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

项目概要/摘要 目标：关于染色体组织对遗传和基因表达的作用的问题 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， 它由各个部分组成，这些部分独立折叠，折叠方式因细胞而异。此外，前 除了 X 和 Y 之外，二倍体生物的染色体成对的同源体，难以轻易分离。 通过成像着色。该应用程序提出了一套工具来跟踪整个染色路径 使用宽场、共聚焦、以序列和同系物特异性方式在单细胞水平上进行一些分析 以及超分辨率显微镜。工具的一方面是寡核苷酸（oligos）文库 虽然可再生，但价格昂贵，此类库将被设计为具有广泛用途，以便它们 实验室之间可以自由共享。简而言之，该提案旨在提供新的工具，以适应 加深我们对染色体功能和染色体组织之间关系的理解 。 健康相关性：细胞核内基因组的组织及其进展 该组织通过发展对基因表达产生深远的影响，因此， 发育和疾病；染色体拓扑和染色体间相互作用影响增强子 启动子相互作用、全局沉默、染色体稳定性和修复、染色体分离、 甚至继承。因此，基于单细胞成像的研究阐明了基因组如何 组织起来将大大有助于进一步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开发上 因此，它们有望实现原本不可能实现的研究和发现。 特别是，他们的目标是通过提高探针效率来促进染色体原位成像 和探头设计，提高数据采集速度和收集数据的数量，并增强 图像分辨率。通过这种方式，他们可以为社区提供可以渲染复杂的工具 基因组，例如人类的基因组，更容易进行分析。简而言之，目标致力于： 目标 1 优化 Oligopaints 目标 2 使用 Oligopaints、OligoSTORM 和 OligoDNA-PAINT 追踪染色体 目标 3 使用 OligoFISSEQ 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