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: 9255294
• 负责人: Kirsten C Sadler Edepli
• 金额: $ 47.78万
• 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 2018-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9255294
• 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; Fingers; Gene Expression; Gene Expression Profiling; Genes; Genomics; Global Change; Goals; Health; 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; Partial Hepatectomy; Patients; Pattern; Phenotype; Phosphorylation; Play; Process; Proliferating; Proteins; Reading; Recovery; Recruitment Activity; Regenerative response; Regulation; Regulator Genes; Repression; Role; Serine; Stimulus; Testing; Toxin; Transcriptional Activation; Transferase; Trauma; Ubiquitin; Virus Diseases; Work; Writing; Zebrafish; base; chromatin remodeling; cofactor; comparative; epigenetic regulation; epigenome; epigenomics; gene induction; genome-wide; improved; improved outcome; insight; liver cell proliferation; liver development; liver transplantation; methylome; mutant; regenerative; research study; 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）：UHRF1对发育和肝脏再生的表观遗传学调控肝脏再生能够从病毒感染、毒素、创伤、缺血和切除等损伤中恢复。在没有损伤的情况下，分化的肝细胞处于静止状态，但当肝脏肿块受损时，例如当肝脏的一部分被切除时，肝细胞“唤醒”并重新进入细胞周期。这伴随着数百个基因的转录激活，这些基因驱动增殖，一旦原始肝脏大小恢复，这些基因就会受到抑制。在胚胎的肝脏发育过程中也发生类似的过程，分化的肝细胞迅速增殖，产生成比例大小的肝脏。虽然肝脏的发育和再生发生在非常不同的刺激下，但它们有重要的相似之处。也就是说，这两个过程的特点是诱导数百个基因同时抑制其他基因，并且需要泛素，如含有PHD和RING Finger domains- 1 （Uhrf1）。Uhrf1通过招募组蛋白修饰酶和DNA甲基转移酶（DNMT1）来“读取”修改后的组蛋白代码并“写入”该代码。这些复杂的功能被认为介导控制基因表达的动态和多层抑制表观遗传标记，并且新出现的证据指出表观遗传修饰在细胞分裂过程中调节染色质动力学中的重要作用。我们假设Uhrf1在肝脏再生和发育过程中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，结合甲基化DNA和Uhrf1的全基因组占用，来确定小鼠肝脏再生和斑马鱼肝脏生长的表观遗传控制机制。在Aim 1中，我们将进行一些肝脏再生的第一批表观遗传学研究，使用我们用肝细胞特异性敲除Uhrf1进行工程小鼠。目的2将确定Uhrf1在斑马鱼肝脏生长过程中如何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鉴定由Uhrf1介导的保守和不同的表观遗传修饰模式。Aim 3的工作是基于我们发现Uhrf1上一个保守丝氨酸的磷酸化对其功能至关重要。我们将阐明磷酸化如何调节Uhrf1基因组占用及其与结合伙伴的相互作用。通过精确定义再生或发育过程中Uhrf1缺失肝细胞的细胞周期缺陷、甲基组和转录组的变化，我们将得出表观遗传调节剂、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脏疾病的潜在治疗，并将深入了解胚胎器官特异性发育过程中表观基因组的模式。