Abstract
R-loops are RNA-DNA hybrid sequences that are emerging players in various biological processes, occurring in both prokaryotic and eukaryotic cells. In viruses, R-loop investigation is limited and functional importance is poorly understood. Here, we performed a computational approach to investigate prevalence, distribution, and location of R-loop forming sequences (RLFS) across more than 6000 viral genomes. A total of 14637 RLFS loci were identified in 1586 viral genomes. Over 70% of RLFS-positive genomes are dsDNA viruses. In the order Herpesvirales, RLFS were presented in all members whereas no RLFS was predicted in the order Ligamenvirales. Analysis of RLFS density in all RLFS-positive genomes revealed unusually high RLFS densities in herpesvirus genomes, with RLFS densities particularly enriched within repeat regions such as the terminal repeats (TRs). RLFS in TRs are positionally conserved between herpesviruses. Validating the computationally-identified RLFS, R-loop formation was experimentally confirmed in the TR and viral Bcl-2 promoter of Kaposi sarcoma-associated herpesvirus (KSHV). These predictions and validations support future analysis of RLFS in regulating the replication, transcription, and genome maintenance of herpesviruses.
Highlights
R-loops are RNA-DNA hybrid sequences that are emerging players in various biological processes, occurring in both prokaryotic and eukaryotic cells
We analyzed a total of 6153 viral genomes, which are 2663 double-stranded DNA, 1556 single-stranded RNA, 905 single-stranded DNA, 278 double-stranded RNA, and 751 other viruses based on the Baltimore classification scheme (Supplementary Table 1)
We identified 14637 merged RLFS (mRLFS) found in 1586 genomes
Summary
R-loops are RNA-DNA hybrid sequences that are emerging players in various biological processes, occurring in both prokaryotic and eukaryotic cells. Validating the computationally-identified RLFS, R-loop formation was experimentally confirmed in the TR and viral Bcl-2 promoter of Kaposi sarcomaassociated herpesvirus (KSHV) These predictions and validations support future analysis of RLFS in regulating the replication, transcription, and genome maintenance of herpesviruses. G-quadruplexes are present in several viral genomes e.g., human immunodeficiency virus (HIV- 1), Epstein–Barr virus (EBV), and human papillomavirus (HPV) Another non-canonical nucleic acid structure called an R-loop or RNA:DNA structure is preferentially formed within G-rich sequences and possesses greater thermodynamic stability than the original DNA:DNA duplex[6]. Both studies highlighted the investigation of R-loop formation in herpesviruses
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