Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Three-dimensional DNA fluorescent in situ hybridization (3D-FISH) has been extensively used for the study of chromosome organization, from large-scale chromosome territories to finer sub-megabase structures, such as topologically associating domains (TADs) or internal TAD features such as chromatin loops. The development of oligo-based technology has rendered this technique highly versatile and allowed to study chromosomal structures at different scale levels, as well as structural variations such as deletions, duplications, or translocations, as those occurring in cancer and chromothripsis. Here, we present a comprehensive Oligopaint FISH protocol, from probe design and production to FISH, microscopy, and specific analysis that can be used with various cell lines.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-0716-4750-9_28 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.
ArXiv
August 2025
Department of Genetics, Yale University, New Haven, CT 06510, USA.
A key output of the NIH-Common Fund 4D Nucleome (4DN) project is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease. Despite this progress, results from Chromatin Tracing FISH-omics experiments are difficult to share, reuse, and subject to third-party downstream analysis due to the lack of standard specifications for data exchange.
View Article and Find Full Text PDFOligopaint FISH to Study Chromosomal Architecture and Structural Variations.
Methods Mol Biol
August 2025
Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France.
Three-dimensional DNA fluorescent in situ hybridization (3D-FISH) has been extensively used for the study of chromosome organization, from large-scale chromosome territories to finer sub-megabase structures, such as topologically associating domains (TADs) or internal TAD features such as chromatin loops. The development of oligo-based technology has rendered this technique highly versatile and allowed to study chromosomal structures at different scale levels, as well as structural variations such as deletions, duplications, or translocations, as those occurring in cancer and chromothripsis. Here, we present a comprehensive Oligopaint FISH protocol, from probe design and production to FISH, microscopy, and specific analysis that can be used with various cell lines.
View Article and Find Full Text PDFWhole Mount Oligopaint Fluorescence In Situ Hybridization of Mouse Oocytes, Eggs, or Early-Stage Embryos.
Methods Mol Biol
July 2025
Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Fluorescence in situ hybridization (FISH) to visualize DNA or chromosomes in cells is well recognized as a valuable and versatile technique. The recent development of Oligopaint FISH is particularly useful for studies of chromosome structure, function, and evolution. Here, we describe a series of protocols for applying the Oligopaint FISH technique to mouse oocytes, eggs, and early-stage embryos.
View Article and Find Full Text PDFThe length and strength of compartmental interactions are modulated by condensin II activity.
PLoS Genet
July 2025
Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
The spatial organization of the genome is crucial for its function and integrity. Although the ring-like SMC complex condensin II has a well-documented role in organizing mitotic chromosomes, its function in interphase chromatin structure has remained more enigmatic. Using a combination of Oligopaint fluorescence in situ hybridization (FISH) and Hi-C, we show that altering condensin II levels in diploid Drosophila cells significantly changes chromosome architecture at large length scales between chromatin compartments.
View Article and Find Full Text PDFOligopaint FISH in Drosophila Testes.
Methods Mol Biol
July 2025
Department of Cell Biology, University of Connecticut School of Medicine, Farmington, CT, USA.
Fluorescence in situ hybridization (FISH) is commonly performed to visualize RNA and DNA. It is routinely used in cytogenetics and karyotyping to check for chromosomal abnormalities and diagnose and identify diseases (Levsky and Singer, J Cell Sci 116:2833-2838, 2003). Oligopaints is a recently established DNA FISH method that has quickly become popular because of its flexibility and economical durability.
View Article and Find Full Text PDF