FIG. 4.

Model for higher-order structure of the 5′-proximal genomic acceptor region and proposed pathways for the switch in cis and in trans. (A) Mapped genomic acceptor window (boxed) for high-frequency template switching in the context of stem-loops I, II, and III in the BCoV genome. The 65-nt leader sequence is shaded, nucleotides making up the leader-associated intergenic core sequence (UCUAAAC) in the loop of stem-loop II are underlined, and the start codon for ORF 1 is boxed. (B) Model for positive-strand-to-positive-strand template switching in cis during synthesis of negative-strand templates for sgmRNA production, as illustrated by Enjuanes et al. (46, 58). The matching donor and acceptor regions are checkered. Base-paired regions between the positive-strand genome and negative-strand nascent RNA are indicated by vertical lines. The transcription complex is depicted by the shaded oval. (C) Model for positive-strand-to-positive-strand template switching in trans.