miCLIP-seq Service

While traditional m6A mapping methods offer broad profiling, they cannot identify exact methylation sites, hindering mechanistic studies. miCLIP‑seq solves this by using crosslinking‑induced mutation signatures to locate m6A residues with single‑base accuracy. CD BioSciences provides comprehensive, end-to-end miCLIP-seq services, from expert experimental design to sophisticated bioinformatic analysis, empowering researchers to decode the precise regulatory roles of m6A in gene expression, cellular function, and disease pathogenesis.

Overview of miCLIP-seq

m6A individual-nucleotide resolution crosslinking and immunoprecipitation sequencing (miCLIP-seq) is an advanced antibody-based technique designed for the high-resolution mapping of N6-methyladenosine (m6A), the most prevalent internal mRNA modification. The core principle involves UV crosslinking to covalently lock the anti-m6A antibody to its bound RNA, followed by immunoprecipitation and reverse transcription. Critically, the crosslinked antibody introduces a characteristic mutation or truncation in the cDNA at the precise m6A site during reverse transcription. By sequencing these cDNAs and mapping these unique mutation signatures, miCLIP-seq enables the transcriptome-wide identification of m6A locations with single-nucleotide accuracy. This technical leap provides unparalleled insights into the epitranscriptome, allowing researchers to investigate the exact placement of m6A within coding sequences, untranslated regions, and splice sites, thereby elucidating its specific effects on RNA stability, splicing, structure, and translation.

Fig.1 Schematic representation of three CLIP-based methods, miCLIP, meCLIP, and m6ACE-seq. (Yang Y, et al., 2024)

Features of miCLIP-seq

miCLIP-seq represents a gold-standard method for epitranscriptomic discovery, specifically engineered to transcend the resolution limits of enrichment-based techniques. It is the method of choice for studies requiring exact m6A localization, validating putative sites from MeRIP-seq data, and investigating the precise molecular mechanisms of m6A readers and writers.

1. Single-Base Resolution: Uniquely identifies the exact adenosine residue methylated, enabling precise genomic coordinate assignment.
2. High Specificity & Low Background: UV crosslinking ensures stringent specificity, reducing non-specific background noise common in standard RIP protocols.
3. Mechanistic Insights: Precise site mapping allows for correlation with structural elements, protein binding motifs, and genetic variants.
4. Validation Power: Serves as a definitive validation tool for m6A sites predicted by lower-resolution methods.

Our Services

CD BioSciences delivers premium, fully managed miCLIP-seq services to unlock the precise landscape of m6A methylation in your biological samples. Utilizing rigorously validated anti-m6A antibodies and an optimized, state-of-the-art miCLIP protocol, we generate high-fidelity data that maps m6A sites with exceptional accuracy and reproducibility. Our service empowers you to move beyond mere detection to precise functional analysis, providing the critical data needed to link specific m6A modifications to phenotypic outcomes in development, disease models, and cellular regulation.

Workflow of miCLIP-seq Service

Our miCLIP‑seq service follows a rigorously validated, end-to-end pipeline designed to maximize specificity and single-nucleotide resolution while minimizing technical artifacts. From initial sample preparation to final data interpretation, each step is optimized and quality-controlled to ensure the delivery of precise, reproducible, and biologically meaningful m6A maps. The integrated workflow encompasses:

Project Consultation & Experimental Design

Our specialists collaborate with you to establish an optimized experimental strategy tailored to your specific biological questions and sample types.

Sample Preparation & Quality Control

We perform rigorous RNA extraction from your provided cells or tissues, followed by comprehensive quality and integrity assessment to ensure input suitability.

UV Crosslinking & RNA Fragmentation

Samples undergo in vitro UV crosslinking to covalently immobilize the m6A antibody-RNA interaction, followed by controlled fragmentation to achieve optimal library preparation size.

Immunoprecipitation & Library Construction

Fragmented RNA is subjected to immunoprecipitation using a highly validated anti-m6A antibody. Enriched RNA is then processed into sequencing libraries, during which reverse transcription captures characteristic mutation signatures at m6A sites.

High‑Throughput Sequencing & Bioinformatics Analysis

Libraries are sequenced on Illumina platforms, and our customized bioinformatics pipeline identifies precise m6A locations through crosslinking-induced mutation calling, peak annotation, motif analysis, and functional enrichment assessment.

Comprehensive Data Delivery & Reporting

You receive all raw and processed data, detailed analytical reports, publication-ready visualizations, and expert interpretation to support your research conclusions.

Supported Sample Types

CD BioSciences provides robust and optimized miCLIP‑seq protocols to accommodate a broad spectrum of biological materials. We support the following sample types:

1. Cultured Cells: Including adherent cell lines, suspension cells, primary cells, and stem cells.
2. Animal Tissues: Fresh, snap-frozen, or RNAlater-preserved tissues from mouse, rat, or other model organisms.
3. Clinical Specimens: Human tissue biopsies, blood samples, or FFPE (formalin-fixed paraffin-embedded) sections, subject to pre-extraction QC.
4. Low-Input & Challenging Samples: Specialized protocols are available for limited materials such as sorted cells, fine-needle aspirates, micro-dissected samples, or early-stage embryos.
5. Plant & Microbial Samples: Including plant tissues, yeast, and selected bacterial cultures (subject to consultation for RNA isolation optimization).

Our Advantages

1. Unmatched Resolution & Accuracy: Our optimized wet-lab and bioinformatic pipelines are fine-tuned to confidently call true single-nucleotide m6A sites, minimizing false positives.
2. Deep Expertise in Epitranscriptomics: Our specialist team understands the technical nuances of miCLIP, ensuring optimal crosslinking efficiency and data interpretation.
3. Integrated Analysis Suite: We provide more than just peak lists; our analysis includes motif discovery, genomic annotation (exon/intron/UTR), conservation analysis, and integration with RNA-seq or RBP data.
4. End-to-End Project Management: From initial consult to final report, a dedicated project manager and scientist guide you through every step, ensuring clarity and success.

In epitranscriptomics research, precisely mapping m6A sites at single‑base resolution is crucial for transitioning from broad correlation studies to mechanistic understanding. In addition to our miCLIP‑seq service, CD BioSciences also provides LC‑MS/MS, MeRIP‑seq, and DART‑seq to meet diverse research needs. This multi‑technology portfolio enables us to design fully customized and integrated research strategies tailored to your specific project goals. Contact us today to discuss your experimental needs and receive a detailed proposal for your high‑impact epitranscriptomic study.

Reference

1. Yang Y, Lu Y, Wang Y, et al. Current progress in strategies to profile transcriptomic m6A modifications[J]. Frontiers in Cell and Developmental Biology, 2024, 12: 1392159.