Genome-wide maps of chromatin modifications in KSHV-transformed primary effusion lymphoma cell lines

The Kaposi's sarcoma-associated herpesviruses causes several cancers including Kaposi's sarcoma and primary effusion lymphoma (PEL). Our work reveals that the cellular transcription factors interferon regulatory factor 4 (IRF4) and basic leucine zipper ATF-like transcription factor (BATF), as well as the viral interferon regulatory factor 3 (vIRF3) are critical oncogenic dependencies specific to PEL cell lines. To understand the functions of these transcription factors, we performed ChIP-Seq on these proteins and other histone modifications in different PEL cell lines. Our results reveal that these oncogenic factors may cooperate to regulate the expression of the same mRNAs through promoter, enhancer, and superenhancer elements. ChIP-Seq of CTCF, and histone modifications in PEL cell lines