Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA

BMC Genomics

Research Article

Joan A Steitz¹  Walter N Moss¹ 

[1] Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 06536, New Haven, Connecticut, USA;

关键词: Epstein-Barr virus (EBV);    Herpesvirus;    RNA;    RNA structure;    Non-coding RNA (ncRNA);    RNA-Seq;    Bioinformatics;    W repeat;    sisRNA;    RNA editing;   

DOI  :  10.1186/1471-2164-14-543

 received in 2013-06-20, accepted in 2013-08-07,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundEpstein-Barr virus (EBV) is a human herpesvirus implicated in cancer and autoimmune disorders. Little is known concerning the roles of RNA structure in this important human pathogen. This study provides the first comprehensive genome-wide survey of RNA and RNA structure in EBV.ResultsNovel EBV RNAs and RNA structures were identified by computational modeling and RNA-Seq analyses of EBV. Scans of the genomic sequences of four EBV strains (EBV-1, EBV-2, GD1, and GD2) and of the closely related Macacine herpesvirus 4 using the RNAz program discovered 265 regions with high probability of forming conserved RNA structures. Secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. The analysis of RNA-Seq data uncovered the first observation of a stable intronic sequence RNA (sisRNA) in EBV. The abundance of this sisRNA rivals that of the well-known and highly expressed EBV-encoded non-coding RNAs (EBERs).ConclusionThis work identifies regions of the EBV genome likely to generate functional RNAs and RNA structures, provides structural models for these regions, and discusses potential functions suggested by the modeled structures. Enhanced understanding of the EBV transcriptome will guide future experimental analyses of the discovered RNAs and RNA structures.

【 授权许可】

CC BY   
© Moss and Steitz; licensee BioMed Central Ltd. 2013