Genome-wide epigenetic control of circadian metabolism by heme receptor Rev-erb

血红素受体 Rev-erb 对昼夜节律代谢的全基因组表观遗传控制

• 批准号: 7934606
• 负责人: MITCHELL A. LAZAR
• 金额: $ 50万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-19 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7934606
• 关键词: Address; Adipocytes; Adipose tissue; Affect; Antibodies; Area; Binding; Biology; Candidate Disease Gene; Circadian Rhythms; Cues; DNA; Data; Data Set; Diabetes Mellitus; Eating; Epidemic; Epigenetic Process; Fasting; Fatty acid glycerol esters; Gene Targeting; Genes; Genetic Transcription; Genome; Genomics; Goals; Laboratories; Leptin; Link; Liver; Liver Extract; Location; Mediating; Metabolic; Metabolic Control; Metabolic Diseases; Metabolism; Molecular; Mus; Nuclear Receptors; Obesity; Pathway interactions; Pattern; Physiological Processes; Physiology; Plasminogen Activator Inhibitor 1; Proteins; Regimen; Regulation; Role; Signal Transduction; Sleep; Testing; Time; Tissues; United States; adipokines; base; chromatin immunoprecipitation; feeding; genome wide association study; genome-wide; genome-wide analysis; glucose metabolism; heme receptor; in vivo; insight; mRNA Expression; mouse genome; promoter; public health relevance; research study; resistin; shift work

DESCRIPTION (provided by applicant): This application addresses the broad Challenge Area (08) Genomics and specific Challenge Topic 08-DK-107: Nuclear Receptor mediated assembly of functional transcriptional units. A major goal of this laboratory is to understand the transcriptional mechanisms by which nuclear receptors (NRs) regulate circadian and metabolic physiology. The heme receptor Rev-erb was identified by the PI in 1989, and has since emerged as an important repressor of key genes controlling circadian rhythm and glucose metabolism. Prior studies of Rev- erb have been based on candidate gene approaches focused on promoters. Thus, it is not surprising that only about ten Rev-erb-target genes are known, given that genome-wide location analyses for other nuclear receptors have revealed that most binding occurs outside of promoters. We hypothesize that Rev-erb functions through binding of hundreds of genes, many tissue-specifically. To address this, we will perform a genome-wide analysis of Rev-erb binding in mouse liver and white adipose tissues. Specific Aim 1 is to identify Rev-erb gene targets on a genome-wide scale in liver at different circadian times, and understand their modes of regulation. We hypothesize that circadian fluctuation of Rev-erb protein level will affect its ability to access recognition sequences in the genome, which, in turn, will have downstream effects on circadian and metabolic processes. We will test this by genome-wide location analysis using chromatin immunoprecipitation (ChIP) followed by sequencing of the isolated DNA (ChIP-seq). Specific Aim 2 is to identify Rev-erb gene targets on a genome-wide scale in liver from fed versus fasted mice and from mice under restricted feeding, and understand their modes of regulation. We hypothesize that metabolic regulation of Rev-erb activity will alter Rev-erb binding at many genes, and will test this by ChIP- seq using liver isolated from fed and fasted mice. Preliminary data reveal that Rev-erb protein level is higher in liver from fasted mice than in liver from fed mice, suggesting that Rev-erb binding activity may be modulated by metabolic signals. Specific Aim 3 is to identify Rev-erb gene targets on a genome-wide scale in white adipose tissue, and understand their modes of regulation. We hypothesize that Rev-erb mediates circadian expression of adipocyte genes and will test this by performing ChIP-seq for adipose Rev- erb at different circadian times and feeding regimens. This will expand our understanding of Rev-erb function in adipose biology and, when combined with the liver data set, it will identify tissue-specific targets and functions for Rev-erb in liver and adipose tissues. These studies can be accomplished in a two-year time frame because we have validated antibodies for ChIP of endogenous Rev-erb in metabolic tissues, and the experimental paradigms involve short-term studies. The genome-wide insights into in vivo tissue-specific regulation of circadian and metabolic genes will be enormous, and contribute greatly to our understanding of how these physiological processes are interrelated, and potentially dysregulated in obesity and diabetes, which are epidemic in the United States. PUBLIC HEALTH RELEVANCE: Metabolic disorders such as diabetes and obesity are affected by sleep patterns and shift work. Thus, it is exciting that the focus of this proposal, the nuclear receptor Rev-erb, has emerged as a critical link between circadian and metabolic physiology. The proposed experiments aim to determine the extent that Rev-erb contributes to, or even controls, circadian and metabolic processes and the crosstalk that occurs between them. Ultimately, greater insight into the regulation of circadian rhythm and metabolism by Rev-erb will contribute greatly to our understanding of how these physiological processes are interrelated, and potentially dysregulated in obesity and diabetes, which are epidemic in the United States.

