Open Access
volume 16, issue 1, publication number 20
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
Cabili Moran N
1, 2, 3
,
Dunagin Margaret C
4
,
Mcclanahan Patrick D
4
,
Biaesch Andrew
4
,
Padovan Merhar Olivia
4
,
Regev Aviv
1, 5
,
Rinn John L.
1, 3
,
Raj Arjun
4
1
Broad Institute of MIT and Harvard, Cambridge, USA
|
2
Department of Systems Biology, Harvard Medical School, Boston, USA
|
3
Department of Stem cell and Regenerative Biology, Harvard University, Cambridge, USA
|
4
School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, USA
|
Publication type: Journal Article
Publication date: 2015-01-29
—
PubMed ID:
25630241
Abstract
BackgroundLong 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.ResultsWe 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.ConclusionsOur 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.
Citations by journals
2
4
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10
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16
18
20
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
19 publications, 3.53%
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Scientific Reports
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Scientific Reports
17 publications, 3.15%
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Nature Communications
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Nature Communications
13 publications, 2.41%
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Methods in Molecular Biology
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Methods in Molecular Biology
12 publications, 2.23%
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Nucleic Acids Research
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Nucleic Acids Research
11 publications, 2.04%
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Non-coding RNA
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Non-coding RNA
9 publications, 1.67%
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RNA Biology
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RNA Biology
9 publications, 1.67%
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Wiley interdisciplinary reviews. RNA
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Wiley interdisciplinary reviews. RNA
8 publications, 1.48%
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Cancers
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Cancers
7 publications, 1.3%
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Frontiers in Oncology
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Frontiers in Oncology
7 publications, 1.3%
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Frontiers in Genetics
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Frontiers in Genetics
6 publications, 1.11%
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Nature Reviews Genetics
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Nature Reviews Genetics
6 publications, 1.11%
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Non-coding RNA Research
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Non-coding RNA Research
6 publications, 1.11%
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Briefings in Bioinformatics
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Briefings in Bioinformatics
6 publications, 1.11%
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Proceedings of the National Academy of Sciences of the United States of America
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Proceedings of the National Academy of Sciences of the United States of America
6 publications, 1.11%
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eLife
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eLife
6 publications, 1.11%
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Cold Spring Harbor perspectives in biology
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Cold Spring Harbor perspectives in biology
6 publications, 1.11%
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Frontiers in Cell and Developmental Biology
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Frontiers in Cell and Developmental Biology
5 publications, 0.93%
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Nature Methods
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Nature Methods
5 publications, 0.93%
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Trends in Genetics
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Trends in Genetics
5 publications, 0.93%
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Cell
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Cell
5 publications, 0.93%
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Frontiers in Endocrinology
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Frontiers in Endocrinology
4 publications, 0.74%
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Cells
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Cells
4 publications, 0.74%
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Cell Reports
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Cell Reports
4 publications, 0.74%
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PLoS ONE
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PLoS ONE
4 publications, 0.74%
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Genome Research
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Genome Research
4 publications, 0.74%
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RNA
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RNA
4 publications, 0.74%
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Molecules
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Molecules
3 publications, 0.56%
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Frontiers in Immunology
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Frontiers in Immunology
3 publications, 0.56%
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2
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6
8
10
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Citations by publishers
20
40
60
80
100
120
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Springer Nature
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Springer Nature
110 publications, 20.41%
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Elsevier
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Elsevier
82 publications, 15.21%
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
47 publications, 8.72%
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Frontiers Media S.A.
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Frontiers Media S.A.
35 publications, 6.49%
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Oxford University Press
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Oxford University Press
31 publications, 5.75%
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Wiley
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Wiley
31 publications, 5.75%
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Cold Spring Harbor Laboratory
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Cold Spring Harbor Laboratory
17 publications, 3.15%
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Taylor & Francis
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Taylor & Francis
16 publications, 2.97%
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Public Library of Science (PLoS)
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Public Library of Science (PLoS)
7 publications, 1.3%
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KeAi Communications Co.
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KeAi Communications Co.
6 publications, 1.11%
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Proceedings of the National Academy of Sciences (PNAS)
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Proceedings of the National Academy of Sciences (PNAS)
6 publications, 1.11%
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eLife Sciences Publications
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eLife Sciences Publications
6 publications, 1.11%
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Annual Reviews
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Annual Reviews
6 publications, 1.11%
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Portland Press
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Portland Press
5 publications, 0.93%
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Bentham Science
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Bentham Science
3 publications, 0.56%
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Spandidos Publications
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Spandidos Publications
3 publications, 0.56%
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SAGE
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SAGE
3 publications, 0.56%
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The American Association of Immunologists
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The American Association of Immunologists
2 publications, 0.37%
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American Society for Pharmacology and Experimental Therapeutics
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American Society for Pharmacology and Experimental Therapeutics
2 publications, 0.37%
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The Company of Biologists
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The Company of Biologists
2 publications, 0.37%
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Wolters Kluwer Health
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Wolters Kluwer Health
2 publications, 0.37%
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Baishideng Publishing Group
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Baishideng Publishing Group
2 publications, 0.37%
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Federation of American Societies for Experimental Biology (FASEB)
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Federation of American Societies for Experimental Biology (FASEB)
2 publications, 0.37%
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American Chemical Society (ACS)
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American Chemical Society (ACS)
2 publications, 0.37%
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Royal Society of Chemistry (RSC)
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Royal Society of Chemistry (RSC)
2 publications, 0.37%
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EMBO press
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EMBO press
2 publications, 0.37%
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Genetics Society of America
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Genetics Society of America
2 publications, 0.37%
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American Association for the Advancement of Science (AAAS)
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American Association for the Advancement of Science (AAAS)
2 publications, 0.37%
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Bio-Protocol
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Bio-Protocol, 2, 0.37%
Bio-Protocol
2 publications, 0.37%
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20
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100
120
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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