Abundant expression of the long noncoding (lnc) PAN (polyadenylated nuclear) RNA 
by the human oncogenic gammaherpesvirus Kaposi's sarcoma-associated herpesvirus 
(KSHV) depends on a cis-element called the expression and nuclear retention 
element (ENE). The ENE upregulates PAN RNA by inhibiting its rapid nuclear decay 
through triple-helix formation with the poly(A) tail. Using structure-based 
bioinformatics, we identified six ENE-like elements in evolutionarily diverse 
viral genomes. Five are in double-stranded DNA viruses, including mammalian 
herpesviruses, insect polydnaviruses, and a protist mimivirus. One is in an 
insect picorna-like positive-strand RNA virus, suggesting that the ENE can 
counteract cytoplasmic as well as nuclear RNA decay pathways. Functionality of 
four of the ENEs was demonstrated by increased accumulation of an intronless 
polyadenylated reporter transcript in human cells. Identification of these ENEs 
enabled the discovery of PAN RNA homologs in two additional gammaherpesviruses, 
RRV and EHV2. Our findings demonstrate that searching for structural elements 
can lead to rapid identification of lncRNAs.