MeRIPSeq

MeRIP-seq, short for methylated RNA immunoprecipitation sequencing, is a high-throughput method used to map RNA methylation, most commonly N6-methyladenosine (m6A), across the transcriptome. It provides a genome-wide view of where methylation occurs on RNA molecules and is widely used to study post-transcriptional regulation of gene expression.

The typical workflow involves fragmenting total RNA to relatively short pieces, immunoprecipitating methylated RNA fragments with an antibody specific for the target modification (commonly anti-m6A), and sequencing the enriched material. An input control (unimmunoprecipitated RNA) is often sequenced in parallel to identify true enrichment. Sequencing reads are aligned to the reference genome or transcriptome, and computational peak-calling identifies regions with significant methylation signal, typically reported as peaks associated with transcripts.

MeRIP-seq provides region-level resolution, usually on the order of 100–200 nucleotides, which is suitable for transcriptome-wide mapping but does not routinely achieve single-nucleotide precision. It is commonly complemented by methods that offer higher resolution, such as Crosslinking and Immunoprecipitation-based approaches. Data analysis includes differential methylation testing between conditions, motif enrichment analyses (notably the DRACH motif associated with m6A), and integration with expression or splicing data to infer regulatory effects.

Limitations include dependence on antibody specificity and potential cross-reactivity, lower resolution, and biases introduced by RNA fragmentation and immunoprecipitation efficiency. Appropriate controls and validation with independent techniques are important for robust interpretation. Variants and related methods, such as miCLIP and m6A-CLIP, offer higher resolution mappings for comparative studies.