RNA Modifications in Genomic RNA of Influenza A Virus and the Relationship between RNA Modifications and Viral Infection
Abstract
:1. Introduction
2. Results
2.1. Inosine
2.2. N1-Methyladenosine (m1A)
2.3. Pseudouridine
2.4. N4-Acetylcytidine (ac4C)
2.5. 7-Methylguanosine (m7G)
2.6. N6-Methyladenosine (m6A) and 5-Methylcytosine (m5C)
3. Discussion
4. Materials and Methods
4.1. Cell Lines and Virus
4.2. Viral Infection and RNA Extraction
4.3. RNA Fragmentation
4.4. Removal of Cap-Structure for m7G-RIP
4.5. Antibodies
4.6. Stringent RNA Immunoprecipitation for Inosine, m1A, and m7G
4.7. Mild RNA Immunoprecipitation for Pseudouridine and ac4C
4.8. Deep-Sequencing Sample Preparation and Sequencing
4.9. Bioinformatics
4.10. Data of Transcriptome Experiments
4.11. Proviral Effect of RNA Modification Host Factors
4.12. Data Availability
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Host Factor | RNA Modification | Function | Expression Level Change by Viral Infection in 6 Transcriptome Studies | Provial Effect in 8 Knockout/Knockdown Screening Studies | Viral Protein with Physical Interaction | ||
---|---|---|---|---|---|---|---|
Studies Reporting Upregulation | Studies Reporting Downregulation | Studies Identifying Host Factor | Reference | Reference [26] | |||
ADAR | inosine | writer | 5 | 0 | 0 | n.d. | |
ADARB1 | inosine | writer | 0 | 1 | 0 | n.d. | |
RRP8 | m1A | writer | 0 | 1 | 0 | n.d. | |
TRMT10C | m1A | writer | 1 | 0 | 0 | n.d. | |
TRMT61A | m1A | writer | 0 | 0 | 2 | [26,27] | n.d. |
TRMT6, TRMT61B | m1A | writer | 0 | 0 | 0 | n.d. | |
ALKBH1, ALKBH3 | m1A | eraser | 0 | 0 | 0 | n.d. | |
DKC1 | pseudouridine | writer | 0 | 1 | 0 | n.d. | |
NOP10 | pseudouridine | writer | 1 | 0 | 0 | n.d. | |
PUS1 | pseudouridine | writer | 0 | 1 | 0 | n.d. | |
PUS3 | pseudouridine | writer | 0 | 1 | 0 | n.d. | |
PUS7 | pseudouridine | writer | 0 | 0 | 0 | NA | |
RPUSD2 | pseudouridine | writer | 0 | 1 | 0 | n.d. | |
GAR1, NHP2, PUS10, TRUB1 | pseudouridine | writer | 0 | 0 | 0 | n.d. | |
NAT10 | ac4C | writer | 0 | 1 | 1 | [26] | PB1, NP, NA, M1 |
WDR4 | m7G | writer | 0 | 2 | 0 | n.d. | |
BUD23, METTL1 | m7G | writer | 0 | 0 | 0 | n.d. | |
METTL3 | m6A | writer | 0 | 1 | 0 | n.d. | |
RBM15 | m6A | writer | 0 | 1 | 0 | n.d. | |
VIRMA | m6A | writer | 0 | 1 | 0 | n.d. | |
WTAP | m6A | writer | 2 | 0 | 2 | [28,29] | n.d. |
METTL14, ZC3H13 | m6A | writer | 0 | 0 | 0 | n.d. | |
YTHDC1 | m6A | reader | 3 | 0 | 1 | [30] | n.d. |
YTHDF1 | m6A | reader | 0 | 0 | 1 | [26] | PB2, NP, NA |
YTHDF2 | m6A | reader | 0 | 0 | 1 | [26] | PB2, NP, NA, M1 |
ALKBH5 | m6A | eraser | 0 | 0 | 0 | n.d. | |
FTO | m6A | eraser | 0 | 1 | 0 | n.d. | |
NOP2 | m5C | writer | 0 | 2 | 0 | NP | |
NSUN2 | m5C | writer | 0 | 0 | 0 | NP, NA | |
NSUN3 | m5C | writer | 1 | 0 | 0 | n.d. | |
NSUN6 | m5C | writer | 1 | 0 | 0 | n.d. | |
NSUN7 | m5C | writer | 3 | 1 | 0 | n.d. | |
TRDMT1 | m5C | writer | 1 | 1 | 1 | [31] | n.d. |
NSUN4, NSUN5 | m5C | writer | 0 | 0 | 0 | n.d. |
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Furuse, Y. RNA Modifications in Genomic RNA of Influenza A Virus and the Relationship between RNA Modifications and Viral Infection. Int. J. Mol. Sci. 2021, 22, 9127. https://doi.org/10.3390/ijms22179127
Furuse Y. RNA Modifications in Genomic RNA of Influenza A Virus and the Relationship between RNA Modifications and Viral Infection. International Journal of Molecular Sciences. 2021; 22(17):9127. https://doi.org/10.3390/ijms22179127
Chicago/Turabian StyleFuruse, Yuki. 2021. "RNA Modifications in Genomic RNA of Influenza A Virus and the Relationship between RNA Modifications and Viral Infection" International Journal of Molecular Sciences 22, no. 17: 9127. https://doi.org/10.3390/ijms22179127