Efficient Site-Specific Nonribozyme Opening of Hepatitis Delta Virus Genomic RNA in Infected Livers

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Abstract
Examination of the 1,679-nucleotide (nt) unit-length hepatitis delta virus (HDV) RNAs in the livers of two HDV-infected woodchucks showed that 96% of the antigenomic RNA but only 50% of the genomic RNA was circular. We subsequently found that at least half of the linear unit-length genomic RNA was open at a unique location. Using a modified form of RNA ligation-mediated amplification of cDNA ends, we showed that the 5′ end was located at nt 1212. Like the previously described ribozyme cleavage site at nt 686, the new site produced a 5′-OH. Nevertheless, we showed that this novel site was not produced by activity of the HDV genomic ribozyme. We speculate that the 5′ end at nt 1212 reflects a preferred site of posttranscriptional endonucleolytic cleavage of genomic RNA.