Enhancer RNA Regulation of Experience-dependent Neuroepigenetic Processes

经验依赖性神经表观遗传过程的增强子 RNA 调节

• 批准号: 10378114
• 负责人: JEREMY J DAY
• 金额: $ 38.23万
• 依托单位: UNIVERSITY OF ALABAMA AT BIRMINGHAM
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10378114
• 关键词: Adaptive Behaviors; Adult; Behavior; Behavioral; Binding; Biological Assay; Biological Models; Biology; Brain; Brain Diseases; CRISPR/Cas technology; Cells; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Cognition Disorders; DNA; DNA Methylation; DNA Sequence; Development; Disease; Distal Enhancer Elements; Electrophoretic Mobility Shift Assay; Enhancers; Ensure; Epigenetic Process; Future; Gene Activation; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Generations; Genes; Genetic Enhancer Element; Genetic Transcription; Genomics; High-Throughput Nucleotide Sequencing; Hippocampus (Brain); Histone Acetylation; Histones; Immediate-Early Genes; Immunoprecipitation; Individual; Investigation; Learning; Link; Lysine; Maps; Memory; Mental Health; Mental disorders; Mitotic; Modeling; Modification; Molecular; Nature; Neuronal Plasticity; Neurons; Parents; Pattern; Phenotype; Physiology; Play; Process; RNA; RNA delivery; RNA-Protein Interaction; Regulation; Regulator Genes; Regulatory Element; Rodent; Role; Signal Transduction; Specificity; Synaptic plasticity; System; Testing; Therapeutic; Tissue-Specific Gene Expression; Transcript; Untranslated RNA; Variant; base; behavioral plasticity; brain health; cognitive process; complex biological systems; conditioned fear; crosslink; experience; experimental study; falls; gene induction; genome sequencing; genome-wide; insight; knock-down; mammalian genome; neuron development; neuropsychiatric disorder; novel; novel strategies; novel therapeutics; programs; promoter; response; screening; single molecule; therapeutic candidate; therapeutically effective; tool; transcription factor; whole genome

Distal enhancer elements in DNA enable higher-order chromatin interactions that facilitate gene expression programs and thus contribute to cellular phenotype and function. Enhancers regulate numerous aspects of cell and tissue-specific gene expression patterns in the developing and adult brain, and have been highly implicated in mental health and disease. In neuronal systems, enhancer elements are subject to widespread, bidirectional transcription that yields non-coding enhancer RNA (eRNA). However, the precise function of eRNAs is still unclear, with different models proposing unique regulatory functions. Emerging evidence suggests that eRNAs function to modify epigenetic states at gene regulatory elements, which are critical for long-term behavioral and neuronal plasticity. Specific Aim 1 of this proposal seeks to utilize whole-genome sequencing approaches to define transcriptional and epigenetic signatures of neuronal activity at enhancers. In addition to revealing new therapeutic candidates, this aim will employ novel targeted eRNA delivery strategies based on CRISPR technology to allow manipulation of eRNAs at specific enhancers to determine their function. Specific Aim 2 will examine interactions between eRNAs and epigenetic profiles at enhancers and promoters of linked genes, which will establish the hierarchical relationships between molecular interactions at enhancers. Specific Aim 3 will examine the contributions of eRNAs to neuronal function and memory formation in the adult brain using hippocampus-dependent contextual fear conditioning, a robust assay of learning and memory that requires activity-dependent gene transcription. This novel approach will demonstrate the necessity of unique eRNAs at specific genes for neuronal activity and behavior, and also enable the first investigation of whether modulation of eRNAs is sufficient to alter memory function. In addition to revealing the exact nature and scope of eRNAs in neuronal gene regulation, this proposal will pave the way for future experiments that will explore how manipulation of enhancers could be used to reprogram circuits that have become maladaptive in mental illness and cognitive disease states.

DNA中的远端增强子元件使促进基因表达的高阶染色质相互作用成为可能 程序，从而有助于细胞表型和功能。增强子调节细胞的许多方面， 和组织特异性基因表达模式在发育和成人大脑，并已高度 与心理健康和疾病有关在神经系统中，增强子元件受到广泛的， 产生非编码增强子RNA（eRNA）的双向转录。然而， eRNA仍不清楚，不同的模型提出了独特的调控功能。新出现的证据 表明eRNA的功能是在基因调控元件上修饰表观遗传状态，这对于 长期的行为和神经可塑性。该提案的具体目标1旨在利用全基因组 测序方法来定义增强子处神经元活性的转录和表观遗传特征。在 除了揭示新的治疗候选药物外，该目标还将采用新的靶向eRNA递送策略 基于CRISPR技术，允许在特定增强子处操纵eRNA，以确定其 功能具体目标2将检查eRNA和增强子处的表观遗传特征之间的相互作用， 连锁基因的启动子，这将建立分子相互作用之间的层次关系， 增强剂。具体目标3将研究eRNA对神经元功能和记忆形成的贡献 在成年人的大脑中使用依赖于校园的背景恐惧条件反射，一个强大的学习和 记忆需要依赖活性的基因转录。这种新方法将证明 神经元活动和行为的特定基因的独特eRNA的必要性，也使第一个 研究eRNA的调节是否足以改变记忆功能。除了揭示 eRNAs在神经元基因调控中的确切性质和范围，这一提议将为未来的研究铺平道路。 实验将探索如何操纵增强子可以用来重新编程电路， 在精神疾病和认知疾病状态下变得不适应。

项目成果

Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine.

D1 中型多棘神经元的不同亚群对可卡因表现出独特的转录反应。

• DOI: 10.1101/2023.01.12.523845
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Phillips3rd,RobertA;Tuscher,JenniferJ;Fitzgerald,NDalton;Wan,Ethan;Zipperly,MorganE;Duke,CoreyG;Ianov,Lara;Day,JeremyJ
• 通讯作者: Day,JeremyJ

Morphine, the microbiome, and fatty acids: short chains make a big link in opioid reward.

吗啡、微生物组和脂肪酸：短链在阿片类药物奖励中发挥着重要作用。

• DOI: 10.1038/s41386-021-01093-4
• 发表时间: 2021
• 期刊: Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology
• 作者: Tuscher,JenniferJ;Day,JeremyJ
• 通讯作者: Day,JeremyJ

Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems.

• DOI: 10.1093/nar/gkaa671
• 发表时间: 2020-09-25
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Carullo NVN;Phillips Iii RA;Simon RC;Soto SAR;Hinds JE;Salisbury AJ;Revanna JS;Bunner KD;Ianov L;Sultan FA;Savell KE;Gersbach CA;Day JJ
• 通讯作者: Day JJ

Delivering progranulin to neuronal lysosomes protects against excitotoxicity.

• DOI: 10.1016/j.jbc.2021.100993
• 发表时间: 2021-09
• 期刊: The Journal of biological chemistry
• 作者: Davis SE;Roth JR;Aljabi Q;Hakim AR;Savell KE;Day JJ;Arrant AE
• 通讯作者: Arrant AE