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

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, Mohammed A. Hannan, Hien G. Hoang, David Colognori, Jeannie T. Lee, William M. Shih, Peng Yin, Xiaowei Zhuang and Chao-ting Wu ()
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Brian J. Beliveau: Harvard Medical School
Alistair N. Boettiger: Harvard University
Maier S. Avendaño: Wyss Institute for Biologically Inspired Engineering, Harvard University
Ralf Jungmann: Wyss Institute for Biologically Inspired Engineering, Harvard University
Ruth B. McCole: Harvard Medical School
Eric F. Joyce: Harvard Medical School
Caroline Kim-Kiselak: Harvard Medical School
Frédéric Bantignies: Harvard Medical School
Chamith Y. Fonseka: Harvard Medical School
Jelena Erceg: Harvard Medical School
Mohammed A. Hannan: Harvard Medical School
Hien G. Hoang: Harvard Medical School
David Colognori: Harvard Medical School
Jeannie T. Lee: Harvard Medical School
William M. Shih: Wyss Institute for Biologically Inspired Engineering, Harvard University
Peng Yin: Wyss Institute for Biologically Inspired Engineering, Harvard University
Xiaowei Zhuang: Harvard University
Chao-ting Wu: Harvard Medical School

Nature Communications, 2015, vol. 6, issue 1, 1-13

Abstract: 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.

Date: 2015
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DOI: 10.1038/ncomms8147

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