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Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

Author

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  • Brian J. Beliveau

    (Harvard Medical School
    Present address: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA & Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Alistair N. Boettiger

    (Harvard University
    Howard Hughes Medical Institute)

  • Maier S. Avendaño

    (Wyss Institute for Biologically Inspired Engineering, Harvard University
    Harvard Medical School)

  • Ralf Jungmann

    (Wyss Institute for Biologically Inspired Engineering, Harvard University
    Harvard Medical School
    Present address: Max Planck Institute of Biochemistry and LMU, Munich, Germany)

  • Ruth B. McCole

    (Harvard Medical School)

  • Eric F. Joyce

    (Harvard Medical School)

  • Caroline Kim-Kiselak

    (Harvard Medical School)

  • Frédéric Bantignies

    (Harvard Medical School
    Institut de Génétique Humaine, CNRS UPR 1142)

  • Chamith Y. Fonseka

    (Harvard Medical School
    Present address: Divisions of Genetics & Rheumatology, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Jelena Erceg

    (Harvard Medical School)

  • Mohammed A. Hannan

    (Harvard Medical School)

  • Hien G. Hoang

    (Harvard Medical School)

  • David Colognori

    (Harvard Medical School
    Howard Hughes Medical Institute
    Massachusetts General Hospital)

  • Jeannie T. Lee

    (Harvard Medical School
    Howard Hughes Medical Institute
    Massachusetts General Hospital)

  • William M. Shih

    (Wyss Institute for Biologically Inspired Engineering, Harvard University
    Harvard Medical School
    Dana-Farber Cancer Institute)

  • Peng Yin

    (Wyss Institute for Biologically Inspired Engineering, Harvard University
    Harvard Medical School)

  • Xiaowei Zhuang

    (Harvard University
    Howard Hughes Medical Institute
    Harvard University)

  • Chao-ting Wu

    (Harvard Medical School)

Abstract

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.

Suggested Citation

  • Brian J. Beliveau & Alistair N. Boettiger & Maier S. Avendaño & Ralf Jungmann & Ruth B. McCole & Eric F. Joyce & Caroline Kim-Kiselak & Frédéric Bantignies & Chamith Y. Fonseka & Jelena Erceg & Mohamm, 2015. "Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes," Nature Communications, Nature, vol. 6(1), pages 1-13, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms8147
    DOI: 10.1038/ncomms8147
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    Cited by:

    1. Cristiana Bersaglieri & Jelena Kresoja-Rakic & Shivani Gupta & Dominik Bär & Rostyslav Kuzyakiv & Martina Panatta & Raffaella Santoro, 2022. "Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Robin Aguilar & Conor K. Camplisson & Qiaoyi Lin & Karen H. Miga & William S. Noble & Brian J. Beliveau, 2024. "Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Juan Du & Keunhwa Kim & Meng Chen, 2024. "Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Hua Yu & Zhen Sun & Tianyu Tan & Hongru Pan & Jing Zhao & Ling Zhang & Jiayu Chen & Anhua Lei & Yuqing Zhu & Lang Chen & Yuyan Xu & Yaxin Liu & Ming Chen & Jinghao Sheng & Zhengping Xu & Pengxu Qian &, 2021. "rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin," Nature Communications, Nature, vol. 12(1), pages 1-21, December.

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