ArticleJournal of visualized experiments : JoVE2013
Robust 3D DNA FISH using directly labeled probes.
Article in Journal of visualized experiments : JoVE, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Pulsatile flow induces chromatin interaction with lamin-associated proteins to enrich H3K9 methylation in endothelial cells.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells.Genes & development · 2025Article
- Increased enhancer-promoter interactions during developmental enhancer activation in mammals.Nature genetics · 2024Article
- Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes.Cell reports · 2023Article
- STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.Nature communications · 2022Article
- Circular RNA circTmem241 drives group III innate lymphoid cell differentiation via initiation of Elk3 transcription.Nature communications · 2022Article
- The 3D Genome: From Structure to Function.International journal of molecular sciences · 2021Review
- Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis.PLoS pathogens · 2021Article
- Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states.Nature communications · 2021Article
- FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains.Frontiers in cell and developmental biology · 2021Review
- Rapid assessment of ocular drug delivery in a novel ex vivo corneal model.Scientific reports · 2020Article
- Article
- Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner.The EMBO journal · 2020Article
- Controlled ploidy reduction of pluripotent 4n cells generates 2n cells during mouse embryo development.Science advances · 2019Article
- Efficient genome-wide first-generation phenotypic screening system in mice using theProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.Nature communications · 2019Article
- A dual colour FISH method for routine validation of sexed Bos taurus semen.BMC veterinary research · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
3D DNA FISH has become a major tool for analyzing three-dimensional organization of the nucleus, and several variations of the technique have been published. In this article we describe a protocol which has been optimized for robustness, reproducibility, and ease of use. Brightly fluorescent directly labeled probes are generated by nick-translation with amino-allyldUTP followed by chemical coupling of the dye. 3D DNA FISH is performed using a freeze-thaw step for cell permeabilization and a heating step for simultaneous denaturation of probe and nuclear DNA. The protocol is applicable to a range of cell types and a variety of probes (BACs, plasmids, fosmids, or Whole Chromosome Paints) and allows for high-throughput automated imaging. With this method we routinely investigate nuclear localization of up to three chromosomal regions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.