title: Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.
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.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Beliveau
authors.affiliation: 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA.
authors.forename: Alistair N
authors.initials: AN
authors.lastname: Boettiger
authors.affiliation: 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Maier S
authors.initials: MS
authors.lastname: Avendaño
authors.affiliation: 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Ralf
authors.initials: R
authors.lastname: Jungmann
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Ruth B
authors.initials: RB
authors.lastname: McCole
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Eric F
authors.initials: EF
authors.lastname: Joyce
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Caroline
authors.initials: C
authors.lastname: Kim-Kiselak
authors.affiliation: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Institut de Génétique Humaine, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Bantignies
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Chamith Y
authors.initials: CY
authors.lastname: Fonseka
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Jelena
authors.initials: J
authors.lastname: Erceg
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Mohammed A
authors.initials: MA
authors.lastname: Hannan
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Hien G
authors.initials: HG
authors.lastname: Hoang
authors.affiliation: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA [3] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
authors.forename: David
authors.initials: D
authors.lastname: Colognori
authors.affiliation: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA [3] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
authors.forename: Jeannie T
authors.initials: JT
authors.lastname: Lee
authors.affiliation: 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors.forename: William M
authors.initials: WM
authors.lastname: Shih
authors.affiliation: 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Yin
authors.affiliation: 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA [3] Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhuang
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Chao-ting
authors.initials: CT
authors.lastname: Wu
mesh_terms: D000818:Animals; D002460:Cell Line; D020223:Chromosome Painting / Q000379:methods*; D002875:Chromosomes / Q000235:genetics*; D004330:Drosophila; D015723:Gene Library; D006239:Haplotypes; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000378:metabolism; D013194:Staining and Labeling
chemical_list: D015345:Oligonucleotide Probes