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N6-methyladenosine (m6A) profiling of ovarian cancer tissues

ABSTRACT: 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 ovarian cancer data as an example data set to benchmart the performance of RADAR and a few alternative methods.

ORGANISM(S): Homo sapiens

PROVIDER: GSE119168 | GEO | 2020/01/13

REPOSITORIES: GEO

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N6-methyladenosine (m6A) profiling of mouse liver

Project description: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.

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Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

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