Mapping the Small RNA Content of Simian Immunodeficiency Virions (SIV)

Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodefi...

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Published inPloS one Vol. 8; no. 9; p. e75063
Main Authors Brameier, Markus, Ibing, Wiebke, Höfer, Katharina, Montag, Judith, Stahl-Hennig, Christiane, Motzkus, Dirk
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 23.09.2013
Public Library of Science (PLoS)
Subjects
Analysis
Base Sequence
Binding sites
Cell culture
Cell Line
Deoxyribonucleic acid
DNA
Enzymes
Exosomes
Exosomes - metabolism
Gene mapping
Genomes
Genomics
Health aspects
High-Throughput Nucleotide Sequencing
HIV
Human immunodeficiency virus
Humans
Immunodeficiency
Infections
Isoacceptors
MicroRNAs
MicroRNAs - genetics
MicroRNAs - metabolism
Molecular Sequence Data
Nucleoli
Nucleotide sequence
Packaging
Physiology
Polyethylene glycol
Ribonucleic acid
RNA
RNA polymerase
RNA, Ribosomal - genetics
RNA, Ribosomal - metabolism
RNA, Small Cytoplasmic - genetics
RNA, Small Cytoplasmic - metabolism
RNA, Small Nucleolar - genetics
RNA, Small Nucleolar - metabolism
RNA, Transfer, Lys - genetics
RNA, Transfer, Lys - metabolism
RNA, Untranslated - metabolism
RNA, Viral - genetics
RNA, Viral - metabolism
Sequences
Signal Recognition Particle - genetics
Signal Recognition Particle - metabolism
Simian immunodeficiency virus
Simian Immunodeficiency Virus - genetics
Stem cells
Virion - genetics
Virions
Viruses
Germany
Online AccessGet full text
ISSN1932-6203
1932-6203
DOI10.1371/journal.pone.0075063

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Abstract Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA(Lys3) and tRNA(Lys) isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
AbstractList Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA(Lys3) and tRNA(Lys) isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac 239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA Lys3 and tRNA Lys isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV .sub.mac 239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA.sup.Lys3 and tRNA.sup.Lys isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA(Lys3) and tRNA(Lys) isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA(Lys3) and tRNA(Lys) isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNALys3 and tRNALys isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
Audience Academic
Author Brameier, Markus
Stahl-Hennig, Christiane
Motzkus, Dirk
Höfer, Katharina
Ibing, Wiebke
Montag, Judith
AuthorAffiliation 1   Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
2   Unit of Infection Models, German Primate Center, Göttingen, Germany
French National Center for Scientific Research - Institut de biologie moléculaire et cellulaire, France
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Competing Interests: The authors have declared that no competing interests exist.
Current address: Molecular and Cellular Physiology, Hannover Medical School, Hannover, Germany
Conceived and designed the experiments: DM. Performed the experiments: WI KH. Analyzed the data: DM MB JM. Contributed reagents/materials/analysis tools: CSH. Wrote the manuscript: MB KH JM CSH DM.
Current address: Department of Vascular and Endovascular Surgery, Düsseldorf University Hospital, Düsseldorf, Germany
Current address: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
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Snippet Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of...
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StartPage e75063
SubjectTerms Analysis
Base Sequence
Binding sites
Cell culture
Cell Line
Deoxyribonucleic acid
DNA
Enzymes
Exosomes
Exosomes - metabolism
Gene mapping
Genomes
Genomics
Health aspects
High-Throughput Nucleotide Sequencing
HIV
Human immunodeficiency virus
Humans
Immunodeficiency
Infections
Isoacceptors
MicroRNAs
MicroRNAs - genetics
MicroRNAs - metabolism
Molecular Sequence Data
Nucleoli
Nucleotide sequence
Packaging
Physiology
Polyethylene glycol
Ribonucleic acid
RNA
RNA polymerase
RNA, Ribosomal - genetics
RNA, Ribosomal - metabolism
RNA, Small Cytoplasmic - genetics
RNA, Small Cytoplasmic - metabolism
RNA, Small Nucleolar - genetics
RNA, Small Nucleolar - metabolism
RNA, Transfer, Lys - genetics
RNA, Transfer, Lys - metabolism
RNA, Untranslated - metabolism
RNA, Viral - genetics
RNA, Viral - metabolism
Sequences
Signal Recognition Particle - genetics
Signal Recognition Particle - metabolism
Simian immunodeficiency virus
Simian Immunodeficiency Virus - genetics
Stem cells
Virion - genetics
Virions
Viruses
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Title Mapping the Small RNA Content of Simian Immunodeficiency Virions (SIV)
URI https://www.ncbi.nlm.nih.gov/pubmed/24086438
https://www.proquest.com/docview/1435431690
https://www.proquest.com/docview/1443406596
https://pubmed.ncbi.nlm.nih.gov/PMC3781035
https://doaj.org/article/0ed141c9b4b54837bdaa001f113bc20c
http://dx.doi.org/10.1371/journal.pone.0075063
Volume 8
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