Genome-wide mapping of RTA binding sites in KSHV+ PEL cells during KSHV reactivation.

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) analysis was performed during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation in KSHV+ recombinant primary effusion B-cell lymphoma cells (PEL). RTA binding sites were identified genome-wide in a recombinant PEL cell line called TRExBCBL1-3xFLAG-RTA cells at 12 hours post-induction (hpi) of RTA expression. The expression of the N-terminally 3xFLAG-tagged RTA was induced by adding 1 μg/ml doxycycline (Dox) to the medium for 12 hours. Cells were cross-linked with formaldehyde and sonicated chromatin prepared. Chromatin immunoprecipitation was performed using FLAG antibody to detect the FLAG epitope tagged RTA protein in the recombinant PEL cells at 12 hpi. Libraries were generated from the genomic DNA material before immunoprecipitation (Input) and from the FLAG-RTA ChIP sample in paralel.