A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs

PeerJ

article

Ryan J. Andrews¹  Collin A. O’Leary¹  Walter N. Moss¹ 

[1] The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University

关键词: RNA;    Herpes viruses;    Motif scan;    RNA structure;    EBV;    KSHV;    PAN;    EBNA1;   

DOI  :  10.7717/peerj.9882

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

90% of adults infected). This ubiquitous virus is implicated in a variety of cancers and autoimmune diseases. Previous analyses of the EBV genome revealed numerous regions with evidence of generating unusually stable and conserved RNA secondary structures and led to the discovery of a novel class of EBV non-coding (nc)RNAs: the stable intronic sequence (sis)RNAs. To gain a better understanding of the roles of RNA structure in EBV biology and pathogenicity, we revisit EBV using recently developed tools for genome-wide motif discovery and RNA structural characterization. This corroborated previous results and revealed novel motifs with potential functionality; one of which has been experimentally validated. Additionally, since many herpesviruses increasingly rival the seroprevalence of EBV (VZV, HHV-6 and HHV-7 being the most notable), analyses were expanded to include all sequenced human Herpesvirus RefSeq genomes, allowing for genomic comparisons. In total 10 genomes were analyzed, for EBV (types 1 and 2), HCMV, HHV-6A, HHV-6B, HHV-7, HSV-1, HSV-2, KSHV, and VZV. All resulting data were archived in the RNAStructuromeDB (https://structurome.bb.iastate.edu/herpesvirus) to make them available to a wide array of researchers.

【 授权许可】

CC BY