Influenza Virus and Chromatin: Role of the CHD1 Chromatin Remodeler in the Virus Life Cycle

Abstract

Influenza A virus requires ongoing cellular transcription to carry out the cap-snatching process. Chromatin remodelers modify chromatin structure to produce an active or inactive conformation, which enables or prevents the recruitment of transcriptional complexes to specific genes; viral transcription thus depends on chromatin dynamics. Influenza virus polymerase associates with chromatin components of the infected cell, such as RNA polymerase II (RNAP II) or the CHD6 chromatin remodeler. Here we show that another CHD family member, CHD1 protein, also interacts with the influenza virus polymerase complex. CHD1 recognizes the H3K4me3 (histone 3 with a trimethyl group in lysine 4) histone modification, a hallmark of active chromatin. Downregulation of CHD1 causes a reduction in viral polymerase activity, viral RNA transcription, and the production of infectious particles. Despite the dependence of influenza virus on cellular transcription, RNAP II is degraded when viral transcription is complete, and recombinant viruses unable to degrade RNAP II show decreased pathogenicity in the murine model. We describe the CHD1-RNAP II association, as well as the parallel degradation of both proteins during infection with viruses showing full or reduced induction of degradation. The H3K4me3 histone mark also decreased during influenza virus infection, whereas a histone mark of inactive chromatin, H3K27me3, remained unchanged. Our results indicate that CHD1 is a positive regulator of influenza virus multiplication and suggest a role for chromatin remodeling in the control of the influenza virus life cycle. IMPORTANCEAlthough influenza virus is not integrated into the genome of the infected cell, it needs continuous cellular transcription to synthesize viral mRNA. This mechanism implies functional association with host genome expression and thus depends on chromatin dynamics. Influenza virus polymerase associates with transcription-related factors, such as RNA polymerase II, and with chromatin remodelers, such as CHD6. We identified the association of viral polymerase with another chromatin remodeler, the CHD1 protein, which positively modulated viral polymerase activity, viral RNA transcription, and virus multiplication. Once viral transcription is complete, RNAP II is degraded in infected cells, probably as a virus-induced mechanism to reduce the antiviral response. CHD1 associated with RNAP II and paralleled its degradation during infection with viruses that induce full or reduced degradation. These findings suggest that RNAP II degradation and CHD1 degradation cooperate to reduce the antiviral response. Influenza A virus contains eight single-stranded RNA segments of negative polarity (viral RNA [vRNA]) that form viral ribonucleoproteins (vRNP) by association with a trimeric polymerase complex that consists of the PA, PB1, and PB2 subunits and the nucleoprotein (NP). These vRNP are the functional units for RNA transcription and replication, which are restricted to the nucleus of the infected cell (1). For viral RNA r...

Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients

“…The recombinant minireplicon assay was performed essentially as described [47]. In brief, cultures of HEK293T cells (2.5 × 10 6 cells) were transfected with a mixture of plasmids expressing the RNP components (pCMVPA, 2.5 ng; pCMVPB1, 12.5 ng; pCMVPB2, 12.5 ng; and pCMVNP, 500 ng) and a genomic plasmid expressing a viral RNA (vRNA)-like chloramphenicol acetyltransferase reporter gene (pHHCAT, 500 ng) using the calcium phosphate technique [48].…”

Downregulation of Aedes aegypti chromodomain helicase DNA binding protein 7/Kismet by Wolbachia and its effect on dengue virus replication

“…Despite extensive characterization of CHD family proteins, their role in shaping host-pathogen interactions has not been much investigated. Yet, there are few reports supporting the involvement of CHD1 in the case of influenza A virus, and both CHD1 and CHD2 in the case of HIV as positive regulators2627. Furthermore, RNAi screen carried out in D. melanogaster S2 cells identified the involvement of CHD7/Kismet in antimicrobial humoral response50.…”

“…Recently, it has been reported that CHD1 and CHD2 proteins play a pivotal role in the replication of influenza and HIV viruses2627. Both viruses replicate inside the nucleus.…”

“…Both viruses replicate inside the nucleus. Interestingly, it has further been demonstrated that CHD1 interacts with RNA polymerase II to facilitate the replication of influenza A virus27. Little is known about the role of CHD7/Kismet in the context of virus infection.…”

“…Members of the CHD family have been found to be involved in replication of Human Immunodeficiency virus (HIV) and Influenza A virus2627. All the CHD protein family members have a pair of chromodomains at their N-terminus along with one sucrose non-fermenting (SNF2) domain in the centre25.…”