Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
Open accessAbstract
Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis.
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A recently developed oligopainting strategy combined with super-resolution microscopy allows the path of the chromatin fibril to be traced at relatively long genomic loci.
“A recently developed oligopainting strategy [149] combined with super-resolution microscopy allows the path of the chromatin fibril to be traced at relatively long genomic loci [150,151].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [149]
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- Authors
- Beliveau, B. J., Boettiger, A. N., Avendaño, M. S., Jungmann, R., McCole, R. B., Joyce, E. F., Kim-Kiselak, C., Bantignies, F., Fonseka, C. Y., Erceg, J., Hannan, M. A., Hoang, H. G., Colognori, D., Lee, J. T., Shih, W. M., Yin, P., Zhuang, X., & Wu, C.-T.
- Affiliations
- Harvard University (US)
- Howard Hughes Medical Institute (US)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Wu, Chao-ting
- ORCID
- Venue
- Nature Communications
- Published
- 2015-05-12
- Volume
- 6
- Issue
- 1
- Pages
- 7147-7147
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC4430122
- OpenAlex
- W2096973725
- Cited by
- 384
- References
- 6
- Citations by year
- 2026: 16 · 2025: 27 · 2024: 29 · 2023: 31 · 2022: 38 · 2021: 51 · 2020: 44 · 2019: 41 · 2018: 41 · 2017: 36 · 2016: 21 · 2015: 9
- FWCI
- 21.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Science Foundation (1054898, 1162459)
- Howard Hughes Medical Institute
- Damon Runyon Cancer Research Foundation
- Alexander von Humboldt-Stiftung
- Centre National de la Recherche Scientifique
- National Institutes of Health (1dp2od007292-01, 1dp2od004641-01)
- Hansjörg Wyss Institute for Biologically Inspired Engineering, Harvard University
- Office of Naval Research (CCF1054898, N00014-13-1- 0593, N000141110914, N000141010827)
- National Cancer Institute (F32CA157188)
- National Institute of General Medical Sciences (RO1GM61936, DP1GM106412, R01 GM61936, R01GM090278, R01GM061936)
- National Institute of Biomedical Imaging and Bioengineering (R01EB018659)
- National Center for Chronic Disease Prevention and Health Promotion (5DP1 GM106412)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R21HD072481)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- fluorescence in situ hybridization, single nucleotide polymorphisms, chromosome positioning, parent-of-origin gene expression, nuclear organization
- MeSH terms
- Animals, Cell Line, Chromosomes, Drosophila, Haplotypes, Staining and Labeling, Oligonucleotide Probes, Gene Library, In Situ Hybridization, Fluorescence, Chromosome Painting, Oligonucleotide Array Sequence Analysis
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