Interrogating genome folding trajectories in health and disease

探究健康和疾病中的基因组折叠轨迹

• 批准号: 10685554
• 负责人: Stavros Lomvardas
• 金额: $ 62.27万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-30 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10685554
• 关键词: 3-Dimensional; Affect; Alleles; Alzheimer disease screening; Alzheimer' s Disease; Alzheimer' s disease model; Alzheimer' s disease patient; Alzheimer' s disease therapeutic; Anosmia; Architecture; Astronomy; Bar Codes; Biological Assay; Cells; Chemicals; Chromatin; Chromosomes; Complement; Complex; DNA; Detection; Development; Developmental Process; Disease; Down-Regulation; Enhancers; Environment; Environmental Risk Factor; Epigenetic Process; Essential Genes; Etiology; Exhibits; Future; Gene Activation; Gene Expression; Gene Expression Regulation; Gene Silencing; Generations; Genes; Genetic; Genetic Enhancer Element; Genetic Transcription; Genome; Genomics; Health; Heterochromatin; Human; Human body; Individual; Label; Link; Maps; Molecular; Mus; Natural regeneration; Nerve Degeneration; Neuronal Differentiation; Neurons; Nose; Nuclear; Odors; Olfactory Epithelium; Olfactory Pathways; Olfactory dysfunction; Organism; Output; Pharmacologic Substance; Prognosis; Property; Receptor Gene; Research; Resolution; Role; Route; Specificity; Stereotyping; Symptoms; System; Technology; Transcriptional Activation; Transcriptional Regulation; Variant; Viral; Volatilization; cell type; diagnostic tool; experimental study; genetic manipulation; humanized mouse; hyposmia; in vivo; insight; interdisciplinary approach; molecular imaging; mouse model; mutant; nerve stem cell; neurotoxicity; novel; olfactory receptor; olfactory sensory neurons; prognostic tool; receptor expression; segregation; single molecule; superresolution imaging; tool

Project Summary Detection and identification of the astronomical number of volatile chemicals that we perceive as odors depends upon the monogenic and monoallelic expression of olfactory receptor (OR) genes in olfactory sensory neurons (OSNs). An intricate network of OSN-specific interchromosomal interactions coordinates the transcriptional activation of only 1 OR allele out of >2000 OR alleles distributed across 18 different chromosomes. Genomic interactions between silent OR genes assemble heterochromatic multi-chromosomal compartments that keep OR genes transcriptionally inactive, whereas genomic interactions between intergenic OR enhancers result in a multi-chromosomal enhancer hub that activates singular OR transcription. Here, we propose to combine Dip-C, a variation of single cell HiC, with viral-based cell tagging technologies, towards the identification of genome folding intermediates across OSN differentiation lineages. This “cradle to crate” genomic analysis will follow individual OSN progenitors and their barcoded progeny, allowing a complete cartography of genomic interactions made by every OR allele en route to transcriptional activation. Single molecule DNA FISH experiments will complement the proposed genomic studies, providing high resolution insight to the genomic choreography that orchestrates singular OR gene choice during development. Finally, we seek to explore how the trajectories of OSN genomic folding become altered and eventually disrupted in a humanized model for Alzheimer’s disease (AD). Olfactory dysfunction, hyposmia, and anosmia constitute well- established prodromal symptoms of AD, but the molecular etiology of this intriguing connection is not known. Using a humanized model for AD we discovered that interchromosomal OR compartments dissipate prior to the onset of neurodegeneration, resulting in strong downregulation of OR transcription. Thus, we propose to apply our single cell interrogation of genome folding transition in the context of AD and to establish the baseline of nuclear architecture in human OSNs. Deciphering how OR compartments assemble in health, and how they become disrupted in disease, may provide the basis for novel prognostic and diagnostic tools for AD, and molecular assays for in vivo screening of AD therapeutics.

项目概要 检测和识别我们认为是气味的大量挥发性化学物质 取决于嗅觉感觉中嗅觉受体（OR）基因的单基因和单等位基因表达 神经元（OSN）。 OSN 特异性染色体间相互作用的复杂网络协调 分布在 18 个不同区域的 >2000 个 OR 等位基因中仅 1 个 OR 等位基因的转录激活 染色体。沉默OR基因之间的基因组相互作用组装异染色质多染色体 保持 OR 基因转录失活的区室，而基因间的基因组相互作用 OR 增强子产生激活单一 OR 转录的多染色体增强子中心。在这里，我们 建议将 Dip-C（单细胞 HiC 的一种变体）与基于病毒的细胞标记技术相结合，以实现 跨 OSN 分化谱系的基因组折叠中间体的鉴定。这个“从摇篮到板条箱” 基因组分析将跟踪单个 OSN 祖细胞及其条形码后代，从而实现完整的分析 每个 OR 等位基因在转录激活过程中产生的基因组相互作用的制图。单身的 分子 DNA FISH 实验将补充拟议的基因组研究，提供高分辨率 深入了解在发育过程中协调单一 OR 基因选择的基因组编排。最后， 我们试图探索 OSN 基因组折叠的轨迹是如何改变并最终被破坏的 阿尔茨海默病（AD）的人源化模型。嗅觉功能障碍、嗅觉减退和嗅觉丧失是很常见的 确定了 AD 的前驱症状，但这种有趣联系的分子病因尚不清楚。 使用 AD 人源化模型，我们发现染色体间 OR 区室在 神经变性的发生，导致 OR 转录的强烈下调。因此，我们建议 在 AD 背景下应用我们对基因组折叠转变的单细胞询问并建立 人类 OSN 核架构的基线。破译手术室隔间如何在健康中组装，以及 它们如何在疾病中被破坏，可能为 AD 的新型预后和诊断工具提供基础， 以及用于 AD 疗法体内筛选的分子测定。