Distribution of genes with differential m6A RNA methylation in the hippocampus of HIV Tg rats.

A) A larger number of genes with down-regulation of m6A methylation was observed in HIV Tg rats than the number of genes with up-regulated methylation, in particular, 201 genes with significant down-regulated methylation (p-value<0.05) while 172 genes were found with significant up-regulated methylation (p-value<0.05). Inset: Distribution of m6A peaks within hippocampal mRNAs of HIV Tg and control rat. Transcript architecture is shown underneath: 5’ untranslated region (UTR); coding sequence (CDS); and 3’ UTR. The density of m6A peaks was greater on the distal CDS and 3’UTR and showed the greatest enrichment in the immediate vicinity of the stop codon at the CDS-3’UTR boundary. B) The distribution of log2 fold change (log2FC) of genes with up-regulated and down-regulated methylation C,D) Correlation between the methylation and expression changes for genes with up-regulated and down-regulated methylation (Pearson correlation = 0.67 and 0.58 respectively). Among the 201 genes with down-regulated methylation, the expression of 127 genes are also down-regulated while the rest remain unchanged; Among the 172 genes with up-regulated methylation, the expression of 83 genes are also up-regulated while expression of 89 genes remain unchanged.