Figure 5. SND1 RNA-binding sites specifically overlap m⁶A peaks (a, b) Genome sequencing tracks from latent (0 hr) and lytic (8 hr and 20 hr post-reactivation) TREx BCBL1-Rta cells depicting input (green) and RIP (blue) coverage.

m⁶A-IP reads (red) are also shown. Blue boxes indicate exons while blue lines represent introns. SND1 overlaps with m⁶A peaks are evident in introns (ARL17A) and 5’UTRs (ABCD1). Note that in ABCD1, SND1 binding and m⁶A peaks are both reduced at 8 hr post-reactivation while at 20 hr post-reactivation methylation and SND1 binding signal are both lost with decreasing expression in inputs. (c, d) Dynamic SND1 binding to m⁶A-modified regions in SND1 target transcripts during KSHV infection. Genome tracks depicting sequencing read coverage from input (green) and RIP (blue) samples. m⁶A-IP reads (pink) are also shown. Note that in contrast to ABCD1, RHOU/DUSP5P1 remain highly expressed even at 20 hr post-reactivation, suggesting the coupled loss of methylation/SND1-binding is independent of the ability to detect these events due to loss of expression. (e) SND1 regions consistently enriched across the three time points studied (0 hr, 8 hr and 20 hr) were defined by applying a fold change RIP/input >2 and>50 mean reads per region (FDR < 1%). Consistently SND1-unbound regions throughout KSHV infection were defined using a fold change RIP/input <0.5 and>50 mean reads per region (FDR < 1%). For all m⁶A overlap analysis, the cut-off for an m⁶A peak was defined as having 50 read paired at the tallest point in the m⁶A peak and a 2-fold enrichment of m⁶A-IP reads over input reads using a FDR < 1%.