N6-methyladenosine (m6A) profiling of mouse liver

We developed RADAR , a method for detecting differential methylated loci in MeRIP-seq data. RADAR uses a flexible model to accommodate increased noise due to RNA immunoprecipitation and are compatible with complex study design. RADAR enabled accurate identification of altered methylation sites in patient samples where covariates need to be accounted for. We use the m6A-profiling of mouse liver data as an example data set to benchmart the performance of RADAR and a few alternative methods. Four mouse liver tissues were collected from wild type mice and four from METTL14 liver specific knockout mice. Total RNA was extracted from the tissue by TRIzol followed by polyT bead mRNA purification. mRNA was subject to fragmentation with Bioruptor ultrasonicator. m6A-immunoprecipitation were performed using EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S). Kapa RNA hyper kit for Illumina was used to construct library from mRNA. The libraries were sequenced by the Hiseq 4000 platform at SE50 mode.