title: Visualizing Long Noncoding RNAs on Chromatin.
abstract: Fluorescence in situ hybridization (FISH) enables the detection of specific nucleic acid sequences within single cells. For example, RNA FISH provides information on both the expression level and localization of RNA transcripts and, when combined with detection of associated proteins and chromatin modifications, can lend essential insights into long noncoding RNA (lncRNA) function. Epigenetic effects have been postulated for many lncRNAs, but shown for only a few. Advances in in situ techniques and microscopy, however, now allow for visualization of lncRNAs that are expressed at very low levels or are not very stable. FISH-based detections of RNA and DNA coupled with immunological staining of proteins/histone modifications offer the possibility to connect lncRNAs to epigenetic effects. Here, we describe an integrated set of protocols to detect, individually or in combination, specific RNAs, DNAs, proteins, and histone modifications in single cells at a high level of sensitivity using conventional fluorescence microscopy.
authors.affiliation: Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hinten
authors.affiliation: Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Maclary
authors.affiliation: Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
authors.forename: Srimonta
authors.initials: S
authors.lastname: Gayen
authors.affiliation: Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
authors.forename: Clair
authors.initials: C
authors.lastname: Harris
authors.affiliation: Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA. Kalantry@umich.edu.
authors.forename: Sundeep
authors.initials: S
authors.lastname: Kalantry
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques / Q000379:methods; D002843:Chromatin / Q000737:chemistry*; D004247:DNA / Q000032:analysis*; D004622:Embryo, Mammalian / Q000737:chemistry / Q000166:cytology / Q000648:ultrastructure; D005260:Female; D005455:Fluorescent Antibody Technique / Q000379:methods; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods*; D062085:RNA, Long Noncoding / Q000032:analysis*
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding; D004247:DNA
keywords: Chromatin; DNA FISH; Epigenetic; Fluorescence in situ hybridization; Histone modifications; Immunofluorescence; Long noncoding RNAs; RNA FISH