Genome-wide analysis of KSHV splicing regulation by ORF57

Kaposi's sarcoma-associated virus (KSHV) ORF57 is a viral RNA-binding protein required for proper posttranscriptional processing of viral transcripts including RNA splicing. To identify the viral splicing events regulated by ORF57 we performed a genome-wide analysis of RNA splicing of viral RNAs in wild type (WT) versus ORF57 knock-out (57KO) primary effusion lymphoma cells line BCBL-1 after induction of KSHV lytic replication by 24h treatment with valproic acid (VA). The obtained reads were mapped to human/KSHV chimeric genome by STAR aligner to identify KSHV splicing events. To detemine ORF57 activity on viral RNA splicing, we compared the number of splice reads mapped to unique splicing junction in WT versus 57KO BCBL-1 cells.