Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination. (4th November 2020)

• Record Type: Journal Article
• Authors: Yang, Yiyan; Yan, Wei; Hall, A Brantley; Jiang, Xiaofang
• Editors: Rasmus, Nielsen
• Is Part Of: Molecular biology and evolution. Volume 38:Number 4(2021)
• Page Start: 1241
• Page End: 1248
• Publication Date: 2020-11-04
• Subjects: Key words: coronavirus -- transcriptional regulatory sequences (TRS) -- recombination; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msaa281
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesized but not yet verified that TRS sites are prone to recombination events. Here, we developed a tool called SuPER to systematically identify TRS in coronavirus genomes and then investigated whether recombination is more common at TRS. We ran SuPER on 506 coronavirus genomes and identified 465 TRS-L and 3, 509 TRS-B. We found that the TRS-L core sequence (CS) and the secondary structure of the leader sequence are generally conserved within coronavirus genera but different between genera. By examining the location of recombination breakpoints with respect to TRS-B CS, we observed that recombination hotspots are more frequently colocated with TRS-B sites than expected.