Beliveau, BrianBoettiger, AlistairAvendaño, Maier S.Jungmann, RalfMcCole, RuthJoyce, Eric F.Kim-Kiselak, CarolineBantignies, FrédéricFonseka, ChamithErceg, JelenaHannan, MohammedHoang, Hien G.Colognori, DavidLee, JeannieShih, WilliamYin, PengZhuang, XiaoweiWu, Chao-ting2015-06-022015Beliveau, B. J., A. N. Boettiger, M. S. Avendaño, R. Jungmann, R. B. McCole, E. F. Joyce, C. Kim-Kiselak, et al. 2015. “Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.” Nature Communications 6 (1): 7147. doi:10.1038/ncomms8147. http://dx.doi.org/10.1038/ncomms8147.2041-1723http://nrs.harvard.edu/urn-3:HUL.InstRepos:16120838Fluorescence 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.en-USJournal Article2015-06-0210.1038/ncomms8147