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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 21, 2023 |
| Title |
ADAR1 biology can hinder effective antiviral RNA interference |
| Organisms |
Homo sapiens; Canis lupus familiaris; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Viruses constantly evolve and adapt to the antiviral defenses of their hosts. The biology of viral circumvention of these selective pressures can often be attributed to the acquisition of novel antagonistic gene products or by rapid genome change that prevents host recognition. To study viral evasion of RNA interference (RNAi)-based defenses, we established a robust antiviral system in mammalian cells using recombinant Sendai virus designed to be targeted by endogenous host microRNAs (miRNAs) with perfect complementarity. Using this system, we previously demonstrated the intrinsic ability of positive-strand RNA viruses to escape this selective pressure via homologous recombination, which was not observed in negative-strand RNA viruses. Here we show that given extensive time, escape of miRNA-targeted Sendai virus was enabled by host adenosine deaminase acting on RNA 1 (ADAR1). Independent of the viral transcript targeted, ADAR1 editing resulted in disruption of the miRNA-silencing motif, suggesting an intolerance for extensive RNA:RNA interactions necessary for antiviral RNAi. This was further supported in N. benthamiana, where exogenous expression of ADAR1 interfered with endogenous RNAi. Together, these results suggest that ADAR1 diminishes the effectiveness of RNAi and may explain why it is absent in species that utilize this antiviral defense system.
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| Overall design |
RNA-sequencing of mammalian cells lines infected with recombinant Sendai viruses that have sequences with perfectly complemenatrity to host miRNAs added into the 3' UTR of the N gene or P gene to produce an artificial miRNA-based antiviral RNAi. Cell lines, which include A549s, STAT1 KO A549s, STAT1/ADAR1 Double KO A549s, MEFs, and MDCKs were infected and RNA was collected at various timepoints post infection to assess host response and changes to viral genome. Samples where differential gene expression in host cells is assessed are in triplicate.
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| Contributor(s) |
Uhl S, tenOever BR |
| Citation(s) |
37017521 |
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| Submission date |
Mar 17, 2023 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Skyler Andrew Uhl |
| E-mail(s) |
skyleruhl@gmail.com
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Microbiology
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| Lab |
Lim & tenOever labs
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| Street address |
1 Gustave L. levy Pl.
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (5)
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| GPL18460 |
Illumina HiSeq 1500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL25760 |
Illumina NovaSeq 6000 (Canis lupus familiaris) |
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| Samples (45)
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| GSM7103647 |
WT A549, rSeV-N5T, 1dpi,1 |
| GSM7103648 |
WT A549, rSeV-N5T, 1dpi,2 |
| GSM7103649 |
WT A549, rSeV-N5T, 1dpi,3 |
| GSM7103650 |
WT A549, rSeV-N5R, 1dpi,1 |
| GSM7103651 |
WT A549, rSeV-N5R, 1dpi,2 |
| GSM7103652 |
WT A549, rSeV-N5R, 1dpi,3 |
| GSM7103653 |
WT A549, rSeV-P5T, 1dpi,1 |
| GSM7103654 |
WT A549, rSeV-P5T, 1dpi,2 |
| GSM7103655 |
WT A549, rSeV-P5T, 1dpi,3 |
| GSM7103656 |
WT A549, MOCK, 2dpi,1 |
| GSM7103657 |
WT A549, MOCK, 2dpi,2 |
| GSM7103658 |
WT A549, MOCK, 2dpi,3 |
| GSM7103659 |
WT A549, rSeV-N5T, 2dpi,1 |
| GSM7103660 |
WT A549, rSeV-N5T, 2dpi,2 |
| GSM7103661 |
WT A549, rSeV-N5T, 2dpi,3 |
| GSM7103662 |
WT A549, rSeV-N5R, 2dpi,1 |
| GSM7103663 |
WT A549, rSeV-N5R, 2dpi,2 |
| GSM7103664 |
WT A549, rSeV-N5R, 2dpi,3 |
| GSM7103665 |
WT A549, rSeV-P5T, 2dpi,1 |
| GSM7103666 |
WT A549, rSeV-P5T, 2dpi,2 |
| GSM7103667 |
WT A549, rSeV-P5T, 2dpi,3 |
| GSM7103668 |
WT A549,Mock AdV transduction,1 |
| GSM7103669 |
WT A549,Mock AdV transduction,2 |
| GSM7103670 |
WT A549,Mock AdV transduction,3 |
| GSM7103671 |
STAT1 ADAR1 double KO A549, Mock AdV transduction,1 |
| GSM7103672 |
STAT1 ADAR1 double KO A549, Mock AdV transduction,2 |
| GSM7103673 |
STAT1 ADAR1 double KO A549, Mock AdV transduction,3 |
| GSM7103674 |
STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1,1 |
| GSM7103675 |
STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1,2 |
| GSM7103676 |
STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1,3 |
| GSM7103677 |
WT A549, Amplicon Seq, rSeV-N5T, 2dpi |
| GSM7103678 |
WT A549, Amplicon Seq, rSeV-N5T, 4dpi |
| GSM7103679 |
WT A549, Amplicon Seq, rSeV-N5T, 8dpi |
| GSM7103680 |
WT A549, rSeV-N5R, 4dpi |
| GSM7103681 |
WT A549, rSeV-N1T, 6dpi |
| GSM7103682 |
WT A549, rSeV-N5T, 10dpi |
| GSM7103683 |
STAT1 KO A549, rSeV-N5T, 4dpi |
| GSM7103684 |
WT A549, rSeV-P5T, 8dpi, 1 |
| GSM7103685 |
WT A549, rSeV-P5T, 8dpi, 2 |
| GSM7103686 |
STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1, rSeV-N5T, 8dpi |
| GSM7103687 |
MDCK, rSeV-N5T, 8dpi |
| GSM7103688 |
MEF, rSeV-N5T, 8dpi |
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| Relations |
| BioProject |
PRJNA945880 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE227592_RAW.tar |
13.3 Mb |
(http)(custom) |
TAR (of CSV, SF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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