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

Nature communications (2015-05-13)
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, Chao-ting Wu
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.

MATERIALS
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