meRIP

MeRIP, short for methylated RNA immunoprecipitation, is a technique used to study N6-methyladenosine (m6A) modifications on RNA. By using an antibody that recognizes m6A, methylated RNA fragments are selectively enriched from a total RNA pool. The enriched material is then analyzed to identify the transcriptome-wide locations of m6A, typically through sequencing (MeRIP-seq) or, less commonly, microarray approaches.

The typical workflow begins with extraction of RNA, which is then fragmented to approximately 100–200 nucleotides. The fragments are incubated with an anti-m6A antibody bound to beads, and the methylated RNA is immunoprecipitated, washed, and eluted. The eluted RNA is converted to cDNA and subjected to sequencing or other profiling methods. An input RNA sample is often sequenced in parallel as a control to identify genuinely enriched regions. Reads are mapped to a reference genome to call peaks representing m6A-enriched regions.

MeRIP data usually reveal peaks that cluster around gene features such as stop codons and 3' untranslated regions and tend to overlap with the DRACH sequence motif (where D is A, G, or U; R is A or G; H is A, C, or U). While MeRIP identifies regions of methylation, its resolution is limited and does not normally pinpoint exact modified nucleotides. Higher-resolution methods, such as miCLIP, have been developed to address this limitation.

Applications of meRIP include exploring how m6A modulates RNA stability, splicing, translation, and gene expression in development, physiology, and disease. Limitations include antibody specificity, potential biases from fragmentation and library preparation, and the need for substantial starting material.