title: ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues.
abstract: Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. Here, we describe a high-resolution fluorescence RNA imaging method, ECHO-liveFISH, to label endogenous nuclear RNA in living mice and chicks. Upon in vivo electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed focally concentrated endogenous 28S rRNA and U3 snoRNA at nucleoli and poly(A) RNA at nuclear speckles. Time-lapse imaging reveals steady-state stability of these RNA foci and dynamic dissipation of 28S rRNA concentrations upon polymerase I inhibition in native brain tissue. Confirming the validity of this technique in a physiological context, the in vivo RNA labeling did not interfere with the function of target RNA nor cause noticeable cytotoxicity or perturbation of cellular behavior.
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Ikumi
authors.initials: I
authors.lastname: Oomoto
authors.affiliation: Brain Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan JSPS Research fellow, Japan Society of Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku,Tokyo 102-0083, Japan.
authors.forename: Asuka
authors.initials: A
authors.lastname: Suzuki-Hirano
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Umeshima
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Yong-Woon
authors.initials: YW
authors.lastname: Han
authors.affiliation: Advanced Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.
authors.forename: Hiroyuki
authors.identifier: http://orcid.org/0000-0003-2636-0728
authors.initials: H
authors.lastname: Yanagisawa
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Peter
authors.initials: P
authors.lastname: Carlton
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Yoshie
authors.initials: Y
authors.lastname: Harada
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Mineko
authors.initials: M
authors.lastname: Kengaku
authors.affiliation: Advanced Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan Research Center for Advanced Science and Technology, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8904, Japan.
authors.forename: Akimitsu
authors.initials: A
authors.lastname: Okamoto
authors.affiliation: Brain Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Shimogori
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan dwang@icems.kyoto-u.ac.jp.
authors.forename: Dan Ohtan
authors.initials: DO
authors.lastname: Wang
mesh_terms: D000818:Animals; D002465:Cell Movement; D002467:Cell Nucleus / Q000235:genetics; D002531:Cerebellum / Q000737:chemistry / Q000166:cytology; D002642:Chick Embryo; D006367:HeLa Cells; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D061986:MCF-7 Cells; D008813:Mice, Inbred ICR; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000737:chemistry; D061848:Optical Imaging; D012313:RNA / Q000032:analysis* / Q000378:metabolism; D012339:RNA, Ribosomal, 28S / Q000032:analysis; D020537:RNA, Small Nucleolar / Q000032:analysis; D059008:Time-Lapse Imaging
chemical_list: D015345:Oligonucleotide Probes; D012339:RNA, Ribosomal, 28S; D020537:RNA, Small Nucleolar; C117378:RNA, U3 small nucleolar; D012313:RNA