Small noncoding RNAs (
sncRNAs), such as
microRNAs (
miRNA), virus-derived
sncRNAs, and more recently identified
tRNA-derived
RNA fragments, are critical to posttranscriptional control of genes. Upon
viral infection, host cells alter their
sncRNA expression as a defense mechanism, while viruses can circumvent host defenses and promote their own propagation by affecting host cellular
sncRNA expression or by expressing viral
sncRNAs. Therefore, characterizing
sncRNA profiles in response to
viral infection is an important tool for understanding host-virus interaction, and for
antiviral strategy development. Human metapneumovirus (hMPV), a recently identified pathogen, is a major cause of lower
respiratory tract infections in infants and children. To investigate whether
sncRNAs play a role in hMPV
infection, we analyzed the changes in
sncRNA profiles of airway epithelial cells in response to hMPV
infection using ultrahigh-throughput sequencing. Of the cloned
sncRNAs,
miRNA was dominant in A549 cells, with the percentage of
miRNA increasing in a time-dependent manner after the
infection. In addition, several hMPV-derived
sncRNAs and corresponding
ribonucleases for their biogenesis were identified. hMPV M2-2
protein was revealed to be a key
viral protein regulating
miRNA expression. In summary, this study revealed several novel aspects of hMPV-mediated
sncRNA expression, providing a new perspective on hMPV-host interactions.