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Programmable Chromosome Painting with Oligopaints

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Imaging Gene Expression

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2038))

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.

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Acknowledgments

The authors would like to thank members of the Joyce laboratory for extensive conversations and experience. This work was supported by an NIH grant to E.J. (R35GM128903).

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Authors and Affiliations

  1. Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Son C. Nguyen & Eric F. Joyce

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  1. Son C. Nguyen
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  2. Eric F. Joyce
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Correspondence to Eric F. Joyce .

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Editors and Affiliations

  1. The Mina & Everard Goodman, Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel

    Yaron Shav-Tal

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Nguyen, S.C., Joyce, E.F. (2019). Programmable Chromosome Painting with Oligopaints. In: Shav-Tal, Y. (eds) Imaging Gene Expression. Methods in Molecular Biology, vol 2038. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9674-2_11

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  • DOI: https://doi.org/10.1007/978-1-4939-9674-2_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9673-5

  • Online ISBN: 978-1-4939-9674-2

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