Fig. 1.

Examining iSLK m⁶A epitrascriptome during KSHV lytic reactivation. (A) Schematic of m⁶A eCLIP set up. iSLK.WT cells were either left latent or lytically reactivated with doxycycline and sodium butyrate for 48 h. Total RNA was collected then incubated with an m⁶A antibody. Samples were ultraviolet cross-linked before being reverse transcribed then attached with 3′ adapters in part of library preparation. Finally, m⁶A-enriched samples were sequenced. (B) Most significant DRACH motifs with m⁶A peaks identified by HOMER in latent and lytic cells. (C) Heat map of a metagene plot depicting the average number of sites mapped to certain genomic regions. The number of sites is calculated for each region of every gene, the lengths of the regions are then normalized, and the average number of sites for a set number of positions along the regions are calculated. (D) Heat map of the most significant m⁶A-enriched functional pathways in latent and lytic cells calculated through an enrichment analysis preformed using the R package clusterProfiler. (E) m⁶A PureCLIP scores of lytically reactivated KSHV genes aligned over an annotated KSHV genome. PureCLIP is the log posterior probability ratio of the m⁶A cross-link sites over the input samples.