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Homo sapiens

ABSTRACT: N6-methyladenosine in Flaviviridae viral RNA genomes regulates infection

PROVIDER: PRJNA325928 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3675080.fastq.gz	Fastqsanger.gz
	SRR3675090.fastq.gz	Fastqsanger.gz
	SRR3675100.fastq.gz	Fastqsanger.gz
	SRR3675081.fastq.gz	Fastqsanger.gz
	SRR3675091.fastq.gz	Fastqsanger.gz

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Discovery of Widespread Host Protein Interactions with the Pre-Replicated Genome of CHIKV using VIR-CLASP

Project description:The pioneer interactions between incoming viral RNA genomes and host proteins are crucial to infection and immune response. Until now, the ability to study these events was lacking. We developed VIR-CLASP (VIRal Cross-Linking And Solid-phase Purification) to characterize the earliest interactions between viral RNA and cellular proteins. We investigated the infection of human cells using Chikungunya virus (CHIKV) and Influenza A virus and identified hundreds of direct RNA-protein interactions. Here, we validate the biological impact of three protein classes that bind CHIKV RNA within minutes of infection. We find CHIKV RNA binds and hijacks the lipid-modifying enzyme FASN for pro-viral activity. We show that CHIKV genomes are N6-methyladenosine modified and that YTHDF1 binds and suppresses its replication. Finally, we find that the innate immune DNA sensor IFI16 associates with CHIKV RNA, reducing viral replication and maturation. Our findings have direct applicability to the investigation of potentially all RNA viruses.

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Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection

Project description:The RNA modification N6-methyladenosine (m6A) can modulate mRNA fate and thus affect many biological processes. We analyzed m6A modification across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, we found that viral activation of innate immune sensing or the endoplasmic reticulum (ER) stress response contributes to the changes in m6A modification in RIOK3 and CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection.

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Project description:N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role in virus life cycle. However, whether m6A methylation can modulate replication of coronaviruses, which contain the largest known RNA genomes, remains elusive. Here, we determined that m6A modifications of porcine epidemic diarrhea coronavirus (PEDV) are exclusively located in the N gene at the 3’-end of genome, and that PEDV infection alters the expression pattern of host proteins involved in m6A modification. Depletion of m6A demethylases significantly increased PEDV replication and gene expression whereas knockdown of m6A methyltransferases slightly decreased PEDV infection. Interestingly, m6A binding proteins YTHDF 2 and 3 significantly inhibited PEDV replication whereas YTHDF1 has an opposite effect. When the major m6A sites in the N gene were mutated, the resultant recombinant PEDVs and PEDV replicons had a significant increase in replication and gene expression. This study illustrates that (i) addition of m6A to PEDV RNA inhibits viral replication, and (ii) both host and viral m6A machinery regulates coronavirus replication.

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N6-methyladenosine modification is not a general trait of viral RNA genomes.

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Project description:N6-methyladenosine (m6A) modification is the most abundant RNA modification in both host mRNA and viral RNA transcripts. Dynamic regulation and recognition of m6A modification widely participate in post-transcriptional regulation of many biological processes. This project aims to define the regulation role of IGF2BP3, a m6A recognition protein, in viral infection, especially in RNA viral infection. In this study, the transcriptomes of Vesicular stomatitis virus (VSV)-infected WT/Igf2bp3-KO RAW264.7 cells and mouse peritoneal macrophages (PMs) were analyzed, suggesting the role of IGF2BP3 in the host's innate immune responses during viral infection and enhancement.

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