描述（由申请人提供）：本申请涉及广泛的挑战领域（08）基因组学和特定的挑战主题08-DK-107：核受体介导的功能转录单元的组装。该实验室的一个主要目标是了解核受体（NR）调节昼夜节律和代谢生理学的转录机制。血红素受体 Rev-erb 于 1989 年被 PI 发现，从此成为控制昼夜节律和葡萄糖代谢的关键基因的重要抑制因子。之前对 Reverb 的研究都是基于关注启动子的候选基因方法。因此，鉴于对其他核受体的全基因组定位分析表明大多数结合发生在启动子之外，因此仅知道大约十个 Rev-erb 靶基因也就不足为奇了。我们假设 Rev-erb 通过结合数百个基因（其中许多是组织特异性的）来发挥作用。为了解决这个问题，我们将对小鼠肝脏和白色脂肪组织中的 Rev-erb 结合进行全基因组分析。具体目标 1 是在不同昼夜节律时间在肝脏全基因组范围内识别 Rev-erb 基因靶标，并了解其调节模式。我们假设 Rev-erb 蛋白水平的昼夜波动将影响其访问基因组中识别序列的能力，进而对昼夜节律和代谢过程产生下游影响。我们将使用染色质免疫沉淀 (ChIP) 进行全基因组定位分析，然后对分离的 DNA 进行测序 (ChIP-seq) 来测试这一点。具体目标 2 是在进食与禁食小鼠以及​​限制进食小鼠的肝脏中在全基因组范围内鉴定 Rev-erb 基因靶标，并了解其调节模式。我们假设 Rev-erb 活性的代谢调节将改变 Rev-erb 在许多基因上的结合，并将使用从进食和禁食小鼠中分离的肝脏通过 ChIP-seq 进行测试。初步数据显示，禁食小鼠肝脏中的 Rev-erb 蛋白水平高于进食小鼠肝脏中的水平，这表明 Rev-erb 结合活性可能受到代谢信号的调节。具体目标 3 是在白色脂肪组织的全基因组范围内识别 Rev-erb 基因靶标，并了解其调节模式。我们假设 Rev-erb 介导脂肪细胞基因的昼夜节律表达，并将通过在不同昼夜节律时间和喂养方案对脂肪 Reverb 进行 ChIP-seq 来测试这一点。这将扩大我们对脂肪生物学中 Rev-erb 功能的理解，并且当与肝脏数据集结合时，它将确定 Rev-erb 在肝脏和脂肪组织中的组织特异性靶点和功能。这些研究可以在两年的时间内完成，因为我们已经验证了代谢组织中内源性 Rev-erb 的 ChIP 抗体，并且实验范式涉及短期研究。对昼夜节律和代谢基因的体内组织特异性调节的全基因组见解将是巨大的，并且极大地有助于我们理解这些生理过程如何相互关联，以及在美国流行的肥胖和糖尿病中潜在的失调。 。 公众健康相关性：糖尿病和肥胖等代谢性疾病受到睡眠模式和轮班工作的影响。因此，令人兴奋的是，该提案的焦点核受体 Rev-erb 已成为昼夜节律和代谢生理学之间的关键联系。拟议的实验旨在确定 Rev-erb 对昼夜节律和代谢过程以及它们之间发生的串扰的贡献甚至控制程度。最终，更深入地了解 Rev-erb 对昼夜节律和新陈代谢的调节将极大地有助于我们了解这些生理过程如何相互关联，以及在美国流行的肥胖和糖尿病中潜在的失调。