Femto-seq: Targeted photo-biotinylation, pulldown and sequencing of locus and region-specific DNA from femtoliter volumes within individual cells

Femto-seq：从单个细胞内的飞升体积中对位点和区域特异性 DNA 进行靶向光生物素化、下拉和测序

• 批准号: 10587721
• 负责人: WARREN R ZIPFEL
• 金额: $ 42.13万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-02-01 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10587721
• 关键词: 3-Dimensional; Architecture; Biological; Biological Assay; Biotin; Biotinylation; Cell Line; Cell Nucleus; Cells; Cellular Stress; Chromatin; Collection; Computer software; Computers and Advanced Instrumentation; Consumption; Custom; Cytosol; DNA; DNA Sequence; DNA sequencing; Data; Dedications; Detection; Disease; Disease susceptibility; Enhancers; Ensure; Environment; Environmental Risk Factor; Eukaryota; Experimental Designs; Fluorescent in Situ Hybridization; Gene Expression; Gene Expression Regulation; Gene Silencing; Genes; Genetic Diseases; Genome; Genomic Segment; Genomics; Goals; Hand; Image; Image Analysis; In Situ; Individual; Knowledge; Label; Lasers; Libraries; Machine Learning; Manuals; Measures; Methods; Microfluidic Microchips; Microfluidics; Microscope; Microscopic; Microscopy; Molecular Conformation; Nuclear; Nuclear Structure; Optics; Physiologic pulse; Population; Population Analysis; Preparation; Procedures; Process; Protocols documentation; Regulation; Reporting; Research Personnel; Resolution; Role; Sampling; Scanning; Series; Shapes; Signal Transduction; Site; Stem Cell Research; Structure; Structure/Function Nuclei; System; Technology; Time; Transgenes; Treatment Protocols; Tube; Validation; cellular imaging; chromosome conformation capture; crosslink; design; design and construction; experimental study; flexibility; gene function; genome-wide; genomic locus; genomic tools; image processing; imaging modality; improved; insight; instrument; interest; multi-photon; new technology; novel; promoter; real-time images; response; sample fixation; software development; technology research and development; three dimensional structure; two-photon

Changes in the spatial organization of the genome are directly involved in gene regulation during differentiation, cellular stress responses and disease initiation. Existing approaches such as chromosome conformation capture (3C) methods and DNA fluorescent in situ hybridization (DNA-FISH) have provided information on the overall 3D structure of the nucleus at the chromatin level, providing critical insights into how our genomes are regulated. Nonetheless, new technologies are needed to uncover the finer details on the role of nuclear architecture, topological domains, and genomic interactions. Studies of gene regulation would benefit from a technology that fills the niche between the ensemble averaged 3C methods and the single cell, low throughput DNA-FISH approach. We have recently developed a novel optical technology we call “Femto-seq” that does just this – it allows users to obtain DNA sequence information from targeted femtoliter volumes within the nucleus of selected cells. Femto-seq provides a new way to examine genomic contacts near a specific gene locus or any nuclear region of interest (e.g. nuclear bodies). Using 3D localized two-photon excitation, we can photochemically biotinylate any region of the nucleus we can fluorescently label and identify in volumes which can be as small as a ½ of a femtoliter. The process is carried out on a population of cells using a combined two-photon/confocal microscope which images, locates fluorescently labeled regions of interest and then irradiates those regions using 700 nm femtosecond pulses to biotinylate the chromatin by photochemically cross-linking the DNA with a psoralen-biotin compound. Nuclei are isolated and the biotinylated DNA from the targeted region pulled down and sequenced. Because the cells are imaged to locate the regions of interest, they can also be screened for other parameters, allowing for the collection of targeted biotinylated DNA only from user selected cells within the cell population, providing single-cell like genomic information from a sub-set of cells within the population. We have proof-of-concept data from a cell line with a fluorescently labeled transgene we used as our targeted region, and show that we can obtain DNA highly enriched in transgene locus sequences. The goals of this Focused Technology Research and Development R01 project are to (Aim 1) design and construct a dual confocal/two- photon microscope capable of targeting and irradiating user selected regions-of-interest in a population of cells in a high-throughput automated fashion, (Aim 2) create a chromatin isolation pipeline based on novel microfluidic designs to efficiently purify and prepare the DNA for sequencing, and (Aim 3) demonstrate the improvement obtained from aims 1 and 2 in a series of Femto-seq experiments designed to produce quantitative metrics of improvement and to uncover new knowledge on how environmental signals may be relayed through the cytosol and into the nucleus. Femto-seq is a unique new way of investigating the spatial and regulatory relationships between DNA sequences and any microscopically visible region-of-interest in the nucleus.

基因组空间组织的变化直接参与分化过程中的基因调控， 细胞应激反应和疾病发生等现有方法。 (3C)方法和DNA荧光原位杂交(DNA-FISH)提供了整体3D信息 染色质水平的细胞核结构，为我们的基因组如何调控提供重要见解。 然而，需要新技术来揭示核结构作用的更详细的细节， 拓扑结构域和基因组相互作用的研究将受益于以下技术： 填补了整体平均 3C 方法和单细胞、低通量 DNA-FISH 之间的空白 我们最近开发了一种称为“Femto-seq”的新型光学技术，它就是这样做的。 允许用户从选定的细胞核内的目标飞升体积中获取 DNA 序列信息 Femto-seq 提供了一种检查特定基因位点或任何细胞核附近基因组接触的新方法。 使用 3D 局部双光子激发，我们可以进行光化学反应。 对细胞核的任何区域进行生物素化，我们可以以小至的体积进行荧光标记和识别 1/2 飞升的过程是使用组合的双光子/共焦对细胞群进行的。 显微镜定位感兴趣的荧光标记区域，然后照射这些区域 使用 700 nm 飞秒脉冲通过光化学交联 DNA 来生物素化染色质 分离补骨脂素-生物素化合物，并从目标区域提取生物素化 DNA。 由于对细胞进行成像来定位感兴趣的区域，因此也可以对它们进行筛选。 其他参数，允许仅从用户选择的细胞内收集目标生物素化 DNA 细胞群体，提供群体内细胞子集的单细胞样基因组信息。 拥有来自带有荧光标记转基因的细胞系的概念验证数据，我们将其用作目标区域， 并表明我们可以获得转基因基因座序列高度富集的 DNA。 技术研发R01项目是（目标1）设计和构建双共焦/双- 光子显微镜能够瞄准和照射用户在细胞群中选择的感兴趣区域 以高通量自动化方式，（目标 2）创建基于新型微流体的染色质分离管道 设计有效纯化和准备用于测序的 DNA，并且（目标 3）展示改进 在一系列 Femto-seq 实验中从目标 1 和 2 获得，旨在产生以下定量指标 改进并发现有关环境信号如何通过细胞质传递的新知识 Femto-seq 是一种研究空间和调控关系的独特新方法。 DNA 序列和细胞核中任何显微镜可见的感兴趣区域之间。