Epigenetic Regulation of Development and Liver Regeneration by UHRF1

UHRF1 对发育和肝脏再生的表观遗传调控

• 批准号: 9293301
• 负责人: Kirsten C Sadler Edepli
• 金额: $ 47.87万
• 依托单位: NEW YORK UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-09 至 2019-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9293301
• 关键词: Affect; Automobile Driving; Binding; Binding Proteins; Biochemical; Biochemical Genetics; Bioinformatics; Biological; Cell Cycle; Cell Cycle Progression; Cell Differentiation process; Cell Proliferation; Cell division; Cells; Chromatin; Chromatin Structure; Code; Complex; DNA; DNA Methylation; DNA Modification Methylases; DNA Modification Process; Data; Data Set; Defect; Development; Embryo; Engineering; Enzymes; Epigenetic Process; Event; Excision; Gene Expression; Gene Expression Profiling; Genes; Genetic Transcription; Genomics; Global Change; Goals; Hepatic; Hepatic Mass; Hepatocyte; Histone Code; Histones; Human; Injury; Ischemia; Knock-out; Liver; Liver Failure; Liver Regeneration; Liver diseases; Mediating; Modeling; Modification; Mus; Natural regeneration; Organ; PHD Finger; Partial Hepatectomy; Patients; Pattern; Phenotype; Phosphorylation; Play; Post-Translational Protein Processing; Process; Proliferating; Proteins; Recovery; Recruitment Activity; Regenerative response; Regulation; Regulator Genes; Repression; Ring Finger Domain; Role; Serine; Stimulus; Testing; Toxin; Transcriptional Activation; Transferase; Trauma; Ubiquitin; Virus Diseases; Work; Writing; Zebrafish; base; chromatin remodeling; cofactor; comparative; epigenetic regulation; epigenome; epigenomics; experimental study; gene induction; genome-wide; improved; improved outcome; insight; liver cell proliferation; liver development; liver transplantation; methylome; mutant; public health relevance; regenerative; response; transcriptome

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.

描述（由申请人提供）：UHRF 1对发育和肝再生的表观遗传调节肝再生能够从病毒感染、毒素、创伤、缺血和切除造成的损伤中恢复。在没有损伤的情况下，分化的肝细胞是静止的，但是当肝脏质量受到损害时，例如当肝脏的一部分被去除时发生，肝细胞“唤醒”并重新进入细胞周期。这伴随着数百个驱动增殖的基因的转录激活，一旦原始肝脏大小恢复，这些相同的基因就会受到抑制。在胚胎的肝脏发育过程中也发生了类似的过程，其中分化的肝细胞迅速增殖以产生成比例大小的肝脏。尽管肝脏发育和再生是针对非常不同的刺激而发生的，但它们有着重要的相似之处。也就是说，这两个过程的特征在于诱导数百个基因并同时抑制其他基因，并且这需要含有PHD和RING Finger结构域-1（Uhrf 1）的泛素样。Uhrf 1既“读取”修饰的组蛋白密码，又通过招募组蛋白修饰酶和DNA甲基转移酶（DNMT 1）来“写入”该密码。这些复杂的功能被认为是介导动态和多层抑制性表观遗传标记，控制基因表达，新出现的证据表明，表观遗传修饰在细胞分裂过程中调节染色质动力学中起着重要作用。我们推测Uhrf 1在肝再生和发育过程中通过甲基化组介导的直接和间接作用调节细胞周期进程。我们将使用基因表达的生化，遗传和生物信息学分析，结合甲基化DNA和Uhrf 1的全基因组占有率，以确定小鼠肝再生和斑马鱼肝生长的表观遗传控制机制。在目标1中，我们将进行一些肝再生的初步表观遗传学研究，使用我们设计的肝细胞特异性敲除Uhrf 1的小鼠。目的2将确定Uhrf 1如何在斑马鱼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，以确定Uhrf 1介导的表观遗传修饰的保守和不同的模式。目标3中的工作是基于我们的发现，即Uhrf 1上保守丝氨酸的磷酸化对其功能至关重要。我们将阐明如何磷酸化调节Uhrf 1基因组占用和它与结合伙伴的相互作用。通过精确定义细胞周期缺陷，在Uhrf 1耗竭肝细胞进行再生或发展的甲基化组和转录组的变化，我们将产生一个表观遗传调节，基因表达变化和细胞增殖之间的因果关系。这与两个重要领域直接相关：我们将通过阐明我们可以操纵再生的机制来推进肝病的潜在疗法，并将深入了解胚胎器官特异性发育期间表观基因组如何形成模式。