Large-Scale Chromatin Immunoprecipitation with Promoter Sequence Microarray Analysis of the Interaction of the NSs Protein of Rift Valley Fever Virus with Regulatory DNA Regions of the Host Genome

Abstract

dRift Valley fever virus (RVFV) is a highly pathogenic Phlebovirus that infects humans and ruminants. Initially confined to Africa, RVFV has spread outside Africa and presently represents a high risk to other geographic regions. It is responsible for high fatality rates in sheep and cattle. In humans, RVFV can induce hepatitis, encephalitis, retinitis, or fatal hemorrhagic fever. The nonstructural NSs protein that is the major virulence factor is found in the nuclei of infected cells where it associates with cellular transcription factors and cofactors. In previous work, we have shown that NSs interacts with the promoter region of the beta interferon gene abnormally maintaining the promoter in a repressed state. In this work, we performed a genome-wide analysis of the interactions between NSs and the host genome using a genome-wide chromatin immunoprecipitation combined with promoter sequence microarray, the ChIP-on-chip technique. Several cellular promoter regions were identified as significantly interacting with NSs, and the establishment of NSs interactions with these regions was often found linked to deregulation of expression of the corresponding genes. Among annotated NSs-interacting genes were present not only genes regulating innate immunity and inflammation but also genes regulating cellular pathways that have not yet been identified as targeted by RVFV. Several of these pathways, such as cell adhesion, axonal guidance, development, and coagulation were closely related to RVFV-induced disorders. In particular, we show in this work that NSs targeted and modified the expression of genes coding for coagulation factors, demonstrating for the first time that this hemorrhagic virus impairs the host coagulation cascade at the transcriptional level.

Virulence Factor NSs of Rift Valley Fever Virus Recruits the F-Box Protein FBXO3 To Degrade Subunit p62 of General Transcription Factor TFIIH

“…In any case, the removal of FBXO3 from the nucleus may have implications for NSs regulation, liberating NSs to pursue another activity such as, e.g., PKR degradation. Interestingly, a recent chromatin immunoprecipitation-DNA sequencing (CHIP-Seq) study revealed that RVFV NSs also downregulates the promoter of the FBXO3 gene (43). Although in our experiments mRNA levels of FBXO3 were unaffected by NSs at 6 h postinfection (p.i.…”

“…In addition to the effects on IFN induction, host transcription, inflammatory cytokine production, p53 regulation, and PKR degradation, RVFV NSs induces chromosomal anomalies (44) and regulates many other genes involved in innate immunity, inflammation, cell adhesion, axonal guidance, development, and blood coagulation (43). Thus, NSs of RVFV is a multifunctional protein that dysregulates and damages the host at several levels.…”

Non-Structural Proteins of Arthropod-Borne Bunyaviruses: Roles and Functions

“…NSs does not only interact with promoters of the innate-immunity regulating genes such as IFN-β, and those involved in inflammation, IL10Rb, but also with the promoters of a number of genes involved in coagulation, cell adhesion and neurological functions. The effect on the expression of these genes can help us to further understand the pathological effects seen upon RVFV infection [59]. …”

The role of signal transducer and activator of transcription 3 in Rift Valley fever virus infection

“…While fos is widely studied in multiple diseases as well as its role in apoptosis, the nuclear receptor family of intracellular transcription factors is understudied, especially in the context of acute infection. Furthermore, a previous study identified NSs as interacting with the nr4a2 promoter through chromatin immunoprecipitation coupled with DNA microarray (ChIP-chip) analysis, prompting further examination of this particular gene (Benferhat et al, 2012). To determine if the observed STAT3 effects are due to a direct interaction of STAT3 with the nr4a2 promoter, ChIP was performed.…”

“…NSs has previously been detected at the IFN-β promoter (Le May et al, 2008) and bound to pericentromeric DNA (Mansuroglu et al, 2010). The interaction of NSs with promoters was also studied on a global scale using the ChIP-on-chip technique (Benferhat et al, 2012). Supplemental data from this publication indicated that NSs was present at the promoter of nr4a2 and fosl2 , a fos family member.…”