使用寡核苷酸探针对染色体进行可编程染色
Programmable Chromosome Painting with Oligopaints.
作者信息
Nguyen Son C, Joyce Eric F
机构信息
Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
出版信息
Methods Mol Biol. 2019;2038:167-180. doi: 10.1007/978-1-4939-9674-2_11.
Abstract
Current methods for chromosome painting via fluorescence in situ hybridization (FISH) are costly, time-consuming, and limited in complexity. In contrast to conventional sources of probe, Oligopaints are computationally designed, synthesized on microarrays, and amplified by PCR. This approach allows for precise control over the sequences they target, which can range from a few kilobases to entire chromosomes with the same basic protocol. We have utilized the flexibility and scalability of Oligopaints to generate low-cost and renewable chromosome paints for Drosophila, mouse, and human chromosomes. These Oligopaint libraries can be customized to label any genomic feature(s) in a chromosome-wide manner. Additionally, this method is compatible with sequential FISH to label entire genomes with a single denaturation step. Here, we outline a protocol and considerations to scale the Oligopaint technology for fluorescent labeling of whole chromosomes.
摘要
当前通过荧光原位杂交（FISH）进行染色体描绘的方法成本高昂、耗时且复杂度有限。与传统的探针来源不同，寡核苷酸探针是通过计算机设计、在微阵列上合成并通过聚合酶链式反应（PCR）进行扩增的。这种方法能够精确控制其靶向的序列，使用相同的基本方案，靶向范围可以从几千个碱基对到整条染色体。我们利用了寡核苷酸探针的灵活性和可扩展性，为果蝇、小鼠和人类染色体生成了低成本且可再生的染色体描绘探针。这些寡核苷酸探针文库可以进行定制，以全染色体范围的方式标记任何基因组特征。此外，该方法与顺序FISH兼容，只需一步变性步骤即可标记整个基因组。在这里，我们概述了一种方案以及将寡核苷酸探针技术扩展用于全染色体荧光标记的注意事项
相似文献
1
Programmable Chromosome Painting with Oligopaints.使用寡核苷酸探针对染色体进行可编程染色
Methods Mol Biol. 2019;2038:167-180. doi: 10.1007/978-1-4939-9674-2_11.
2
Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.用于使用寡核苷酸 FISH 探针可视化基因组的通用设计和合成平台。
Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21301-6. doi: 10.1073/pnas.1213818110. Epub 2012 Dec 11.
3
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.使用寡核苷酸荧光原位杂交（Oligopaint FISH）探针进行染色体的单分子超分辨率成像及原位单倍型可视化
Nat Commun. 2015 May 12;6:7147. doi: 10.1038/ncomms8147.
4
PCR in situ followed by microdissection allows whole chromosome painting probes to be made from single microdissected chromosomes.原位聚合酶链反应（PCR）结合显微切割技术，可从单个显微切割的染色体制作全染色体涂染探针。
Mamm Genome. 1999 Jun;10(6):628-31. doi: 10.1007/s003359901058.
5
Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships.玉米的整条染色体显带揭示了重排、核域和染色体之间的关系。
Proc Natl Acad Sci U S A. 2019 Jan 29;116(5):1679-1685. doi: 10.1073/pnas.1813957116. Epub 2019 Jan 17.
6
Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis.基于寡核苷酸多重 PCR 的灵活染色体显带及其在黄瓜比较染色体分析中的应用。
Plant J. 2020 Apr;102(1):178-186. doi: 10.1111/tpj.14600. Epub 2019 Dec 8.
7
COBRA: combined binary ratio labeling of nucleic-acid probes for multi-color fluorescence in situ hybridization karyotyping.COBRA：用于多色荧光原位杂交核型分析的核酸探针组合二元比率标记法
Nat Protoc. 2006;1(1):264-75. doi: 10.1038/nprot.2006.41.
8
Phylogenomic analysis by chromosome sorting and painting.通过染色体分选和涂染进行系统基因组分析。
Methods Mol Biol. 2008;422:13-29. doi: 10.1007/978-1-59745-581-7_2.
9
Generation of chromosome paints: approach for increasing specificity and intensity of signals.染色体涂染的产生：提高信号特异性和强度的方法。
Biotechniques. 2003 Mar;34(3):530-2, 534, 536. doi: 10.2144/03343st05.
10
Development and application of whole-chromosome painting of chromosomes 7A and 8A of based on chromosome-specific single-copy oligonucleotides.基于染色体特异性单拷贝寡核苷酸的 7A 和 8A 染色体整条染色体涂抹技术的开发和应用。
Genome. 2024 Jun 1;67(6):178-188. doi: 10.1139/gen-2023-0116. Epub 2024 Feb 23.
引用本文的文献
1
B cell stimulation changes the structure and higher-order organization of the inactive X chromosome.B细胞刺激会改变失活X染色体的结构和高级组织形式。
Cell Rep. 2025 Mar 25;44(3):115351. doi: 10.1016/j.celrep.2025.115351. Epub 2025 Feb 26.
