Open Access
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 typeJournal Article
Publication date2015-01-29
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.

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