recruiting histone modifying enzymes and DNA methyl transferase (DNMT1). These complex functions are thought to mediate dynamic and multi-layered repressive epigenetic marks that control gene expression and, emerging evidence points to an important role for epigenetic modifications in regulating chromatin dynamics during cell division. We hypothesize that Uhrf1 regulates cell cycle progression via both direct and indirect effects mediated through the methylome during liver regeneration and development. We will use biochemical, genetic and bioinformatic analysis of gene expression combined with genome wide occupancy of methylated DNA and Uhrf1 to identify the mechanism underlying epigenetic control of liver regeneration in mice and hepatic outgrowth in zebra fish. In Aim 1, we will undertake some of the first epigenetic studies in liver regeneration using mice we engineered with hepatocyte-specific knock out of Uhrf1. Aim 2 will determine how Uhrf1 regulates the same epigenetic modifications during hepatic outgrowth in zebra fish. We will then pioneer the use of comparative epigenomics to identify conserved and divergent patterns of epigenetic modifications mediated by Uhrf1. Work in Aim 3 is based on our discovery that phosphorylation of a conserved serine on Uhrf1 is essential for its function. We will elucidate how phosphorylation regulates Uhrf1 genomic occupancy and its interaction with binding partners. By precisely defining the cell cycle defects, changes in the methylome and transcriptome in Uhrf1 depleted hepatocytes undergoing regeneration or development, we will generate causative relationships between an epigenetic regulator, gene expression changes and cell proliferation. This has direct relevance to two important fields: we will advance potentia therapies for liver disease by elucidating a mechanism by which we may manipulate regeneration and will provide insight into how the epigenome is patterned during organ specific development in embryos.