Coronavirus cis-Acting RNA Elements

Adv Virus Res. 2016:96:127-163. doi: 10.1016/bs.aivir.2016.08.007. Epub 2016 Sep 6.


Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA-RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.

Keywords: Coronavirus; Genome packaging; RNA structure; RNA virus; Replication; cis-Acting element.

Publication types

  • Review

MeSH terms

  • Coronavirus / genetics*
  • Coronavirus / metabolism
  • Coronavirus Infections / virology
  • Epithelial Cells / metabolism
  • Epithelial Cells / virology
  • Gene Expression Regulation, Viral*
  • Genome Size
  • Genome, Viral*
  • Host-Pathogen Interactions
  • Humans
  • Nucleic Acid Conformation
  • RNA, Viral / biosynthesis
  • RNA, Viral / genetics*
  • Regulatory Elements, Transcriptional*
  • Transcription, Genetic*
  • Virus Replication


  • RNA, Viral