title: Nanoscale imaging of RNA with expansion microscopy.
abstract: The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be covalently attached to a swellable polyelectrolyte gel synthesized throughout a biological specimen. Then, postexpansion, fluorescent in situ hybridization (FISH) imaging of RNA can be performed with high yield and specificity as well as single-molecule precision in both cultured cells and intact brain tissue. Expansion FISH (ExFISH) separates RNAs and supports amplification of single-molecule signals (i.e., via hybridization chain reaction) as well as multiplexed RNA FISH readout. ExFISH thus enables super-resolution imaging of RNA structure and location with diffraction-limited microscopes in thick specimens, such as intact brain tissue and other tissues of importance to biology and medicine.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Chen
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Asmamaw T
authors.initials: AT
authors.lastname: Wassie
authors.affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Allison J
authors.initials: AJ
authors.lastname: Cote
authors.affiliation: Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Anubhav
authors.identifier: 0000-0002-1545-3163
authors.initials: A
authors.lastname: Sinha
authors.affiliation: Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Shahar
authors.initials: S
authors.lastname: Alon
authors.affiliation: Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Shoh
authors.initials: S
authors.lastname: Asano
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA.|Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Evan R
authors.initials: ER
authors.lastname: Daugharthy
authors.affiliation: Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Jae-Byum
authors.initials: JB
authors.lastname: Chang
authors.affiliation: Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Marblestone
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Arjun
authors.initials: A
authors.lastname: Raj
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Boyden
mesh_terms: D000178:Acrylamides / Q000737:chemistry*; D000818:Animals; D001921:Brain / Q000166:cytology / Q000378:metabolism*; D002478:Cells, Cultured; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods*; D036103:Nanotechnology / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry; D061848:Optical Imaging / Q000379:methods*; D012313:RNA / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism
chemical_list: D000178:Acrylamides; D015345:Oligonucleotide Probes; D012313:RNA