The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

The m⁶A landscape of PAN RNA expressed at latent and lytic stages of KSHV replication. (A) The graphs represent m⁶A_RATIO (y-axis) against PAN RNA sequence (x-axis). The peaks correspond to the RT stop 1 nt downstream from m⁶A. The threshold line (red) for calling m⁶A peaks is set at 0.2 and it was calculated by dividing the average m⁶A_RATIO values calculated for all PAN nucleotides divided by the total number of nucleotides. (B) The charts represent the signal-to-noise ratio for sequences overlapping m⁶A peaks within a specified nucleotide window (x-axis). (C) The average m⁶A_RATIO values for each modification at specified time points (n = 2). Time points of KSHV infection are color-coded as follows: uninduced stage/latency—0 h pi in blue; lytic stages: immediate early—8 h pi in orange; early—24 h pi in gray; late—48 h pi in yellow; late—72 h pi in green.