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Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing.

Journal article
Authors Cecilia Lässer
Ganesh V Shelke
Ashish Yeri
Dae-Kyum Kim
Rossella Crescitelli
Stefania Raimondo
Margareta Sjöstrand
Yong Song Gho
Kendall Van Keuren Jensen
Jan Lötvall
Published in RNA biology
Volume 14
Issue 1
Pages 58-72
ISSN 1555-8584
Publication year 2017
Published at Krefting Research Centre
Pages 58-72
Language en
Links dx.doi.org/10.1080/15476286.2016.12...
www.ncbi.nlm.nih.gov/entrez/query.f...
Keywords Exosomes, extracellular RNA, extracellular vesicles, microarray, next-generation sequencing, proteomics, RNA, transcriptomics
Subject categories Cell Biology

Abstract

Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analyzed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the 2 exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

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