Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
Department of Microbiology and Immunology and Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
Sci Rep. 2020 Apr 14;10(1):6389. doi: 10.1038/s41598-020-63101-9.
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.
R 环是 RNA-DNA 杂交序列，是各种生物学过程中的新兴参与者，存在于原核和真核细胞中。在病毒中，对 R 环的研究有限，其功能的重要性也知之甚少。在这里，我们通过计算方法研究了超过 6000 种病毒基因组中 R 环形成序列（RLFS）的普遍性、分布和位置。在 1586 种病毒基因组中鉴定出了 14637 个 RLFS 基因座。超过 70%的 RLFS 阳性基因组是双链 DNA 病毒。在疱疹病毒目中，所有成员都存在 RLFS，而在 Ligamenvirales 目中则没有预测到 RLFS。对所有 RLFS 阳性基因组中 RLFS 密度的分析表明，疱疹病毒基因组中的 RLFS 密度异常高，RLFS 密度在重复区域（如末端重复序列（TRs））中特别丰富。疱疹病毒之间的 TR 中的 RLFS 位置保守。通过实验验证了计算机预测的 RLFS，证实了卡波西肉瘤相关疱疹病毒（KSHV）的 TR 和病毒 Bcl-2 启动子中的 R 环形成。这些预测和验证支持未来对 RLFS 在调节疱疹病毒复制、转录和基因组维持中的作用进行分析。
