Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity.

Autor:	Zeng W; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2280, USA., Jiang S; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2280, USA., Kong X; Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA 92697-1700, USA., El-Ali N; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2280, USA., Ball AR Jr; Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA 92697-1700, USA., Ma CI; Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA 92697-1700, USA., Hashimoto N; Department of Regenerative Medicine, National Center for Geriatrics and Gerontology, 7-430 Morioka, Oobu, Aichi 474-8522, Japan., Yokomori K; Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA 92697-1700, USA kyokomor@uci.edu., Mortazavi A; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA ali.mortazavi@uci.edu.; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2280, USA.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2016 Dec 01; Vol. 44 (21), pp. e158. Date of Electronic Publication: 2016 Aug 26.
DOI:	10.1093/nar/gkw739
Abstrakt:	Myoblasts are precursor skeletal muscle cells that differentiate into fused, multinucleated myotubes. Current single-cell microfluidic methods are not optimized for capturing very large, multinucleated cells such as myotubes. To circumvent the problem, we performed single-nucleus transcriptome analysis. Using immortalized human myoblasts, we performed RNA-seq analysis of single cells (scRNA-seq) and single nuclei (snRNA-seq) and found them comparable, with a distinct enrichment for long non-coding RNAs (lncRNAs) in snRNA-seq. We then compared snRNA-seq of myoblasts before and after differentiation. We observed the presence of mononucleated cells (MNCs) that remained unfused and analyzed separately from multi-nucleated myotubes. We found that while the transcriptome profiles of myoblast and myotube nuclei are relatively homogeneous, MNC nuclei exhibited significant heterogeneity, with the majority of them adopting a distinct mesenchymal state. Primary transcripts for microRNAs (miRNAs) that participate in skeletal muscle differentiation were among the most differentially expressed lncRNAs, which we validated using NanoString. Our study demonstrates that snRNA-seq provides reliable transcriptome quantification for cells that are otherwise not amenable to current single-cell platforms. Our results further indicate that snRNA-seq has unique advantage in capturing nucleus-enriched lncRNAs and miRNA precursors that are useful in mapping and monitoring differential miRNA expression during cellular differentiation. (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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