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

基因组空间组织的变化直接参与了分化过程中的基因调控， 细胞应激反应和疾病的启动。现有的方法，如染色体构象捕获 (3C)方法和DNA荧光原位杂交(DNA-FISH)提供了总体3D的信息 核染色质水平的结构，为我们的基因组如何调控提供了关键的见解。 尽管如此，需要新的技术来揭示关于核建筑作用的更详细的细节， 拓扑域和基因组相互作用。基因调控的研究将受益于一项技术 填补了整体平均3C方法和单细胞低通量DNA-FISH之间的利基 接近。我们最近开发了一种新的光学技术，我们称之为“Femto-seq”，它就是这样做的 允许用户从选定的细胞核内的目标毫微升体积中获取DNA序列信息 细胞。Femto-seq提供了一种检查特定基因座或任何核附近的基因组接触的新方法。 感兴趣的区域(例如，核机构)。利用三维局域双光子激发，我们可以在光化学上 生物素标记细胞核的任何区域，我们可以荧光标记和识别体积，可以小到 1/2毫微升。这一过程是使用组合的双光子/共焦对一组细胞进行的 显微镜，成像，定位荧光标记的感兴趣区域，然后照射这些区域 使用700 nm飞秒脉冲通过光化学方法将DNA与 补骨脂素-生物素复合体。分离细胞核，并从目标区域拉下生物素DNA 并进行了测序。由于对细胞进行成像以定位感兴趣区域，因此还可以对它们进行筛选 其他参数，允许仅从用户选择的 细胞群体，提供来自群体内细胞子集的单细胞样基因组信息。我们 有一个细胞系的概念验证数据，该细胞系带有荧光标记的转基因作为我们的靶区， 并表明我们可以获得高度富含转基因基因座序列的DNA。这次聚焦的目标是 技术研发R01项目是(目标1)设计和建造一个双共焦/两个- 能够瞄准和照射一组细胞中的用户选择的感兴趣区域的光子显微镜 以高通量自动化方式，(AIM 2)基于新型微流控技术创建染色质分离管道 设计高效地提纯和准备DNA以进行测序，并(目标3)展示改进 从目标1和目标2通过一系列Femto-Seq实验获得，旨在产生定量指标 改进并发现有关环境信号如何通过细胞质传递的新知识 并进入了原子核。Femto-seq是调查空间和监管关系的一种独特的新方法。 DNA序列和细胞核中任何显微可见的感兴趣区之间的差异。

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.