2
CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association.CTCF/RAD21 组织染色质 - 核斑点关联的基态。
Nat Struct Mol Biol. 2025 Feb 21. doi: 10.1038/s41594-024-01465-6.
3
Nuclear speckles regulate functional programs in cancer.核斑点调节癌症中的功能程序。
Nat Cell Biol. 2025 Feb;27(2):322-335. doi: 10.1038/s41556-024-01570-0. Epub 2025 Jan 2.
4
Inter-chromosomal contacts demarcate genome topology along a spatial gradient.染色体间接触沿着空间梯度划定基因组拓扑结构。
Nat Commun. 2024 Nov 13;15(1):9813. doi: 10.1038/s41467-024-53983-y.
5
Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species.在全着丝粒的鳞翅目昆虫中，精子发生过程中的染色体分离通过一种独特的中心动力学机制发生。
PLoS Genet. 2024 Jun 24;20(6):e1011329. doi: 10.1371/journal.pgen.1011329. eCollection 2024 Jun.
6
A feedback loop between heterochromatin and the nucleopore complex controls germ-cell-to-oocyte transition during Drosophila oogenesis.异染色质和核孔复合物之间的反馈环控制果蝇卵子发生过程中的生殖细胞到卵母细胞的转变。
Dev Cell. 2023 Nov 20;58(22):2580-2596.e6. doi: 10.1016/j.devcel.2023.08.014. Epub 2023 Sep 5.
7
Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding.使用一种名为寡带的新核型分析方法对加拿大种猪核心群进行细胞遗传学筛查。
Genet Sel Evol. 2023 Jul 10;55(1):47. doi: 10.1186/s12711-023-00819-w.
8
Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.驯鹿基因组的染色体水平组装及对有角类动物和反刍动物进化见解的验证。
BMC Genomics. 2023 Mar 23;24(1):142. doi: 10.1186/s12864-023-09189-5.
9
Nucleoporins facilitate ORC loading onto chromatin.核孔蛋白促进 ORC 加载到染色质上。
Cell Rep. 2022 Nov 8;41(6):111590. doi: 10.1016/j.celrep.2022.111590.
10
Dosage compensation in is achieved by partial repression of both Z chromosomes in males.在[具体物种]中，剂量补偿是通过部分抑制雄性个体中的两条Z染色体来实现的。
Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2113374119. doi: 10.1073/pnas.2113374119. Epub 2022 Mar 3.
本文引用的文献
1
A multiplexed DNA FISH strategy for assessing genome architecture in .一种用于评估. 基因组结构的多重化 DNA FISH 策略。
Elife. 2019 May 14;8:e42823. doi: 10.7554/eLife.42823.
2
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.用超高分辨率成像、接触图谱和整合建模沿着染色体行走。
PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. eCollection 2018 Dec.
3
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.超分辨率染色质追踪揭示了单细胞中的域和协同相互作用。
Science. 2018 Oct 26;362(6413). doi: 10.1126/science.aau1783.
4
Condensin II drives large-scale folding and spatial partitioning of interphase chromosomes in Drosophila nuclei.凝聚素 II 驱动果蝇核内间期染色体的大规模折叠和空间分隔。
PLoS Genet. 2018 Jul 12;14(7):e1007393. doi: 10.1371/journal.pgen.1007393. eCollection 2018 Jul.
5
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.通过内含子 seqFISH 研究新生转录组的动态和空间基因组学。
Cell. 2018 Jul 12;174(2):363-376.e16. doi: 10.1016/j.cell.2018.05.035. Epub 2018 Jun 7.
6
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.OligoMiner 为设计基因组规模的寡核苷酸原位杂交探针提供了一个快速、灵活的环境。
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2183-E2192. doi: 10.1073/pnas.1714530115. Epub 2018 Feb 20.
7
Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression.核纤层相关结构域：与染色体结构、异染色质及基因抑制的联系
Cell. 2017 May 18;169(5):780-791. doi: 10.1016/j.cell.2017.04.022.
8
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.单核Hi-C技术揭示了从卵母细胞到合子转变过程中独特的染色质重排。
Nature. 2017 Apr 6;544(7648):110-114. doi: 10.1038/nature21711. Epub 2017 Mar 29.
9
Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.Xist 将 X 染色体募集到核纤层，从而实现全染色体沉默。
Science. 2016 Oct 28;354(6311):468-472. doi: 10.1126/science.aae0047. Epub 2016 Aug 4.
10
Spatial organization of chromatin domains and compartments in single chromosomes.单条染色体中染色质结构域和区室的空间组织
Science. 2016 Aug 5;353(6299):598-602. doi: 10.1126/science.aaf8084. Epub 2016 Jul 21.
Zotero 插件