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Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

BACKGROUND: Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct...

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Autores principales: Cabili, Moran N, Dunagin, Margaret C, McClanahan, Patrick D, Biaesch, Andrew, Padovan-Merhar, Olivia, Regev, Aviv, Rinn, John L, Raj, Arjun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369099/
https://www.ncbi.nlm.nih.gov/pubmed/25630241
http://dx.doi.org/10.1186/s13059-015-0586-4
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author Cabili, Moran N
Dunagin, Margaret C
McClanahan, Patrick D
Biaesch, Andrew
Padovan-Merhar, Olivia
Regev, Aviv
Rinn, John L
Raj, Arjun
author_facet Cabili, Moran N
Dunagin, Margaret C
McClanahan, Patrick D
Biaesch, Andrew
Padovan-Merhar, Olivia
Regev, Aviv
Rinn, John L
Raj, Arjun
author_sort Cabili, Moran N
collection PubMed
description BACKGROUND: Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visualization of lncRNAs in single cells at single-molecule resolution. RESULTS: We use single-molecule RNA-FISH to systematically quantify and categorize the subcellular localization patterns of a representative set of 61 lncRNAs in three different cell types. Our survey yields high-resolution quantification and stringent validation of the number and spatial positions of these lncRNA, with an mRNA set for comparison. Using this highly quantitative image-based dataset, we observe a variety of subcellular localization patterns, ranging from bright sub-nuclear foci to almost exclusively cytoplasmic localization. We also find that the low abundance of lncRNAs observed from cell population measurements cannot be explained by high expression in a small subset of ‘jackpot’ cells. Additionally, nuclear lncRNA foci dissolve during mitosis and become widely dispersed, suggesting these lncRNAs are not mitotic bookmarking factors. Moreover, we see that divergently transcribed lncRNAs do not always correlate with their cognate mRNA, nor do they have a characteristic localization pattern. CONCLUSIONS: Our systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0586-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-43690992015-03-22 Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution Cabili, Moran N Dunagin, Margaret C McClanahan, Patrick D Biaesch, Andrew Padovan-Merhar, Olivia Regev, Aviv Rinn, John L Raj, Arjun Genome Biol Research BACKGROUND: Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visualization of lncRNAs in single cells at single-molecule resolution. RESULTS: We use single-molecule RNA-FISH to systematically quantify and categorize the subcellular localization patterns of a representative set of 61 lncRNAs in three different cell types. Our survey yields high-resolution quantification and stringent validation of the number and spatial positions of these lncRNA, with an mRNA set for comparison. Using this highly quantitative image-based dataset, we observe a variety of subcellular localization patterns, ranging from bright sub-nuclear foci to almost exclusively cytoplasmic localization. We also find that the low abundance of lncRNAs observed from cell population measurements cannot be explained by high expression in a small subset of ‘jackpot’ cells. Additionally, nuclear lncRNA foci dissolve during mitosis and become widely dispersed, suggesting these lncRNAs are not mitotic bookmarking factors. Moreover, we see that divergently transcribed lncRNAs do not always correlate with their cognate mRNA, nor do they have a characteristic localization pattern. CONCLUSIONS: Our systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0586-4) contains supplementary material, which is available to authorized users. BioMed Central 2015-01-29 2015 /pmc/articles/PMC4369099/ /pubmed/25630241 http://dx.doi.org/10.1186/s13059-015-0586-4 Text en © Cabili et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Cabili, Moran N
Dunagin, Margaret C
McClanahan, Patrick D
Biaesch, Andrew
Padovan-Merhar, Olivia
Regev, Aviv
Rinn, John L
Raj, Arjun
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
title Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
title_full Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
title_fullStr Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
title_full_unstemmed Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
title_short Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
title_sort localization and abundance analysis of human lncrnas at single-cell and single-molecule resolution
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369099/
https://www.ncbi.nlm.nih.gov/pubmed/25630241
http://dx.doi.org/10.1186/s13059-015-0586-4
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