In vivo RNA-directed transcription, with template switching, by a mammalian RNA polymerase.

These studies support the interpretation that a host polymerase, most likely RNA polymerase II, can not only carry out transcription that is RNA directed, but also achieve template switching on a discontinuous RNA template, and even perform non-templated nucleotide incorporation. As part of an in vivo analysis of the initiation of replication of the RNA genome of human hepatitis delta virus (HDV), a series of linear RNAs containing HDV sequences was tested in order to explain the ability of this host polymerase to initiate RNA-directed RNA synthesis in vivo and produce replicating circular HDV species. The data support the hypothesis that the input linear template RNAs were not converted to circles before transcription but rather that in the process of transcription, the polymerase was able to make an intra-molecular template switch. Furthermore, in certain cases this switch produced small deletions of template sequences, and in some cases even insertion of non-templated sequences. Thus, in an in vivo situation, polymerase II has several important capabilities in addition to what is considered typical DNA-directed transcription.