Analysis of paramyxovirus transcription and replication by high-throughput sequencing
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We have developed a high-throughput sequencing (HTS) workflow for investigating paramyxovirus transcription and replication. We show that sequencing of oligo-dT selected polyadenylated mRNAs, without considering the orientation of the RNAs from which they had been generated, cannot accurately be used to analyse the abundance of viral mRNAs because genomic RNA co-purifies with the viral mRNAs. The best method is directional sequencing of infected cell RNA that has physically been depletion of ribosomal and mitochondrial RNA followed by bioinformatic steps to differentiate data originating from genomes from viral mRNAs and antigenomes. This approach has the advantage that the abundance of viral mRNA (and antigenomes) and genomes can be analysed and quantified from the same data. We investigated the kinetics of viral transcription and replication during infection of A549 cells with parainfluenza virus type 2 (PIV2), PIV3, PIV5 or mumps virus, and determined the abundance of individual viral mRNAs and readthrough mRNAs. We found that the mRNA abundance gradients differed significantly between all four viruses, but that for each virus the pattern remained relatively stable throughout infection. We suggest that rapid degradation of nonpolyadenylated mRNAs may be primarily responsible for the shape of the mRNA abundance gradient in parainfluenza virus 3, whereas a combination of this factor and disengagement of RNA polymerase at intergenic sequences, particularly those at the NP:P and P:M gene boundaries, may be responsible in the other viruses.
Wignall-Fleming , E B , Hughes , D J , Vattipally , S , Modha , S , Goodbourn , S , Davison , A J & Randall , R E 2019 , ' Analysis of paramyxovirus transcription and replication by high-throughput sequencing ' , Journal of Virology , vol. 93 , no. 17 , e00571-19 . https://doi.org/10.1128/JVI.00571-19
Journal of Virology
Copyright © 2019 Wignall-Fleming et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
DescriptionThis work was supported by the Wellcome Trust (grant nos. 101788/Z/13/Z, 101792/Z/13/Z and 109056/Z/15/A) and the Medical Research Council (grant no. G0801822, MRC-University of Glasgow Centre for Virus Research).
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