Technologies for visualizing the genome in situ

原位可视化基因组技术

• 批准号: 9922960
• 负责人: CHAO-TING WU
• 金额: $ 62.85万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2021-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9922960
• 关键词: Affect; Age; Biological; Caliber; Cell Nucleus; Cells; Chromatin; Chromosomal Stability; Chromosome Segregation; Chromosome Structures; Chromosomes; Church; Clinical; Collaborations; Communities; Complement; Complex; DNA; DNA analysis; Data; Development; Diploidy; Disease; Drosophila genus; Effectiveness; Enhancers; Family; Fluorescent Probes; Fluorescent in Situ Hybridization; Free Will; Gene Expression; Genetic Transformation; Genome; Genomic Segment; Goals; Health; Homologous Gene; Human; Image; Image Enhancement; Imaging technology; In Situ; Laboratories; Lead; Libraries; Microscopy; Nucleosomes; Oligonucleotides; Organ; Organism; Paint; Protocols documentation; Resolution; Resources; Role; Signal Transduction; Single Nucleotide Polymorphism; Speed; Technology; Visual; Y Chromosome; Yin; autosome; base; cellular imaging; confocal imaging; data acquisition; design; improved; in situ sequencing; innovation; insight; new technology; promoter; repaired; technology development; tool

PROJECT SUMMARY/ABSTRACT Goals: Questions regarding the role of chromosome organization on inheritance and gene expres- sion raise many technical challenges. Not only is chromosomal DNA the largest biomolecule in the cell, it is comprised of segments that fold independently in ways that vary from cell to cell. Furthermore, ex- cepting the X and Y, chromosomes of diploid organisms come in pairs of homologs that defy easy dis- tinction via imaging. This application proposes a suite of tools for tracing the path of entire chromo- somes at the single cell level in a sequence- and homolog-specific fashion using widefield, confocal, as well as super-resolution microscopy. As one aspect of the tools are libraries of oligonucleotides (oligos) which, while renewable, are expensive, such libraries will be designed to be broadly useful so that they can be shared freely among laboratories. In brief, this proposal aims to provide new tools that will ad- vance our understanding of the relationship between chromosome function and chromosome organiza- tion. Health relatedness: The organization of the genome within the nucleus and the progression of that organization through development has profound consequences for gene expression and, thus, development and disease; chromosome topology and interchromosomal interactions affect enhancer- promoter interactions, global silencing, chromosome stability and repair, chromosome segregation, and, thus, even inheritance. As such, single-cell imaging-based studies that elucidate how the genome is organized will do much to further our understanding and treatment of disease. Innovation: The proposed aims are focused heavily on the development of new technologies and, thus, they hold promise for enabling studies and discoveries that might not otherwise be possible. In particular, they aim to facilitate the imaging of chromosomes in situ by improving probe effectiveness and probe design, increasing speed of data acquisition and quantity of data collected, and enhancing image resolution. In this way, they may provide the community with tools that can render complex genomes, such as those of humans, more accessible for analysis. In brief, the aims are dedicated to: Aim 1 Optimizing Oligopaints Aim 2 Tracing chromosomes using Oligopaints, OligoSTORM, and OligoDNA-PAINT Aim 3 Tracing chromosomes using OligoFISSEQ

项目摘要/摘要 目标：有关染色体组织在遗传和基因表达中的作用的问题 - Sion提出了许多技术挑战。染色体DNA不仅是细胞中最大的生物分子 它由段组成，这些段以各种细胞之间不同的方式独立折叠。此外， X和Y，二倍体生物的染色体有成对的同源物，无视容易的疾病 通过成像进行刺激。该应用程序提出了一套工具，用于追踪整个铬的路径 使用广场，共焦点，以序列和同源性的方式处于单细胞水平的单元格 以及超分辨率显微镜。由于工具的一个方面是寡核苷酸（寡核苷酸）的库 虽然可再生能够昂贵，但此类库将被设计为广泛有用，以便它们 可以在实验室中自由共享。简而言之，该建议旨在提供新工具，以 我们对染色体功能与染色体组织之间关系的理解 - tion。 健康相关性：核内基因组的组织和 通过发展的组织对基因表达产生了深远的影响，因此， 发展与疾病；染色体拓扑和染色体相互作用会影响增强子 - 启动子相互作用，全局沉默，染色体稳定性和修复，染色体隔离， 因此，甚至继承。因此，基于单细胞成像的研究阐明了基因组 组织有很大的作用，可以进一步了解我们对疾病的理解和治疗。 创新：拟议的目标主要集中在新技术的发展上 因此，他们有望实现可能是不可能的研究和发现。 特别是，它们旨在通过提高探针效率来促进原位染色体的成像 和探针设计，数据获取速度的提高和收集的数据数量以及增强 图像分辨率。通过这种方式，他们可以为社区提供可以使复杂的工具 基因组，例如人类的基因组，更容易访问进行分析。简而言之，目的是致力于： 目标1优化寡聚 AIM 2使用寡聚，寡聚剂和寡素 - paint染色体追踪染色体 AIM 3使用寡素染色体追踪染色体

项目成果

Transcription-mediated supercoiling regulates genome folding and loop formation.

• DOI: 10.1016/j.molcel.2021.06.009
• 发表时间: 2021-08-05
• 期刊: MOLECULAR CELL
• 影响因子: 16
• 作者: Victoria Neguembor, Maria;Martin, Laura;Castells-Garcia, Alvaro;Aurelio Gomez-Garcia, Pablo;Vicario, Chiara;Carnevali, Davide;Abed, Jumana AlHaj;Granados, Alba;Sebastian-Perez, Ruben;Sottile, Francesco;Solon, Jerome;Wu, Chao-ting;Lakadamyali, Melike;Cosma, Maria Pia
• 通讯作者: Cosma, Maria Pia

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.

• DOI: 10.1038/s41594-022-00839-y
• 发表时间: 2022-10
• 期刊: NATURE STRUCTURAL & MOLECULAR BIOLOGY
• 影响因子: 16.8
• 作者: Victoria Neguembor, Maria;Pablo Arcon, Juan;Buitrago, Diana;Lema, Rafael;Walther, Jurgen;Garate, Ximena;Martin, Laura;Romero, Pablo;Abed, Jumana AlHaj;Gut, Marta;Blanc, Julie;Lakadamyali, Melike;Wu, Chao-ting;Brun Heath, Isabelle;Orozco, Modesto;Dans, Pablo D.;Cosma, Maria Pia
• 通讯作者: Cosma, Maria Pia

Paircounting.

配对计数。

• DOI: 10.1016/j.tig.2019.07.010
• 发表时间: 2019
• 期刊: Trends in genetics : TIG
• 作者: Nguyen,HuyQ;Lee,SDean;Wu,C-Ting
• 通讯作者: Wu,C-Ting