Abstract
Viral interfering RNA (viRNA) has been identified from several viral genomes via directly deep RNA sequencing of the virus-infected cells, including zika virus (ZIKV). Once produced by endoribonuclease Dicer, viRNAs are loaded onto the Argonaute (AGO) family proteins of the RNA-induced silencing complexes (RISCs) to pair with their RNA targets and initiate the cleavage of target genes. However, the identities of functional ZIKV viRNAs and their viral RNA targets remain largely unknown. Our recent study has shown that ZIKV capsid protein interacted with Dicer and antagonized its endoribonuclease activity, which requires its histidine residue at the 41st amino acid. Accordingly, the engineered ZIKV-H41R loss-of-function (LOF) mutant virus no longer suppresses Dicer enzymatic activity nor inhibits miRNA biogenesis in NSCs. By combining AGO-associated RNA sequencing, deep sequencing analysis in ZIKV-infected human neural stem cells (NSCs), and miRanda target scanning, we defined 29 ZIKV derived viRNA profiles in NSCs, and established a complex interaction network between the viRNAs and their viral targets. More importantly, we found that viRNA production from the ZIKV mRNA is dependent on Dicer function and is a limiting factor for ZIKV virulence in NSCs. As a result, much higher levels of viRNAs generated from the ZIKV-H41R virus-infected NSCs. Therefore, our mapping of viRNAs to their RNA targets paves a way to further investigate how viRNAs play the role in anti-viral mechanisms, and perhaps other unknown biological functions.
Highlights
Zika virus (ZIKV), a member of the Flaviviridae family, is a single-stranded positive-sense RNA virus
As Viral interfering RNA (viRNA) are loaded into the RNA-induced silencing complexes (RISCs) for pairing with their RNA targets and initiating cleavage of the target genes, we decided to perform AGO-associated RNA sequencing in zika virus (ZIKV)-infected neural stem cells (NSCs) (Figure 1A)
Due to the undetectable viRNAs in mammalian somatic cells infected with some wild-type human viruses such as EV71, IAV, and Sindbis virus (Parameswaran et al, 2010; Girardi et al, 2013; Backes et al, 2014; Bogerd et al, 2014), the role of RNA interference (RNAi) as a critical mammalian antiviral defense mechanism remains under-debate
Summary
Zika virus (ZIKV), a member of the Flaviviridae family, is a single-stranded positive-sense RNA virus. The most concern of ZIKV is its ability to induce fetal microcephaly and congenital Zika syndrome (Rasmussen et al, 2016; Hoen et al, 2018). ZIKV has an intrinsic tropism for neural stem and progenitor cells (NSCs) in cell cultures, brain organoids and fetal brain slices (Cugola et al, 2016; Dang et al, 2016; Garcez et al, 2016; Liang et al, 2016; Qian et al, 2016; Tang et al, 2016), whereas ZIKV has much lower infectivity to more differentiated immature or mature neurons (Li et al, 2016a; Muffat et al, 2018). Mammalian multipotent stem cells, including NSCs, intrinsically produce little interferon (IFN) and response poorly to IFN treatment compare to somatic cells (Hong and Carmichael, 2013; Wu et al, 2019), and these cells often rely on other machineries once the virus breaches the surveillance (Ding and Voinnet, 2007)
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