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Some host genes were predicted to be targeted by multiple viral siRNAs at distinct locations within the gene.
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We envision that multiple factors could affect the functionality of viral siRNAs and therefore limit their regulatory potential on host targets in vivo.
Successful viruses are able to suppress or evade the production or action of viral siRNAs.
This study demonstrates the ability of a viral miRNA to regulate multiple viral genes.
Antiviral silencing starts with the DCL-dependent production of viral siRNAs (vsiRNAs) (Hamilton and Baulcombe 1999; Parent et al. 2015) (Fig. 1).
Alternatively it could be because AGO2 binds to viral siRNAs that target the viral RNAs directly.
Sequencing of 5'RACE products revealed multiple cleavage sites within the predicted TMV-siRNA-interacting region in CPSF30 mRNA, with only one of them corresponded to the predicted canonical site for a cleavage directed by TMV-Cg-siR221, one of three viral siRNAs predicted to interact with the target (Fig 5C, upper panel).
Sequestration of TMV-Cg-derived siRNAs by the ∼120 KDa protein could therefore limit the activity of viral siRNAs.
Finally, the extent to which viral siRNAs could modulate host gene expression will also depend on the abundance of functional viral siRNAs.
Indeed, viral siRISCs loaded primarily with sense viral siRNAs were observed from plants infected with a tombusvirus [17].
Our results therefore argue against a model with highly structured viral genomic RNA being the precursors of viral siRNAs.
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