Genome-wide analysis of the 5’ and 3’ ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts.

We adapted tag-based methods in conjunction with SOLiD and Illumina deep sequencing platforms to determine the precise 5’ and 3’ ends of VACV early mRNAs and map the transcription start sites (TSSs) and polyadenylation sites (PASs). We annoated Individual and clustered TSSs preceding 104 annotated open reading frames (ORFs). Large number of TSSs occurred in anomalous locations that may expand the functional repertoire of the VACV genome. Discrete and clustered PASs occurred about 40 nt after an UUUUUNU termination signal. However, a large number of PASs were not preceded by this motif, suggesting alternative polyadenylation mechanisms. Pyrimidine-rich sequences were found immediately upstream of both types of PASs, signifying an additional feature of VACV 3’ end formation and polyadenylation.