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Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E8987-E8995. doi: 10.1073/pnas.1712108114. Epub 2017 Oct 10.

Broad role for YBX1 in defining the small noncoding RNA composition of exosomes.

Author information

1
Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720.
2
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720.
3
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712.
4
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712.
5
Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720; schekman@berkeley.edu lambowitz@austin.utexas.edu.
6
Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.
7
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712; schekman@berkeley.edu lambowitz@austin.utexas.edu.

Abstract

RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation. We found that EV-associated transcripts are dominated by full-length, mature transfer RNAs (tRNAs) and other small noncoding RNAs (ncRNAs) encapsulated within vesicles. A substantial proportion of the reads mapping to protein-coding genes, long ncRNAs, and antisense RNAs were due to DNA contamination on the surface of vesicles. Nevertheless, sequences mapping to spliced mRNAs were identified within HEK293T cell EVs and exosomes, among the most abundant being transcripts containing a 5' terminal oligopyrimidine (5' TOP) motif. Our results indicate that the RNA-binding protein YBX1, which is required for the sorting of selected miRNAs into exosomes, plays a role in the sorting of highly abundant small ncRNA species, including tRNAs, Y RNAs, and Vault RNAs. Finally, we obtained evidence for an EV-specific tRNA modification, perhaps indicating a role for posttranscriptional modification in the sorting of some RNA species into EVs. Our results suggest that EVs and exosomes could play a role in the purging and intercellular transfer of excess free RNAs, including full-length tRNAs and other small ncRNAs.

KEYWORDS:

RNA-binding protein; RNA-seq; extracellular vesicle; posttranscriptional modification; thermostable group II intron reverse transcriptase

PMID:
29073095
PMCID:
PMC5663387
DOI:
10.1073/pnas.1712108114
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

Conflict of interest statement: Thermostable group II intron reverse transcriptase (TGIRT) enzymes and methods for their use are the subject of patents and patent applications that have been licensed by the University of Texas and East Tennessee State University to InGex, LLC. A.M.L., some former and present members of the A.M.L. laboratory, and the University of Texas are minority equity holders in InGex, LLC and receive royalty payments from the sale of TGIRT enzymes and kits and from the sublicensing of intellectual property to other companies.

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