RIP-seq

RNA immunoprecipitation (RIP) is a technique for studying intracellular RNA-protein interactions, particularly suited for investigating post-transcriptional regulatory network dynamics. It enables identification of target RNA molecules—including lncRNAs, mRNAs, and other non-coding RNAs—bound by specific proteins. RIP employs antibodies targeting proteins of interest to precipitate RNA-protein complexes, which are then isolated and purified. Bound RNAs can be analyzed by qPCR (RIP-qPCR), microarray (RIP-chip), or sequencing (RIP-seq). RIP is analogous to chromatin immunoprecipitation (ChIP), but targets RNA-protein rather than DNA-protein interactions. RIP-seq provides transcriptome-wide profiling of protein-bound RNA regions or species and enables differential analysis across samples.

cr：illumina

Workflow

Cells are lysed, and antibodies targeting the protein of interest are employed to precipitate the corresponding RNA-protein complexes. Immunoprecipitation is performed using Protein A/G magnetic beads and the corresponding antibody. RNA is subsequently extracted, reverse transcribed into cDNA, ligated with adapters at both ends, amplified by PCR, and purified using magnetic beads to construct sequencing libraries. High-throughput sequencing is then conducted, followed by bioinformatics analysis and experimental validation. The comprehensive RIP-seq service provided by EPIBIOTEK® includes all upstream RIP experimental procedures. Clients need only provide cell samples, and EpiBiotek performs professional RIP experiments to identify RNA regions or species specifically bound by particular proteins across the whole transcriptome, as well as differential binding patterns among multiple samples.

Sample Requirements

Cells

≥1×10^7 cells/sample

Bioinformatics Analysis

1. Adapter trimming and QC of raw reads. 2. Reference genome alignment. 3. Gene expression quantification. 4. RIP-target analysis. 5. GO analysis of RIP-targets. 6. KEGG enrichment analysis of RIP-targets.

EPIBIOTEK® Project Publications

1. Ma M, Duan Y, Peng C, et al. Mycobacterium tuberculosis inhibits METTL14-mediated m6A methylation of Nox2 mRNA and suppresses anti-TB immunity. Cell Discov. 2024;10(1):36. Published 2024 Mar 29. doi:10.1038/s41421-024-00653-4 2. Shao N, Xi L, Lv Y, et al. USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation. Nat Commun. 2025;16(1):1313. Published 2025 Feb 3. doi:10.1038/s41467-025-56564-9 3. Zhang H, Luo X, Yang W, et al. YTHDF2 upregulation and subcellular localization dictate CD8 T cell polyfunctionality in anti-tumor immunity. Nat Commun. 2024;15(1):9559. Published 2024 Nov 5. doi:10.1038/s41467-024-53997-6 4. Yuan J, Xie BM, Ji YM, et al. piR-26441 inhibits mitochondrial oxidative phosphorylation and tumorigenesis in ovarian cancer through m6A modification by interacting with YTHDC1. Cell Death Dis. 2025;16(1):25. Published 2025 Jan 18. doi:10.1038/s41419-025-07340-6 5. Yang Y, Jianxu Z, Hao L, et al. EF24 targets METTL3 to reprogram m6A methylation and induce ferroptosis: an epitranscriptomic mechanism with therapeutical potential for glioma. Cell Commun Signal. 2025;24(1):32. Published 2025 Dec 12. doi:10.1186/s12964-025-02583-4