Alternative RNA splicing of KSHV ORF57 produces two different RNA isoforms

- A native KSHV ORF57 transcript has a small constitutive intron and a large suboptimal intron.
- RNA splicing to include or exclude the suboptimal intron results in two ORF57 isoforms.
- The RNA1, a major isoform derived from splicing of the constitutive intron, encodes full-length ORF57 protein.
- The RNA2 derived from double splicing is a non-coding RNA.
- The suboptimal intron in RNA1 can be activated to splice in certain expression vectors.

In lytically infected B cells Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 gene encodes two RNA isoforms by alternative splicing of its pre-mRNA, which contains a small, constitutive intron in its 5′ half and a large, suboptimal intron in its 3′s half. The RNA1 isoform encodes full-length ORF57 and is a major isoform derived from splicing of the constitutive small intron, but retaining the suboptimal large intron as the coding region. A small fraction (<5%) of ORF57 RNA undergoes double splicing to produce a smaller non-coding RNA2 due to lack of a translational termination codon. Both RNAs are cleaved and polyadenylated at the same cleavage site CS83636. The insertion of ORF57 RNA1 into a restriction cutting site in certain mammalian expression vectors activates splicing of the subopitmal intron and produces a truncated ORF57 protein.

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