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R-loop Forming Structure Prediction in Viral Genomes

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Thidathip Wongsurawat1, Piroon Jenjaroenpun1, Preecha Patumcharoenpol1, David Ussery1, and Intawat Nookaew1

Background: An R-loop is a triple-stranded nucleic acid structure comprising nascent RNA hybridized with its corresponding DNA template strand, while leaving the non-template DNA single-stranded. R-loop formation has been observed in a wide range of organisms, from bacteria to mammals. Possible roles of R-loops in transcription, telomere maintenance, genome instability, epigenetic regulation as well as disease involvement have been demonstrated. In viruses, R-loop detection is rare and their functional importance is poorly understood. Thus, we aim to investigate the prevalence and distribution of R-loop in the viral genomes.

Results: We use 6,153 viral complete genomes collected from NCBI as a reference set. R-loop prediction by QmRLFS-finder ( is performed on these genomes. A total of 1,586 out of 6,153 genomes contain at least one R-loop. The number of R-loops and the ratio of R-loop length per kb of the viral genome are presented. We find that herpesviruses are enriched with R-loops, especially human herpesvirus. In addition, the distribution of these R-loops throughout the genome is not uniform.

Conclusion: We report here the results of a search for the existence and prevalence of R-loops in viral genomes. The pervasiveness of R-loops, their enrichment at specific genomic locations suggest that these structural entities may represent a novel class of functional elements in herpesviruses. Future analysis will be focused on the R-loop-positive genes and regulatory elements of these viruses.

This work is funded in part from the Arkansas Research Alliance and the Helen Adams & Arkansas Research Alliance Professor & Chair.

1Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205