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: 10266185
• 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/10266185
• 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; Bar Codes; Biological Assay; Cells; Chemicals; Chromatin; Chromosomes; Complement; Complex; DNA; Detection; Development; Developmental Process; Diagnostic; 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; Image; Individual; Label; Link; Maps; Molecular; Mus; Natural regeneration; Nerve Degeneration; Neurons; Nose; Nuclear; Odors; Olfactory Epithelium; Olfactory Pathways; Olfactory dysfunction; Organism; Output; Pharmacologic Substance; Prognosis; Property; Receptor Gene; Research; Resolution; Role; Route; Specificity; Structure; Symptoms; System; Technology; Transcriptional Activation; Transcriptional Regulation; Variant; Viral; base; cell type; 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; receptor expression; segregation; single molecule; 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.

项目摘要 检测和识别天文数字的挥发性化学物质，我们认为是气味 依赖于嗅觉感受器（OR）基因的单基因和单等位基因表达， 神经元（OSNs）。一个复杂的OSN特异性染色体间相互作用网络协调了 >2000个OR等位基因中只有1个OR等位基因的转录激活分布在18个不同的 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基因转录不活跃的区室，而基因间的基因组相互作用 OR增强子导致激活单一OR转录的多染色体增强子中心。这里我们 我建议将联合收割机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， 鉴定跨OSN分化谱系的基因组折叠中间体。这种“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，从而允许完整的 每个OR等位基因在转录激活过程中的基因组相互作用的制图。单个 分子DNA FISH实验将补充拟议的基因组研究，提供高分辨率 深入了解基因组编排，编排单一或基因的选择在发展过程中。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在一个过程中被破坏的。 阿尔茨海默病（AD）的人源化模型。嗅觉障碍，嗅觉减退，嗅觉丧失- AD的前驱症状，但这种有趣的联系的分子病因学尚不清楚。 使用AD的人源化模型，我们发现染色体间OR区室在AD发生之前消失。 神经变性的发作，导致OR转录的强烈下调。因此，我们建议 应用我们对AD背景下基因组折叠转变的单细胞询问， 人类OSN核结构的基线。解读OR隔室如何在健康状态下组装， 它们在疾病中是如何被破坏的，可能为AD的新的预后和诊断工具提供基础， 以及用于体内筛选AD治疗剂的分子测定。