Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model

Figure 1

Comparison of the differential methylation analysis in DNA and RNA. The first column shows the DNA related differential analysis in ChIP-Seq or MeDIP-Seq, where the total DNA is often considered the same under two experimental conditions, so the differential analysis can be performed by directly comparing the absolute amount of methylated RNAs in the two IP samples. In contrast, for RNA (the second column), the background is total RNA, which can vary significantly under different conditions, and therefore, the absolute amount of methylated RNA for a specific site does not necessarily correlate with the degree of methylation. For the example shown in the above figure, while amount of methylated RNA increases under the cancer condition, the relative amount (percentage of methylated RNA) decreases, indicating a hypomethylation at RNA level. As a result, the differential analysis of RNA methylome in MeRIP-Seq should be performed by comparing the percentages of methylated RNA to reflect the influence of methylation enzymatic regulation.